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1

SAF-Box, a conserved protein domain that specifically recognizes scaffold attachment region DNA  

Microsoft Academic Search

SARs (scaffold attachment regions) are candidate DNA elements for partitioning eukaryotic genomes into independent chromatin loops by attaching DNA to proteins of a nuclear scaffold or matrix. The interaction of SARs with the nuclear scaffold is evolutionarily conserved and appears to be due to specific DNA binding proteins that recognize SARs by a mechanism not yet understood. We describe a

MICHAEL KIPP; FRANK GOHRING; THORSTEN OSTENDORP; Drunen van C. M; ROEL VAN DRIEL; MICHAEL PRZYBYLSKI; F. O. Fackelmaer

2000-01-01

2

The stability region of the Streptomyces lividans plasmid pIJ101 encodes a DNA-binding protein recognizing a highly conserved short palindromic sequence motif  

PubMed Central

Conjugation is a driving force in the evolution and shaping of bacterial genomes. In antibiotic producing streptomycetes even small plasmids replicating via the rolling-circle mechanism are conjugative. Although they encode only genes involved in replication and transfer, the molecular function of most plasmid encoded proteins is unknown. In this work we show that the conjugative plasmid pIJ101 encodes an overlooked protein, SpdA2. We show that SpdA2 is a DNA binding protein which specifically recognizes a palindromic DNA sequence (sps). sps is localized within the spdA2 coding region and highly conserved in many Streptomyces plasmids. Elimination of the palindrome or deletion of spdA2 in plasmid pIJ303 did not interfere with conjugative plasmid transfer or pock formation, but affected segregational stability. PMID:25295034

Thoma, Lina; Sepulveda, Edgardo; Latus, Annette; Muth, Günther

2014-01-01

3

Conservation Regional Conservation SavingsRegional Conservation Savings  

E-print Network

1 Northwest Power and Conservation Council Regional Conservation SavingsRegional Conservation the Plan''s Targets?s Targets? March 14, 2008 slide 2 Northwest Power and Conservation Council 55thth Plan Conservation ResourcePlan Conservation Resource Acquisition TargetsAcquisition Targets 20052005 ­­ 2009 = 700 a

4

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

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.

Korber, Bette [Los Alamos National Laboratory; Szinger, James [Los Alamos National Laboratory

2009-01-01

5

Anschutz Library receives plaque recognizing outstanding efforts in energy conservation and sustainability  

E-print Network

. The Student Environmental Advisory Board, a KU student organization, spearheaded a Student Senate initiative to reduce dependence on unsustainable energy in 2007. The initiative uses student fees to purchase wind power credits from one of Westar Energy... Articles, Books,… Friends & Benefactors Suggestions Anschutz Library receives plaque recognizing outstanding efforts in energy conservation and sustainabil i ty On Friday, August 14, Chevron Energy Solutions (CES) will present a plaque to Anschutz Library...

2009-01-01

6

75 FR 59143 - Magnuson-Stevens Fishery Conservation and Management Act; Regional Fishery Management Councils...  

Federal Register 2010, 2011, 2012, 2013, 2014

...member of a Regional Fishery Management Council established under the...Magnuson-Stevens Fishery Conservation and Management Act, hereby promise to conserve...of the Nation. I recognize my responsibility to serve as...Magnuson-Stevens Fishery Conservation and Management Act and other applicable...

2010-09-27

7

Crystal structure reveals conservation of amyloid-? conformation recognized by 3D6 following humanization to bapineuzumab  

PubMed Central

Introduction Immunotherapy targeting amyloid-? peptide is under active clinical investigation for treatment of Alzheimer’s disease (AD). Among the hypotheses being investigated for impact on clinical outcome are the preferred epitope or conformation of amyloid-? to target for treatment, and the mechanism of action underlying immunotherapy. Bapineuzumab (humanized 3D6), a neo-epitope specific antibody recognizing amyloid-?1-5 with strong preference for an exposed Asp residue at the N-terminus of the peptide, has undergone advanced clinical testing for treatment of AD. Methods To gain further insight into the epitope conformation, we interrogated structural details of amino-terminal epitopes in amyloid-? using x-ray crystallography of 3D6Fab:amyloid-? complexes. Humanization of 3D6 was carried out using standard procedures integrating recombinant methods, sequence informatics, and homology modeling predictions to identify important mouse framework residues for retention in the finished humanized product. Results Here we report the crystal structure of a recombinant Fab fragment of 3D6 in complex with amyloid-?1-7 solved at 2.0 Å resolution. The N-terminus of amyloid-? is bound to 3D6 as a 310 helix. The amino-terminal Asp residue is buried deepest in the antibody binding pocket, with the C? atom of residue 6 visible at the entrance to the binding pocket near the surface of the antibody. We further evaluate homology model based predictions used to guide humanization of 3D6 to bapineuzumab, with actual structure of the Fab. The structure of the Fab:amyloid-? complex validates design of the humanized antibody, and confirms the amyloid-? epitope recognized by 3D6 as previously mapped by ELISA. Conclusions The conformation of amyloid-? antigen recognized by 3D6 is novel and distinct from other antibodies recognizing N-terminal epitopes. Our result provides the first report demonstrating structural conservation of antigen contact residues, and conformation of antigen recognized, between the parent murine antibody and its humanized version. PMID:25024748

2014-01-01

8

Title: Toronto and Region Conservation Authority Data Data Creator /  

E-print Network

Title: Toronto and Region Conservation Authority Data Data Creator / Copyright Owner: Toronto and Region Conservation Authority Publisher: Toronto and Region Conservation Authority Edition: N/A Versions/A Abstract: The dataset represents various natural features within the Toronto and Region Conservation

9

5 CFR 5501.103 - Gifts from federally recognized Indian tribes or Alaska Native villages or regional or village...  

Code of Federal Regulations, 2012 CFR

...federally recognized Indian tribes or Alaska Native villages or regional or village...federally recognized Indian tribes or Alaska Native villages or regional or village corporations. (a) Tribal or Alaska Native gifts. In addition...

2012-01-01

10

5 CFR 5501.103 - Gifts from federally recognized Indian tribes or Alaska Native villages or regional or village...  

Code of Federal Regulations, 2014 CFR

...federally recognized Indian tribes or Alaska Native villages or regional or village...federally recognized Indian tribes or Alaska Native villages or regional or village corporations. (a) Tribal or Alaska Native gifts. In addition...

2014-01-01

11

5 CFR 5501.103 - Gifts from federally recognized Indian tribes or Alaska Native villages or regional or village...  

Code of Federal Regulations, 2013 CFR

...federally recognized Indian tribes or Alaska Native villages or regional or village...federally recognized Indian tribes or Alaska Native villages or regional or village corporations. (a) Tribal or Alaska Native gifts. In addition...

2013-01-01

12

5 CFR 5501.103 - Gifts from federally recognized Indian tribes or Alaska Native villages or regional or village...  

Code of Federal Regulations, 2011 CFR

...federally recognized Indian tribes or Alaska Native villages or regional or village...federally recognized Indian tribes or Alaska Native villages or regional or village corporations. (a) Tribal or Alaska Native gifts. In addition...

2011-01-01

13

Localization of T cell epitope regions of chicken ovomucoid recognized by mice.  

PubMed

We localized the T cell epitope regions of chicken ovomucoid (OVM), a potent egg allergen, with the overlapping pin-peptides covering the entire sequence of OVM and three strains of mice with different haplotypes. In C3H/He (H-2k) mice, the T cells recognized relatively broad regions on OVM; the dominant regions were 49-93 and 97-114 residues, and the subdominant regions were 7-21, 37-48, 94-96, 115-123 and 145-177 residues. In contrast, a more limited number of T cell epitope regions were localized in BALB/c (H-2d) and C57BL/6 (H-2b) mice. The T cells from BALB/c mice recognized 100-114 and 157-171 residues, and the T cells from C57BL/6 mice recognized only 157-180 residues. These results were confirmed by using peptides separately synthesized and purified on the putative epitope regions. The roles of the carbohydrate moieties and cysteine residues involved in the disulfide bridges of OVM were also examined, and we found that they were not important in recognition by the T cell/antigen presenting cell. PMID:12784609

Mizumachi, Koko; Kurisaki, Jun-ichi

2003-04-01

14

Conservation Focus: Priorities for Policy-Relevant Conservation Research: a View from SCB Regional Sections  

E-print Network

Conservation Focus: Priorities for Policy-Relevant Conservation Research: a View from SCB Regional Sections Gaining Traction: Retreading the Wheels of Marine Conservation PHAEDRA DOUKAKIS, E. C. M. PARSONS Conservation Science, School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794

15

The Habitat Conservation Division, Northeast Region is working to protect, conserve and restore habitats of our  

E-print Network

The Habitat Conservation Division, Northeast Region is working to protect, conserve and restore habitats of our living marine resources. Primary Activities The Habitat Conservation Division collaborates with regional fishery management councils to: Identify and describe Essential Fish Habitat (EFH) for each

16

Cytauxzoon felis infections are present in bobcats ( Lynx rufus) in a region where cytauxzoonosis is not recognized in domestic cats  

Microsoft Academic Search

This study was performed to determine the prevalence of Cytauxzoon felis (C. felis) infections in bobcats (Lynx rufus) from a region where C. felis is recognized in domestic cats, North Carolina (NC), and a region where C. felis is not recognized in domestic cats, Pennsylvania (PA). Samples from NC (n=32) were obtained post-mortem via cardiac puncture from legally trapped bobcats.

Adam J. Birkenheuer; Henry S. Marr; Camille Warren; Anne E. Acton; Eric M. Mucker; Jan G. Humphreys; Melissa D. Tucker

2008-01-01

17

PLANNING FOR WATER CONSERVATION Greater Vancouver Regional District  

E-print Network

PLANNING FOR WATER CONSERVATION Greater Vancouver Regional District by Andrew K. Doi B. A (BMPs) for water conservation are used as evaluative criteria. These BMPs were drawn from California's urban water conservation system. This researched examines 4 case study municipalities from the GVRD

18

Epitope mapping reveals conserved regions of an auxin-binding protein.  

PubMed

There is now good evidence that maize (Zea mays) auxin-binding protein (ABP) functions as a receptor. We have synthesized sequential overlapping hexapeptides to map the epitopes recognized by a number of antisera to ABP. Only a few regions of the protein are recognized, and these are shown to be exposed on the surface. Three epitopes predominate, and these are clustered around, but do not include, the glycosylation site. A comparison is made between these maps of sera against purified ABP, maps of sera raised against recombinant maize ABP expressed in Escherichia coli and computer antigenicity predictions. Our anti-(maize ABP) serum recognizes ABP counterparts in other plant species. We have used immunoblotting to affinity-purify the immunoglobulins which cross-react from the antiserum. Epitope mapping of these immunoglobulins suggests that two of the three predominant epitopes may be conserved in both monocotyledonous and dicotyledonous plants. The possible functional significance of these conserved epitopes is discussed. PMID:1377914

Napier, R M; Venis, M A

1992-06-15

19

Conservation of Extended Promoter Regions of Nodulation Genes in Rhizobium  

Microsoft Academic Search

A 47-base-pair (bp) conserved sequence in the 5'-flanking regions of three transcriptional units coding for nodulation functions (nodABC, nodEFG, and nodH) has been identified in Rhizobium meliloti strain 41. The conserved region contains subsequences of 7 bp, 5 bp, and 25 bp. The conserved 25-bp sequence was synthesized and used as a hybridization probe; three additional copies of the sequence

Katalin Rostas; Eva Kondorosi; Beatrix Horvath; Andras Simoncsits; Adam Kondorosi

1986-01-01

20

SNPs Occur in Regions with Less Genomic Sequence Conservation  

PubMed Central

Rates of SNPs (single nucleotide polymorphisms) and cross-species genomic sequence conservation reflect intra- and inter-species variation, respectively. Here, I report SNP rates and genomic sequence conservation adjacent to mRNA processing regions and show that, as expected, more SNPs occur in less conserved regions and that functional regions have fewer SNPs. Results are confirmed using both mouse and human data. Regions include protein start codons, 3? splice sites, 5? splice sites, protein stop codons, predicted miRNA binding sites, and polyadenylation sites. Throughout, SNP rates are lower and conservation is higher at regulatory sites. Within coding regions, SNP rates are highest and conservation is lowest at codon position three and the fewest SNPs are found at codon position two, reflecting codon degeneracy for amino acid encoding. Exon splice sites show high conservation and very low SNP rates, reflecting both splicing signals and protein coding. Relaxed constraint on the codon third position is dramatically seen when separating exonic SNP rates based on intron phase. At polyadenylation sites, a peak of conservation and low SNP rate occurs from 30 to 17 nt preceding the site. This region is highly enriched for the sequence AAUAAA, reflecting the location of the conserved polyA signal. miRNA 3? UTR target sites are predicted incorporating interspecies genomic sequence conservation; SNP rates are low in these sites, again showing fewer SNPs in conserved regions. Together, these results confirm that SNPs, reflecting recent genetic variation, occur more frequently in regions with less evolutionarily conservation. PMID:21674007

Castle, John C.

2011-01-01

21

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

PubMed

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

Lessmann, Janeth; Muñoz, Jesús; Bonaccorso, Elisa

2014-06-01

22

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

PubMed Central

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

Lessmann, Janeth; Muñoz, Jesús; Bonaccorso, Elisa

2014-01-01

23

Rocky Mountain Conservation Region Geospatial Information: KML Files  

NSDL National Science Digital Library

This portal features a selection of downloadable Keyhole Markup Language (KML) files containing geospatial data formatted for use in Google Earth. Selections include geospatial coverages for the Nature Conservancy's Rocky Mountain Conservation Region such as natural land cover and terrestrial ecoregion boundaries for prairies, basins, plateaus, and deserts in the western and southwestern United States.

24

Setting Priorities for Regional Conservation Planning in the Mediterranean Sea  

PubMed Central

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-based plans for the south and eastern Mediterranean is an urgent requirement for true regional conservation planning. PMID:23577060

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

25

Setting priorities for regional conservation planning in the Mediterranean Sea.  

PubMed

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-based plans for the south and eastern Mediterranean is an urgent requirement for true regional conservation planning. PMID:23577060

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

26

Suitability for conservation as a criterion in regional conservation network selection  

Microsoft Academic Search

The process of selecting candidate areas for inclusion in a regional conservation network should include not only delineating\\u000a appropriate land units for selection and defining targets for representing features of interest, but also determining the\\u000a suitability of land units for conservation purposes. We developed an explicit rating of conservation suitability by applying\\u000a fuzzy-logic functions in a knowledge base to ecological

Hope C. Humphries; Patrick S. Bourgeron; Keith M. Reynolds

2008-01-01

27

Occurrence of protein structure elements in conserved sequence regions  

PubMed Central

Background Conserved protein sequence regions are extremely useful for identifying and studying functionally and structurally important regions. By means of an integrated analysis of large-scale protein structure and sequence data, structural features of conserved protein sequence regions were identified. Results Helices and turns were found to be underrepresented in conserved regions, while strands were found to be overrepresented. Similar numbers of loops were found in conserved and random regions. Conclusion These results can be understood in light of the structural constraints on different secondary structure elements, and their role in protein structural stabilization and topology. Strands can tolerate fewer sequence changes and nonetheless keep their specific shape and function. They thus tend to be more conserved than helices, which can keep their shape and function with more changes. Loop behavior can be explained by the presence of both constrained and freely changing loops in proteins. Our detailed statistical analysis of diverse proteins links protein evolution to the biophysics of protein thermodynamic stability and folding. The basic structural features of conserved sequence regions are also important determinants of protein structure motifs and their function. PMID:17210087

Sitbon, Einat; Pietrokovski, Shmuel

2007-01-01

28

Conservation voltage reduction: Estimating methodology for a large regional application  

SciTech Connect

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.

De Steese, J.G. (Pacific Northwest Lab., Richland, WA (United States)); Kennedy, B.W. (Bonneville Power Administration, Portland, OR (United States)); Merrick, S.B. (Westinghouse Hanford Co., Richland, WA (United States))

1992-04-01

29

Conservation voltage reduction: Estimating methodology for a large regional application  

SciTech Connect

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.

De Steese, J.G. [Pacific Northwest Lab., Richland, WA (United States); Kennedy, B.W. [Bonneville Power Administration, Portland, OR (United States); Merrick, S.B. [Westinghouse Hanford Co., Richland, WA (United States)

1992-04-01

30

Aquaporins: Are regions of the protein conserved?  

NSDL National Science Digital Library

The osmotic controlled passage of polar water through fundamentally nonpolar biologic lipid bilayers (membranes) wasn't understood until the work of Peter Agre and Roderick MacKinnon on aquaporins resulting in the Nobel prize in Chemistry in 2003. We decided to examine conservation in aquaporins. A Google search provided us with both the PDB id (1h6i) of the human aquaporin A chain from RBCs, and a clearer understanding that the aquaprorins represent a related group of proteins present in multiple species. At http://www.rcsb.org/pdb/ we conducted an initial investigation of the structure of 1h6i. At consurf (http://consurf.tau.ac.il/) we were able to obtain the protein sequences for the best 20 matches in nearly FASTA form. After text editing we ran Clustalw and retrieved both rooted and unrooted trees. In the trees, it is easy to see the families of aquaporins (type 1, 2 etc; see tree.doc below).

Jerry Hall (Lane Community College; )

2004-10-24

31

Broadly reactive human CD8 T cells that recognize an epitope conserved between VZV, HSV and EBV.  

PubMed

Human herpesviruses are important causes of potentially severe chronic infections for which T cells are believed to be necessary for control. In order to examine the role of virus-specific CD8 T cells against Varicella Zoster Virus (VZV), we generated a comprehensive panel of potential epitopes predicted in silico and screened for T cell responses in healthy VZV seropositive donors. We identified a dominant HLA-A*0201-restricted epitope in the VZV ribonucleotide reductase subunit 2 and used a tetramer to analyze the phenotype and function of epitope-specific CD8 T cells. Interestingly, CD8 T cells responding to this VZV epitope also recognized homologous epitopes, not only in the other ?-herpesviruses, HSV-1 and HSV-2, but also the ?-herpesvirus, EBV. Responses against these epitopes did not depend on previous infection with the originating virus, thus indicating the cross-reactive nature of this T cell population. Between individuals, the cells demonstrated marked phenotypic heterogeneity. This was associated with differences in functional capacity related to increased inhibitory receptor expression (including PD-1) along with decreased expression of co-stimulatory molecules that potentially reflected their stimulation history. Vaccination with the live attenuated Zostavax vaccine did not efficiently stimulate a proliferative response in this epitope-specific population. Thus, we identified a human CD8 T cell epitope that is conserved in four clinically important herpesviruses but that was poorly boosted by the current adult VZV vaccine. We discuss the concept of a "pan-herpesvirus" vaccine that this discovery raises and the hurdles that may need to be overcome in order to achieve this. PMID:24675761

Chiu, Christopher; McCausland, Megan; Sidney, John; Duh, Fuh-Mei; Rouphael, Nadine; Mehta, Aneesh; Mulligan, Mark; Carrington, Mary; Wieland, Andreas; Sullivan, Nicole L; Weinberg, Adriana; Levin, Myron J; Pulendran, Bali; Peters, Bjoern; Sette, Alessandro; Ahmed, Rafi

2014-03-01

32

Optimal dynamic allocation of conservation funding among priority regions.  

PubMed

The optimal allocation of conservation resources between biodiverse conservation regions has generally been calculated using stochastic dynamic programming, or using myopic heuristics. These solutions are hard to interpret and may not be optimal. To overcome these two limitations, this paper approaches the optimal conservation resource allocation problem using optimal control theory. A solution using Pontryagin's maximum principle provides novel insight into the general properties of efficient conservation resource allocation strategies, and allows more extensive testing of the performance of myopic heuristics. We confirmed that a proposed heuristic (minimize short-term loss) yields near-optimal results in complex allocation situations, and found that a qualitative allocation feature observed in previous analyses (bang-bang allocation) is a general property of the optimal allocation strategy. PMID:18712571

Bode, Michael; Wilson, Kerrie; McBride, Marissa; Possingham, Hugh

2008-10-01

33

Energy Conservation Training Institute: commentary and review. [FEA Region V Institute meeting in Chicago  

Microsoft Academic Search

Throughout the spring of 1976, the Federal Energy Administration, as part of its on-going support of energy conservation, contracted with the Conservation Foundation of Washington, D.C., to sponsor eight regional Energy Conservation Training Institutes. The purpose of the Institutes was to train citizens in energy conservation strategies. The Region V Institute was sponsored by the Conservation Foundation and was locally

R. Pauls; S. Pauls

1976-01-01

34

A monoclonal antibody recognizes a highly conserved neutralizing epitope on hemagglutinin of H6N1 avian influenza virus.  

PubMed

Neutralizing antibodies on the globular head of the hemagglutinin (HA) of avian influenza virus (AIV) are crucial for controlling this disease. However, most neutralizing antibodies lack cross reaction. This report describes the identification of a hemagglutinin epitope on the globular head near the receptor binding site of the H6N1 AIV. A monoclonal antibody named EB2 was prepared against the H6N1 AIV HA. Flow cytometry of AIV-infected chicken embryo fibroblast, DF-1 cells and specific-pathogen-free embryonated eggs were used to verify the neutralizing activity of this mAb. To narrow down the binding region, partially overlapping HA fragments and synthetic peptides were used to map the epitope by immune-blotting. The linear motif RYVRMGTESMN, located on the surface on the globular head of the HA protein, was identified as the epitope bound by EB2 mAb. Alignment of the EB2-defined epitope with other H6 AIVs showed that this epitope was conserved and specific to H6. We propose that this motif is a linear B-cell epitope of the HA protein and is near the receptor binding site. The identified epitope might be useful for clinical applications and as a tool for further study of the structure and function of the AIV HA protein. PMID:25465660

He, Jie-Long; Hsieh, Ming-Shou; Juang, Rong-Huay; Wang, Ching-Ho

2014-12-01

35

Use of flow cytometry to identify monoclonal antibodies that recognize conserved epitopes on orthologous leukocyte differentiation antigens in goats, lamas, and rabbits  

Microsoft Academic Search

Flow cytometry was used to screen a panel of 320 mAbs, submitted to the Animal Homologues Section of the HLDA8, for mAbs that recognize epitopes conserved on orthologous leukocyte differentiation antigens (LDA) in goats, lamas, and rabbits. Nineteen mAbs specific for CD11a (1), CD14 (3), CD18 (1), CD21 (1), CD29 (2), CD44 (2), CD47 (3), CD49d (1), CD172a (1), CD45RB

William C. Davis; Karel Drbal; Abdel-El-Aziz A. E. Mosaad; Abdel-Rahman M. Elbagory; Ahmed Tibary; George M. Barrington; Yong Ho Park; Mary Jo Hamilton

2007-01-01

36

The relevance of the Mediterranean Region to colonial waterbird conservation  

USGS Publications Warehouse

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 data banks for seabirds, wading birds, ducks, and geese; (2) implementing a wetland inventory for many Countries with little quantitative data on wetlands; (3) improving habitat quality assessments; (4) improving relationships with industry, the private citizenry, and government officials to further an appreciation for the value of wetlands and waterbirds; (5) enhancing training efforts, especially in underdeveloped Countries; (6) evaluating the effects of hunting and other disturbances to nesting and feeding waterbirds in different regions; (7) setting up 'sister-reserve' (twinned) sites in Europe and Africa to foster international linkages and training; and (8) fostering local-regional conservation programs to preserve reed beds, wet woodlots, and other key habitats.

Erwin, R.M.

1996-01-01

37

Cytauxzoon felis infections are present in bobcats (Lynx rufus) in a region where cytauxzoonosis is not recognized in domestic cats.  

PubMed

This study was performed to determine the prevalence of Cytauxzoon felis (C. felis) infections in bobcats (Lynx rufus) from a region where C. felis is recognized in domestic cats, North Carolina (NC), and a region where C. felis is not recognized in domestic cats, Pennsylvania (PA). Samples from NC (n=32) were obtained post-mortem via cardiac puncture from legally trapped bobcats. Samples from PA (n=70) were collected post-mortem onto Nobuto blood collecting strips by the PA Game Commission. Each sample was tested using a C. felis specific PCR assay as well as a PCR assay targeting host DNA to rule out the presence of PCR inhibitors. Three samples were excluded due to the presence of PCR inhibitors. Thirty-three percent (10/30) of the samples from NC and 7% (5/69) of the samples from PA tested positive for the presence of C. felis. The proportion of C. felis positive bobcats from NC was significantly different than that from PA (P<0.005). Despite the lower prevalence of C. felis infections in bobcats from PA this finding is unique and indicates the potential for C. felis infections in domestic cats in the northeastern USA if the appropriate tick vectors are present. Veterinary practitioners in PA should be on alert for cytauxzoonosis in domestic cats. Further studies about the epidemiology and transmission of C. felis infections among both domestic cats and bobcats are needed. PMID:18295403

Birkenheuer, Adam J; Marr, Henry S; Warren, Camille; Acton, Anne E; Mucker, Eric M; Humphreys, Jan G; Tucker, Melissa D

2008-05-01

38

Use of flow cytometry to identify monoclonal antibodies that recognize conserved epitopes on orthologous leukocyte differentiation antigens in goats, llamas, and rabbits.  

PubMed

Flow cytometry was used to screen a panel of 320 mAbs, submitted to the Animal Homologues Section of the HLDA8, for mAbs that recognize epitopes conserved on orthologous leukocyte differentiation antigens (LDA) in goats, lamas, and rabbits. Nineteen mAbs specific for CD11a (1), CD14 (3), CD18 (1), CD21 (1), CD29 (2), CD44 (2), CD47 (3), CD49d (1), CD172a (1), CD45RB (1), CD61 (1), RACT48A, and GBSP71A reacted with goat LDA. Twenty three mAbs specific for CD7 (1), CD9 (2), CD11a (1), CD14 (3), CD18 (4), CD29 (1), CD32 (1), CD44 (1), CD47 (4), CD49d (2), CD50 (1), CD80 (1), CD172a (1), and GBSP71A reacted with llama LDA. Eighteen mAbs specific for CD9 (2), CD11a (1), CD14 (2), CD18 (4), CD21 (1), CD44 (2), CD45RB (1), CD49d (1), CD209 (1), RACT48A, and GBSP71A reacted with rabbit LDA. The specificities of two cross reactive mAbs that recognize different conserved epitopes on all leukocytes in two species (RACT48A) and all three species (GBSP71A) have not been determined. The patterns of reactivity of most of the mAbs were consistent with patterns of reactivity noted on human leukocytes. The specificity of some cross reactive mAbs generated in non-human species were validated on human leukocytes. Further studies are needed to verify that CD7, CD32, CD45RB, CD50, and CD209 recognize orthologous molecules in the indicated species. PMID:17686528

Davis, William C; Drbal, Karel; Mosaad, Abdel-El-Aziz A E; Elbagory, Abdel-Rahman M; Tibary, Ahmed; Barrington, George M; Park, Yong Ho; Hamilton, Mary Jo

2007-09-15

39

Water Conservation Policy in an Arid Metropolitan Region: A Historical and Geographical Assessment of Phoenix, Arizona  

E-print Network

Water Conservation Policy in an Arid Metropolitan Region: A Historical and Geographical Assessment and geographical methods is used to examine water conservation policy trends in the ten most populous municipalities in the greater Phoenix region. Residential water conservation policies and programs across

Hall, Sharon J.

40

Human dimension of conservation planning: the case of Madagascar at national and regional scales  

E-print Network

conservation planning efficiency in the Mediterranean Basin.Efficiency and concordance of alternative methods for minimizing opportunity costs in conservation planning.planning exercise either at regional scale when looking at the efficiency

Ramaharitra Tondrasoa, Tendro

2012-01-01

41

C3bi receptor (complement receptor type 3) recognizes a region of complement protein C3 containing the sequence Arg-Gly-Asp.  

PubMed Central

Human phagocytes express a receptor termed complement receptor type 3 (CR3) that recognizes the complement protein fragment C3bi. We show here that CR3 recognizes a region of C3 that contains the sequence Arg-Gly-Asp (RGD). CR3 is down-modulated upon spreading of macrophages on surfaces coated with a synthetic 21-residue peptide from C3 (residues 1383-1403). This peptide was also attached to erythrocytes by coupling myristic acid to its amino terminus and allowing the myristoylated peptide to bind to erythrocytes through hydrophobic interactions. Erythrocytes coated with this RGD-containing segment of C3 were bound by macrophages, and binding could be blocked by specific monoclonal antibodies against CR3. Since CR3 recognizes a peptide sequence that contains the RGD triplet, it appears to be a member of a larger family of adhesion-promoting receptors that recognize RGD-containing proteins. However, since CR3 does not recognize a hexapeptide containing RGD, we presume that residues beyond the RGD triplet contribute to binding. We have compared the RGD-containing region of fibronectin and vitronectin, proteins known to be recognized by means of their RGD-containing regions, with those in human and murine C3. A striking homology is observed over an approximately equal to 50 amino acid sequence present in all four proteins. We suggest that this extended region of homology contains a structure recognized by adhesion-promoting receptors. PMID:3550803

Wright, S D; Reddy, P A; Jong, M T; Erickson, B W

1987-01-01

42

A Syntenic Region Conserved from Fish to Mammalian X Chromosome  

PubMed Central

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

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

2014-01-01

43

A syntenic region conserved from fish to Mammalian x chromosome.  

PubMed

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

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

2014-01-01

44

A Human Antibody Recognizing a Conserved Epitope of H5 Hemagglutinin Broadly Neutralizes Highly Pathogenic Avian Influenza H5N1 Viruses  

PubMed Central

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

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

2012-01-01

45

ACHIEVING GLOBAL AND REGIONAL PERSPECTIVES ON FOREST BIODIVERSITY AND CONSERVATION  

Microsoft Academic Search

Forests are arguably the single most important repository of global biodiversity, attracting the attention of conservation planners as well as foresters. Diversity is an essential factor in maintaining forest function, so its conservation and management are important issues in forest planning. Because species and ecosystems are no respecters of national boundaries, and international collaboration is required to ensure their preservation,

V. KAPOS; S. F. IREMONGER

46

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...

47

A High-Affinity CDR-Grafted Antibody against Influenza A H5N1 Viruses Recognizes a Conserved Epitope of H5 Hemagglutinin  

PubMed Central

Highly pathogenic avian influenza (HPAI) H5N1 virus infection is still a potential threat to public health worldwide. While vaccines and antiviral drugs are currently under development, neutralizing antibodies could offer an alternative strategy to prevent and treat H5N1 virus infection. In the present study, we had developed a humanized antibody against H5N1 viruses from mouse-derived hybridoma in order to minimize its immunogenicity for potential clinical application. The humanized antibody hH5M9 was generated by transferring the mouse complementarity determining region (CDR) residues together with four key framework region (FR) residues onto the FR of the human antibody. This humanized antibody exhibited high affinity and specificity comparable to the parental mouse or chimeric counterpart with broad and strong neutralization activity against all H5N1 clades and subclades except for Egypt clades investigated. Furthermore, through epitope mapping we identified a linear epitope on the top region of hemagglutinin (HA) that was H5N1 specific and conserved. Our results for the first time reported a humanized antibody against H5N1 viruses by CDR grafting method. With the expected lower immunogenicity, this humanized antibody was expected to be more efficacious than murine or human-mouse chimeric antibodies for future application in humans. PMID:24558425

Xiong, Feifei; Xia, Liliang; Wang, Jingfang; Wu, Biao; Wang, Dengyu; Yuan, Longfang; Cheng, Yating; Zhu, Hongying; Che, Xiaoyan; Zhang, Qinghua; Zhao, Guoping; Wang, Ying

2014-01-01

48

INTEGRATING GRASSLAND AND SHRUBLAND BIRD CONSERVATION WITH THE NORTHERN BOBWHITE CONSERVATION INITIATIVE FOR THE CENTRAL HARDWOODS BIRD CONSERVATION REGION  

Microsoft Academic Search

Much attention has focused on management options to increase Northern Bobwhite (Colinus virginianus) habitat availability including the organization of the Southeast Quail Study Group Technical Committee and the creation of the Northern Bobwhite Conservation Initiative (NBCI). As the NBCI moves from the planning stages to implementation, there is a need to understand how management options for Northern Bobwhite populations will

JAMES J. GIOCOMO; DAVID A. BUEHLER; JANE FITZGERALD

49

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...

50

Recognizing Energy  

NSDL National Science Digital Library

Energy is such a common notion. We talk about it all the time. Should you buy energy-efficient windows? The country needs an energy policy. That little kid at the store who screaming at the top of his lungs sure has a lot of energy. This chapter deals with recognizing and defining energy. This free selection from Stop Faking It! Finally Understanding Science So You Can Teach It: Energy includes the Table of Contents and Preface.

William C. Robertson, Ph.D.

2002-01-01

51

Conserving migrating shorebirds in the Yellow Sea region  

Microsoft Academic Search

The Yellow Sea Region lies between North and South Korea to the east and China to the west, and covers an area of 458 000 sq km. Biodiversity in the inter-tidal zone of the Yellow Sea Region is high: excellent feeding and roosting areas accom- modate many different species of waterbirds, and preliminary records indicate that the coastal zone of

C. Kelin; X. Qiang

52

Continuity or Change: what a future Conservative Continuity or Change: what a future Conservative Continuity or Change: what a future Conservative Continuity or Change: what a future Conservative government might mean for regional, housing and  

Microsoft Academic Search

Abstract Abstract Abstract This paper reviews current Conservative Party thinking in relation to four policy areas: urban and regional policy; housing policy; labour market and welfare policy; and the third sector. It seeks to explore aspects of continuity and change, both with the current New Labour government and the Conservative government of 1979-1997. A remarkable degree of continuity is revealed,

Richard Crisp; Rob Macmillan; David Robinson; Peter Wells

53

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

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

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

1992-01-01

54

Conservation of an immunoglobulin variable-region gene family indicates a specific, noncoding function.  

PubMed Central

Blot-hybridization and DNA sequence analyses reveal the particular evolutionary conservation of a group of immunoglobulin heavy-chain variable-region (VH) genes in all mammalian species examined. These particular genes are group III genes--the VH7183 family in the mouse and the homologous VH III family in human. This conservation is localized to sequences encoding framework regions 1 and 3 of the antibody variable region and is exerted at the nucleotide level. Because selection acting at the amino acid level alone cannot explain the conservation of these sequences, these sequences must have a noncoding function. The preferential rearrangement of VH7183 and VH III genes, together with the similarity of the conserved sequences to elements implicated in recombination in other systems, suggest that these sequences function to target the series of rearrangements that assemble complete immunoglobulin genes. Images PMID:2798416

Tutter, A; Riblet, R

1989-01-01

55

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

PubMed

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. PMID:20557656

White, W T; Kyne, P M

2010-06-01

56

South West Woodland Renaissance Helping to conserve the region's woodlands  

E-print Network

and target urban markets, tourist markets and seasonal selling opportunities through events across the South, supports a grants programme which is used to fund targeted schemes that support regional development and market knowledge within and about the industry. · To identify and roll-out best practice across

57

An Evolutionary Model for Protein-Coding Regions with Conserved RNA Structure  

E-print Network

. Introduction Some genome regions direct both the synthesis of a protein and the formation of biologicallyAn Evolutionary Model for Protein-Coding Regions with Conserved RNA Structure Jakob Skou Pedersen, University of Oxford, Oxford, England Here we present a model of nucleotide substitution in protein

Hein, Jotun

58

Old and New World arenaviruses share a highly conserved epitope in the fusion domain of the glycoprotein 2, which is recognized by Lassa virus-specific human CD4+ T-cell clones  

Microsoft Academic Search

Data from human studies and animal experiments indicate a dominant role of T-cells over antibodies in controlling acute Lassa virus infection and providing immunity to reinfection. Knowledge of the epitopes recognized by T-cells may therefore be crucial to the development of a recombinant Lassa virus vaccine. In order to study human T-cell reactivity to the most conserved structural protein of

Jan ter Meulen; Marlis Badusche; Judith Satoguina; Thomas Strecker; Oliver Lenz; Cornelius Loeliger; Mohamed Sakho; Kekoura Koulemou; Lamine Koivogui; Achim Hoerauf

2004-01-01

59

Strategy for Sea Turtle Conservation in the WIO Region (J. A. Mortimer) --page 1 A Strategy to Conserve and Manage the Sea Turtle Resources  

E-print Network

Strategy for Sea Turtle Conservation in the WIO Region (J. A. Mortimer) -- page 1 A Strategy to Conserve and Manage the Sea Turtle Resources of the Western Indian Ocean Region A report produced for IUCN of five species of sea turtles occur in the Western Indian Ocean (WIO). These have long been a resource

Prestwich, Ken

60

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

DOE Data Explorer

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

Loots, Gabriela G. (LLNL); Ovcharenko, I. (LLNL)

61

Conservation.  

ERIC Educational Resources Information Center

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,…

National Audubon Society, New York, NY.

62

SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions  

PubMed Central

Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E. PMID:22977176

Davey, Norman E.; Cowan, Joanne L.; Shields, Denis C.; Gibson, Toby J.; Coldwell, Mark J.; Edwards, Richard J.

2012-01-01

63

High-frequency expression of a conserved kappa light-chain variable-region gene in chronic lymphocytic leukemia  

SciTech Connect

Malignant B lymphocytes from several patients with chronic lymphocytic leukemia (CLL) were examined for reactivity with murine monoclonal antibody 17.109. This antibody, prepared against the rheumatoid factor (RF) paraprotein Sie, recognizes a cross reactive idiotype on 48% of human IgM RF paraproteins, but does not react with IgM paraproteins without RF activity or substantially with normal pooled immunoglobulin. The 17.109-reactive idiotype is a marker for a kappa III variable-region gene, designated V/sub kappa/RF, that is conserved in outbred human populations. In a limited study of 31 CLL patients, the leukemic cells from 5 of 20 patients with kappa light chain-expressing CLL were recognized by the 17.109 monoclonal antibody. Despite having malignant cells specifically reactive with this antibody, patients with 17.109-positive CLL did not have elevated serum levels of circulating antibody bearing 17.109-reactive determinants. Total RNAs isolated from the CLL B lymphocytes, or from hybridomas produced by fusing the CLL cells with the WI-L2-729-HF/sub 2/ cell line, were fractionated electrophoretically and examined by blot hybridization. Under stringent hybridization conditions capable of discerning a single base-pair mismatch, RNA from the 17.109-idiotype-positive CLL cells hybridized to synthetic oligonucleotide probes corresponding to framework and complementary-determining regions in the V/sub kappa/RF gene. The high frequency of the 17.109-associated idiotype and the V/sub kappa/RF gene in CLL suggests that the disease may arise from B lymphocytes that express a restricted set of inherited immunoglobulin variable-region genes with little or no somatic mutation.

Kipps, T.J.; Fong, S.; Tomhave, E.; Chen, P.P.; Goldfien, R.D.; Carson, D.A.

1987-05-01

64

High-frequency expression of a conserved kappa light-chain variable-region gene in chronic lymphocytic leukemia.  

PubMed Central

Malignant B lymphocytes from several patients with chronic lymphocytic leukemia (CLL) were examined for reactivity with murine monoclonal antibody 17.109. This antibody, prepared against the rheumatoid factor (RF) paraprotein Sie, recognizes a crossreactive idiotype on 48% of human IgM RF paraproteins, but does not react with IgM paraproteins without RF activity or substantially with normal pooled immunoglobulin. The 17.109-reactive idiotype is a marker for a kappa III variable-region gene, designated V kappa RF, that is conserved in outbred human populations. In a limited study of 31 CLL patients, the leukemic cells from 5 of 20 patients with kappa light chain-expressing CLL were recognized by the 17.109 monoclonal antibody. Despite having malignant cells specifically reactive with this antibody, patients with 17.109-positive CLL did not have elevated serum levels of circulating antibody bearing 17.109-reactive determinants. Total RNAs isolated from the CLL B lymphocytes, or from hybridomas produced by fusing the CLL cells with the WI-L2-729-HF2 cell line, were fractionated electrophoretically and examined by blot hybridization. Under stringent hybridization conditions capable of discerning a single base-pair mismatch, RNA from the 17.109-idiotype-positive CLL cells hybridized to synthetic oligonucleotide probes corresponding to framework and complementary-determining regions in the V kappa RF gene. The high frequency of the 17.109-associated idiotype and the V kappa RF gene in CLL suggests that the disease may arise from B lymphocytes that express a restricted set of inherited immunoglobulin variable-region genes with little or no somatic mutation. Images PMID:3106980

Kipps, T J; Fong, S; Tomhave, E; Chen, P P; Goldfien, R D; Carson, D A

1987-01-01

65

Achieving Conservation when Opportunity Costs Are High: Optimizing Reserve Design in Alberta's Oil Sands Region  

PubMed Central

Recent studies have shown that conservation gains can be achieved when the spatial distributions of biological benefits and economic costs are incorporated in the conservation planning process. Using Alberta, Canada, as a case study we apply these techniques in the context of coarse-filter reserve design. Because targets for ecosystem representation and other coarse-filter design elements are difficult to define objectively we use a trade-off analysis to systematically explore the relationship between conservation targets and economic opportunity costs. We use the Marxan conservation planning software to generate reserve designs at each level of conservation target to ensure that our quantification of conservation and economic outcomes represents the optimal allocation of resources in each case. Opportunity cost is most affected by the ecological representation target and this relationship is nonlinear. Although petroleum resources are present throughout most of Alberta, and include highly valuable oil sands deposits, our analysis indicates that over 30% of public lands could be protected while maintaining access to more than 97% of the value of the region's resources. Our case study demonstrates that optimal resource allocation can be usefully employed to support strategic decision making in the context of land-use planning, even when conservation targets are not well defined. PMID:21858046

Schneider, Richard R.; Hauer, Grant; Farr, Dan; Adamowicz, W. L.; Boutin, Stan

2011-01-01

66

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

PubMed Central

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

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

2014-01-01

67

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

USGS Publications Warehouse

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 Regions appear to provide reasonable strata for summary of BBS data.

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

2003-01-01

68

An Escherichia coli replication protein that recognizes a unique sequence within a hairpin region in phi X174 DNA.  

PubMed Central

Protein n', a prepriming DNA replication enzyme of Escherichia coli, is a phi X174 DNA-dependent ATPase. Restriction of phi X174 DNA have led to the identification of a 55-nucleotide fragment that carries the protein n' recognition sequence. Molecular hybridization and sequence analysis have located this sequence within the untranslated region between genes F and G, a map location analogous to that of the unique complementary strand origin of phage G4 DNA. Within the 55-nucleotide fragment is a sequence of 44 nucleotides that forms a stable hairpin structure. This duplex may be the signal for protein n' to initiate the prepriming events that led to the start of phi X174 complementary DNA strand replication. Images PMID:6444725

Shlomai, J; Kornberg, A

1980-01-01

69

Conservation Assessment for the Big Bend-Ro Bravo Region 19 Aquatic and  

E-print Network

)/ Rio Grande Wild and Scenic River (right) Photo: Jeffery Bennett #12;Conservation Assessment Mountains in Colorado and New Mexico and much of the western half of New Mexico. Water diver- sions to the long-term regional drought, have put extreme pressure on the Rio Grande's aquatic ecology. Fortunately

Pasternack, Gregory B.

70

Regional assessment and conservation implications of landscape characteristics of African national parks  

Microsoft Academic Search

The spatial characteristics of African protected areas classified as national parks (category II) by the World Conservation Union (IUCN) were quantified on a regional basis. Four groups of spatial statistics were used; park size, park abundance, park shape and park spacing. Eastern Africa has the greatest number of small national parks (< 100 km2 and 100–1000 km2), western Africa most

W. Roy Siegfried; Grant A. Benn; Caroline M. Gelderblom

1998-01-01

71

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

USGS Publications Warehouse

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.

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

2004-01-01

72

WILDLIFE CONSERVATION AND LAND-USE CHANGES IN THE TRANSHIMALAYAN REGION OF LADAKH, INDIA  

Microsoft Academic Search

4 ABSTRACT Changes in economy and land use are under way in the Indian Transhimalayan region of Ladakli, creating both negative and positive prospects for wildlife conservation in this sparsely populated and previously remote area. New livestock breeds, irrigation developments, farming practices, foreign tourists, and a large military presence are changing the way people view and use the mountainous land

JOSEPH L. Fox; SEEMA BHATT; ALOK CHANDOLA

1994-01-01

73

Evolution and structural conservation of the control region of insect mitochondrial DNA  

Microsoft Academic Search

The control regions of mitochondrial DNA of two insects, Schistocerca gregaria and Chorthippus parallelus, have been isolated and sequenced. Their sizes are 752 by and 1,512 bp, respectively, with the presence of a tandem repeat in C. parallelus. (The sequences of the two repeats are highly conserved, having a homology of 97.5%.) Comparison of their nucleotide sequences revealed the presence

De-Xing Zhang; Jacek M. Szymura; Godfrey M. Hewitt

1995-01-01

74

Carnivores as Focal Species for Conservation Planning in the Rocky Mountain Region  

Microsoft Academic Search

Viability analysis of well-selected focal species can complement ecosystem- level conservation planning by revealing thresholds in habitat area and landscape connec- tivity. Mammalian carnivores are good candidates for focal species because their distri- butional patterns often strongly reflect regional-scale population processes. We incorporated focal species analysis of four carnivore species, fisher (Martes pennanti), lynx (Lynx can- adensis), wolverine (Gulo gulo),

Carlos Carroll; Reed F. Noss; Paul C. Paquet

2001-01-01

75

Rapid Profiling of the Antigen Regions Recognized by Serum Antibodies Using Massively Parallel Sequencing of Antigen-Specific Libraries  

PubMed Central

There is a need for techniques capable of identifying the antigenic epitopes targeted by polyclonal antibody responses during deliberate or natural immunization. Although successful, traditional phage library screening is laborious and can map only some of the epitopes. To accelerate and improve epitope identification, we have employed massive sequencing of phage-displayed antigen-specific libraries using the Illumina MiSeq platform. This enabled us to precisely identify the regions of a model antigen, the meningococcal NadA virulence factor, targeted by serum antibodies in vaccinated individuals and to rank hundreds of antigenic fragments according to their immunoreactivity. We found that next generation sequencing can significantly empower the analysis of antigen-specific libraries by allowing simultaneous processing of dozens of library/serum combinations in less than two days, including the time required for antibody-mediated library selection. Moreover, compared with traditional plaque picking, the new technology (named Phage-based Representation OF Immuno-Ligand Epitope Repertoire or PROFILER) provides superior resolution in epitope identification. PROFILER seems ideally suited to streamline and guide rational antigen design, adjuvant selection, and quality control of newly produced vaccines. Furthermore, this method is also susceptible to find important applications in other fields covered by traditional quantitative serology. PMID:25473968

Domina, Maria; Lanza Cariccio, Veronica; Benfatto, Salvatore; D'Aliberti, Deborah; Venza, Mario; Borgogni, Erica; Castellino, Flora; Biondo, Carmelo; D'Andrea, Daniel; Grassi, Luigi; Tramontano, Anna; Teti, Giuseppe; Felici, Franco; Beninati, Concetta

2014-01-01

76

Assessing and Prioritizing Ecological Communities for Monitoring in a Regional Habitat Conservation Plan  

NASA Astrophysics Data System (ADS)

In nature reserves and habitat conservation areas, monitoring is required to determine if reserves are meeting their goals for preserving species, ecological communities, and ecosystems. Increasingly, reserves are established to protect multiple species and communities, each with their own conservation goals and objectives. As resources are always inadequate to monitor all components, criteria must be applied to prioritize both species and communities for monitoring and management. While methods for prioritizing species based on endangerment or risk have been established, approaches to prioritizing ecological communities for monitoring are not well developed, despite a long-standing emphasis on communities as target elements in reserve design. We established guidelines based on four criteria derived from basic principles of conservation and landscape ecology—extent, representativeness, fragmentation, and endangerment—to prioritize communities in the San Diego Multiple Species Conservation Plan (MSCP). The MSCP was one of the first multiple-species habitat conservation areas established in California, USA, and it has a complex spatial configuration because of the patterns of surrounding land use, which are largely urbanized. In this case study, high priority communities for monitoring include coastal sage scrub (high endangerment, underrepresented within the reserve relative to the region, and moderately fragmented), freshwater wetlands, and coastal habitats (both have high fragmentation, moderate endangerment and representativeness, and low areal extent). This framework may be useful to other conservation planners and land managers for prioritizing the most significant and at-risk communities for monitoring.

Hierl, Lauren A.; Franklin, Janet; Deutschman, Douglas H.; Regan, Helen M.; Johnson, Brenda S.

2008-07-01

77

Comparative Sequence Analysis of 634 kb of the Mouse Chromosome 16 Region of Conserved Synteny with the Human Velocardiofacial Syndrome Region on Chromosome 22q11.2  

Microsoft Academic Search

Mouse genomic DNA sequence extending 634 kb on proximal mouse chromosome 16 was compared to the corresponding human sequence from chromosome 22q11.2. Haploinsufficiency for this region results in velocardiofacial syndrome (VCFS) in humans. The mouse region is rearranged into three conserved blocks relative to human, but gene content and position are highly conserved within these blocks. Examination of the boundaries

James Lund; Feng Chen; Axin Hua; Bruce Roe; Marcia Budarf; Beverly S. Emanuel; Roger H. Reeves

2000-01-01

78

Antigenic structure of the central conserved region of protein G of bovine respiratory syncytial virus.  

PubMed Central

Epitopes were resolved at the amino acid level for nine monoclonal antibodies (MAbs) directed against the central conserved region of protein G of bovine respiratory syncytial virus (BRSV-G). Peptide binding studies showed which amino acids in the epitope contributed to antibody binding. The details of the epitopes were compared with the high-resolution structure of a synthetic peptide corresponding to the central conserved region of BRSV-G, and this indicated which face of the central conserved region is the antigenic structure. The major linear epitope of the central conserved region of BRSV-G is located at the tip of the loop, overlapping a relatively flat surface formed by a double disulfide-bonded cystine noose. At least one, but possibly two sulfur atoms of a disulfide bridge that line the conserved pocket at the center of the flat surface, is a major contributor to antibody binding. Some of the residue positions in the epitope have mutated during the evolution of RSV-G, which suggests that the virus escaped antibody recognition with these mutations. Mutations that occur at positions 177 and 180 may have only a local effect on the antigenic surface, without influencing the structure of the backbone, whereas mutations at positions 183 and 184 will probably have major structural consequences. The study explains the antigenic, structural, and functional importance of each residue in the cystine noose which provides information for peptide vaccine design. Additionally, analysis of the epitopes demonstrated that two point mutations at positions 180 and 205 define the preliminary classification of BRSV subgroups. PMID:9094683

Langedijk, J P; Meloen, R H; Taylor, G; Furze, J M; van Oirschot, J T

1997-01-01

79

Primary Structure of the Variable Region of Monoclonal Antibody 2B10, Capable of Inducing Anti-Idiotypic Antibodies That Recognize the C-Terminal Region of MSA1 ofPlasmodium falciparum  

Microsoft Academic Search

Previously, we reported on the properties of a monoclonal antibody, 2B10, which has the same determinant on the human erythrocyte as MSA-1 ofPlasmodium falciparum(FCR3 strain); the binding of both ligands to erythrocytereceptorswastotallysialicaciddependent.Inthiswork,rabbitanti-2B10idiotypicantibodieswere 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

SHIDONG SU; SHUTONG YANG; RUCHUANG DING; ANDEUGENE A. DAVIDSON

80

Building on IUCN Regional Red Lists to Produce Lists of Species of Conservation Priority: a Model with Irish Bees  

Microsoft Academic Search

A World Conservation Union (IUCN) regional red list is an objective assessment of regional extinc- tion 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 conserva- tion action. We developed a simple eight-step priority-setting process and

ÚNA FITZPATRICK; TOMÁS E. MURRAY; ROBERT J. PAXTON; MARK J. F. BROWN

2007-01-01

81

Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome  

PubMed Central

The H1N1 subtype of influenza A virus has caused two of the four documented pandemics and is responsible for seasonal epidemic outbreaks, presenting a continuous threat to public health. Co-circulating antigenically divergent influenza strains significantly complicates vaccine development and use. Here, by combining evolutionary, structural, functional, and population information about the H1N1 proteome, we seek to answer two questions: (1) do residues on the protein surfaces evolve faster than the protein core residues consistently across all proteins that constitute the influenza proteome? and (2) in spite of the rapid evolution of surface residues in influenza proteins, are there any protein regions on the protein surface that do not evolve? To answer these questions, we first built phylogenetically-aware models of the patterns of surface and interior substitutions. Employing these models, we found a single coherent pattern of faster evolution on the protein surfaces that characterizes all influenza proteins. The pattern is consistent with the events of inter-species reassortment, the worldwide introduction of the flu vaccine in the early 80’s, as well as the differences caused by the geographic origins of the virus. Next, we developed an automated computational pipeline to comprehensively detect regions of the protein surface residues that were 100% conserved over multiple years and in multiple host species. We identified conserved regions on the surface of 10 influenza proteins spread across all avian, swine, and human strains; with the exception of a small group of isolated strains that affected the conservation of three proteins. Surprisingly, these regions were also unaffected by genetic variation in the pandemic 2009 H1N1 viral population data obtained from deep sequencing experiments. Finally, the conserved regions were intrinsically related to the intra-viral macromolecular interaction interfaces. Our study may provide further insights towards the identification of novel protein targets for influenza antivirals. PMID:24282564

Warren, Samantha; Wan, Xiu-Feng; Conant, Gavin; Korkin, Dmitry

2013-01-01

82

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

PubMed Central

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

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

2014-01-01

83

Mass conservation and atmospheric dynamics in the Regional Atmospheric Modeling System (RAMS)  

Microsoft Academic Search

This paper examines the spatio-temporal patterns of atmospheric carbon dioxide transport predicted by the Regional Atmospheric Modeling System (RAMS). Forty-eight hour simulations over northern New England incorporating a simple representation of the diurnal summertime surface carbon dioxide forcing arising from biological activity indicate that, in its native formulation, RAMS exhibits a significant degree of mass non-conservation. Domain-wide rates of non-physical

David Medvigy; Paul R. Moorcroft; Roni Avissar; Robert L. Walko

2005-01-01

84

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

PubMed Central

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

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

1989-01-01

85

Sequence conservation of the region targeted by the Abbott RealTime HCV viral load assay.  

PubMed

The Abbott RealTime (RT) HCV assay targets the 5' untranslated region (UTR) of the HCV genome. Here, we analyzed the sequence variability of the assay target regions from 1,092 specimens. Thermodynamic modeling of the percentage of primers/probes bound at the assay annealing temperature was performed to assess the potential effect of sequence variability. An analysis of this large data set revealed that the primer and probe binding sites of the RealTime HCV viral load assay are highly conserved and that naturally occurring sequence polymorphisms are not expected to discernibly impact assay performance. PMID:24430453

Cloherty, Gavin; Parkin, Neil; Rhoads, James; Esping, Claudia; Steinhart, Corklin; Schneider, George; Yuen, Lily; Hackett, John

2014-04-01

86

Sequence Conservation of the Region Targeted by the Abbott RealTime HCV Viral Load Assay  

PubMed Central

The Abbott RealTime (RT) HCV assay targets the 5? untranslated region (UTR) of the HCV genome. Here, we analyzed the sequence variability of the assay target regions from 1,092 specimens. Thermodynamic modeling of the percentage of primers/probes bound at the assay annealing temperature was performed to assess the potential effect of sequence variability. An analysis of this large data set revealed that the primer and probe binding sites of the RealTime HCV viral load assay are highly conserved and that naturally occurring sequence polymorphisms are not expected to discernibly impact assay performance. PMID:24430453

Parkin, Neil; Rhoads, James; Esping, Claudia; Steinhart, Corklin; Schneider, George; Yuen, Lily; Hackett, John

2014-01-01

87

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

PubMed

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 a controversial conservation strategy, and would be difficult in what is largely a highly fragmented area geographically. PMID:25540698

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

2014-11-01

88

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

PubMed Central

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 a controversial conservation strategy, and would be difficult in what is largely a highly fragmented area geographically. PMID:25540698

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

2014-01-01

89

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

NASA Astrophysics Data System (ADS)

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 open space remains to accommodate the expected population growth. Redevelopment conserved more naturally vegetated open space. The redevelopment scenario also permits the lowest increase in energy demand because buildings taken out in the process are reconfigured to higher levels of energy efficiency. However, redevelopment requires substantial increases in residential densities to confine the spatial footprint of the expected future urban growth. These three urban growth scenario footprints differ in their impact to natural vegetation and open space. To incorporate the influence of climate change on remaining natural ecosystems in this urbanizing landscape, we projected the stability of existing, mapped, vegetation types in the region under future climates by examining where projected ranges of the dominant plant species comprising each California Wildlife Habitat Relationship type will all remain together, and where they will begin to dis-associate due to biogeographic response to changing climate. This permits identification of stable and unstable zones of vegetation. The combination of climate stable, high conservation priority and likelihood of urban development provides a way to prioritize conservation land acquisitions.

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

2011-12-01

90

[Optimization of conservation network system for inter-basin wetland ecosystem in Huang-Huai-Hai Region].  

PubMed

By using systematic conservation planning (SCP) method, and taking catchment as planning unit, an optimization of conservation network system for the inter-basin wetland ecosystem in Huang-Huai-Hai Region was conducted, with a comprehensive consideration of 3-dimensional (lateral, longitudinal and vertical) connectivity and Inter-basin Water Transfer Project and by the methods of irreplaceability analysis and gap identification. The efficacy of the optimized conservation network system was evaluated, as compared with the existing conservation network system. According to the principles of irreplaceability and connectivity, the wetland conservation gaps could be divided into two types, i.e. , be conserved in priority and in general. After the optimization, the conservation status of the inter-basin wetland ecosystem in Huang-Huai-Hai Region had an overall improvement. The conserved percentage of the wetland types was from about 20% up to 46.8%, and, for each wetland type, its conserved level increased to some extent, almost above 40%. Both in the near future and in the long term, more attention should be paid to the conservation of lake wetland. In addition, the integration of ecosystem service function and biodiversity and the combination of protection with restoration would be the main task for the wetland ecosystem conservation planning in the future. PMID:22586975

Song, Xiao-Long; Li, Xiao-Wen; Zhang, Ming-Xiang; Yang, Dian-Lin; Zhang, Li-Na; Zhang, Gui-Long

2012-02-01

91

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

PubMed

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. PMID:17883497

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

2007-10-01

92

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

USGS Publications Warehouse

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.

Mushet, David M.; Neau, Jordan L.

2014-01-01

93

Plant diversity and conservation status of Himalayan Region Poonch Valley Azad Kashmir (Pakistan).  

PubMed

The plant diversity of Himalayan region has been reduced to greater extent due to environmental degradation and human exploitation. Anthropogenic disturbance was the major factor responsible for fragmentation of forest vegetation into small patches. Little research has been conducted in the Himalayan region of Poonch Valley of North eastern Pakistan with reference to plants biodiversity and its conservation. The present research was carried out to provide a checklist of vegetation for biodiversity conservation. A total of 430 vascular and 5 nonvascular plant species with 5 species of Bryophytes (5 families), 13 species of Pteridophytes (6 families), 4 species of Gymnosperms (1 family) and 413 species of angiosperms (95 families) were enumerated from the Poonch valley Azad Kashmir. The genera were classified into three categories according to the number of species. 25 plant communities with phytosociological parameters and diversity indices were reported. Present study revealed that there were 145 threatened, 30 endangered, 68 vulnerable and 47 rare species. It is recorded that extensive grazing, uprooting of plants and soil slope erosion intensify the environmental problems. Since there is maximum exploitation of vegetation, the valley showed a decline in plant diversity. The study was also indicated that the main threats to the biodiversity are expansion of settlement and army installations in the forest area of the valley. For sustainable use In-situ and Ex-situ conservation, controlled harvesting and afforestation may be the solution. Moreover, forest area should be declared prohibited for settlements and army installations. PMID:25176378

Khan, Muhammad Azam; Khan, Mir Ajab; Hussain, Mazhar; Mujtaba, Ghulam

2014-09-01

94

The juxtamembrane regions of human receptor tyrosine kinases exhibit conserved interaction sites with anionic lipids  

PubMed Central

Receptor tyrosine kinases (RTKs) play a critical role in diverse cellular processes and their activity is regulated by lipids in the surrounding membrane, including PIP2 (phosphatidylinositol-4,5-bisphosphate) in the inner leaflet, and GM3 (monosialodihexosylganglioside) in the outer leaflet. However, the precise details of the interactions at the molecular level remain to be fully characterised. Using a multiscale molecular dynamics simulation approach, we comprehensively characterise anionic lipid interactions with all 58 known human RTKs. Our results demonstrate that the juxtamembrane (JM) regions of RTKs are critical for inducing clustering of anionic lipids, including PIP2, both in simple asymmetric bilayers, and in more complex mixed membranes. Clustering is predominantly driven by interactions between a conserved cluster of basic residues within the first five positions of the JM region, and negatively charged lipid headgroups. This highlights a conserved interaction pattern shared across the human RTK family. In particular predominantly the N-terminal residues of the JM region are involved in the interactions with PIP2, whilst residues within the distal JM region exhibit comparatively less lipid specificity. Our results suggest that JM–lipid interactions play a key role in RTK structure and function, and more generally in the nanoscale organisation of receptor-containing cell membranes. PMID:25779975

Hedger, George; Sansom, Mark S. P.; Koldsø, Heidi

2015-01-01

95

The juxtamembrane regions of human receptor tyrosine kinases exhibit conserved interaction sites with anionic lipids.  

PubMed

Receptor tyrosine kinases (RTKs) play a critical role in diverse cellular processes and their activity is regulated by lipids in the surrounding membrane, including PIP2 (phosphatidylinositol-4,5-bisphosphate) in the inner leaflet, and GM3 (monosialodihexosylganglioside) in the outer leaflet. However, the precise details of the interactions at the molecular level remain to be fully characterised. Using a multiscale molecular dynamics simulation approach, we comprehensively characterise anionic lipid interactions with all 58 known human RTKs. Our results demonstrate that the juxtamembrane (JM) regions of RTKs are critical for inducing clustering of anionic lipids, including PIP2, both in simple asymmetric bilayers, and in more complex mixed membranes. Clustering is predominantly driven by interactions between a conserved cluster of basic residues within the first five positions of the JM region, and negatively charged lipid headgroups. This highlights a conserved interaction pattern shared across the human RTK family. In particular predominantly the N-terminal residues of the JM region are involved in the interactions with PIP2, whilst residues within the distal JM region exhibit comparatively less lipid specificity. Our results suggest that JM-lipid interactions play a key role in RTK structure and function, and more generally in the nanoscale organisation of receptor-containing cell membranes. PMID:25779975

Hedger, George; Sansom, Mark S P; Koldsø, Heidi

2015-01-01

96

Conserved regulatory elements in the promoter region of the N-CAM gene  

SciTech Connect

Genomic clones containing 5[prime]-flanking sequences, the first exon, and the entire first intron from the chicken N-CAM gene were characterized by restriction mapping and DNA sequencing. A > 600-bp segment that includes the first exon is very G + C-rich and contains a large proportion of CpG dinucleotides, suggesting that it represents a CpG island. SP-1 and AP-1 consensus elements are present, but no TATA- or CCAAT-like elements were found within 300 bp upstream of the first exon. Comparison of the chicken promoter region sequence with similar regions of the human, rat, and mouse N-CAM genes revealed that some potential regulatory elements including a [open quotes]purine box[close quotes] seen in mouse and rat N-CAM genes, one of two homeodomain binding regions seen in mammalian N-CAM genes, and several potential SP-1 sites are not conserved within this region. In contrast, high CpG content, a homeodomain binding sequence, an SP-1 element, an octomer element, and an AP-1 element are conserved in all four genes. The first intron of the chicken gene is 38 kb, substantially smaller than the corresponding intron from mammalian N-CAM genes. Together with previous studies, this work completes the cloning of the chicken N-CAM gene, which contains at least 26 exons distributed over 85 kb. 49 refs., 5 figs.

Colwell, G.; Li, B.; Forrest, D.; Brackenbury, R. (Univ. of Cincinnati Medical Center, OH (United States))

1992-12-01

97

Novel bacterial lipoprotein structures conserved in low-GC content gram-positive bacteria are recognized by Toll-like receptor 2.  

PubMed

Bacterial lipoproteins/lipopeptides inducing host innate immune responses are sensed by mammalian Toll-like receptor 2 (TLR2). These bacterial lipoproteins are structurally divided into two groups, diacylated or triacylated lipoproteins, by the absence or presence of an amide-linked fatty acid. The presence of diacylated lipoproteins has been predicted in low-GC content gram-positive bacteria and mycoplasmas based on the absence of one modification enzyme in their genomes; however, we recently determined triacylated structures in low-GC gram-positive Staphylococcus aureus, raising questions about the actual lipoprotein structure in other low-GC content gram-positive bacteria. Here, through intensive MS analyses, we identified a novel and unique bacterial lipoprotein structure containing an N-acyl-S-monoacyl-glyceryl-cysteine (named the lyso structure) from low-GC gram-positive Enterococcus faecalis, Bacillus cereus, Streptococcus sanguinis, and Lactobacillus bulgaricus. Two of the purified native lyso-form lipoproteins induced proinflammatory cytokine production from mice macrophages in a TLR2-dependent and TLR1-independent manner but with a different dependence on TLR6. Additionally, two other new lipoprotein structures were identified. One is the "N-acetyl" lipoprotein structure containing N-acetyl-S-diacyl-glyceryl-cysteine, which was found in five gram-positive bacteria, including Bacillus subtilis. The N-acetyl lipoproteins induced the proinflammatory cytokines through the TLR2/6 heterodimer. The other was identified in a mycoplasma strain and is an unusual diacyl lipoprotein structure containing two amino acids before the lipid-modified cysteine residue. Taken together, our results suggest the existence of novel TLR2-stimulating lyso and N-acetyl forms of lipoproteins that are conserved in low-GC content gram-positive bacteria and provide clear evidence for the presence of yet to be identified key enzymes involved in the bacterial lipoprotein biosynthesis. PMID:22303020

Kurokawa, Kenji; Ryu, Kyoung-Hwa; Ichikawa, Rie; Masuda, Akiko; Kim, Min-Su; Lee, Hanna; Chae, Jun-Ho; Shimizu, Takashi; Saitoh, Tatsuya; Kuwano, Koichi; Akira, Shizuo; Dohmae, Naoshi; Nakayama, Hiroshi; Lee, Bok Luel

2012-04-13

98

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

SciTech Connect

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.

Loots, G; Ovcharenko, I

2006-08-08

99

Energy Conservation: An Examination of Energy Conservation Mechanisms As They Relate to School Districts in Region XI.  

ERIC Educational Resources Information Center

This report attempts to supply information on energy conservation mechanisms that can be employed in schools to the public schools of Minnesota. The report begins by presenting guidelines for developing an energy conservation plan. The two models include the concept of Total Educational Energy Management as developed by the Colorado Department of…

Kerns, Marilyn

100

Discovery of functional non-coding conserved regions in the ?-synuclein gene locus  

PubMed Central

Several single nucleotide polymorphisms (SNPs) and the Rep-1 microsatellite marker of the ?-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

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

2014-01-01

101

In embryonic stem cells, ZFP57/KAP1 recognize a methylated hexanucleotide to affect chromatin and DNA methylation of imprinting control regions.  

PubMed

The maintenance of H3K9 and DNA methylation at imprinting control regions (ICRs) during early embryogenesis is key to the regulation of imprinted genes. Here, we reveal that ZFP57, its cofactor KAP1, and associated effectors bind selectively to the H3K9me3-bearing, DNA-methylated allele of ICRs in ES cells. KAP1 deletion induces a loss of heterochromatin marks at ICRs, whereas deleting ZFP57 or DNMTs leads to ICR DNA demethylation. Accordingly, we find that ZFP57 and KAP1 associated with DNMTs and hemimethylated DNA-binding NP95. Finally, we identify the methylated TGCCGC hexanucleotide as the motif that is recognized by ZFP57 in all ICRs and in several tens of additional loci, several of which are at least ZFP57-dependently methylated in ES cells. These results significantly advance our understanding of imprinting and suggest a general mechanism for the protection of specific loci against the wave of DNA demethylation that affects the mammalian genome during early embryogenesis. PMID:22055183

Quenneville, Simon; Verde, Gaetano; Corsinotti, Andrea; Kapopoulou, Adamandia; Jakobsson, Johan; Offner, Sandra; Baglivo, Ilaria; Pedone, Paolo V; Grimaldi, Giovanna; Riccio, Andrea; Trono, Didier

2011-11-01

102

A-to-I RNA editing alters less-conserved residues of highly conserved coding regions: Implications for dual functions in evolution  

PubMed Central

The molecular mechanism and physiological function of recoding by A-to-I RNA editing is well known, but its evolutionary significance remains a mystery. We analyzed the RNA editing of the Kv2 K+ channel from different insects spanning more than 300 million years of evolution: Drosophila melanogaster, Culex pipiens (Diptera), Pulex irritans (Siphonaptera), Bombyx mori (Lepidoptera), Tribolium castaneum (Coleoptera), Apis mellifera (Hymenoptera), Pediculus humanus (Phthiraptera), and Myzus persicae (Homoptera). RNA editing was detected across all Kv2 orthologs, representing the most highly conserved RNA editing event yet reported in invertebrates. Surprisingly, five of these editing sites were conserved in squid (Mollusca) and were possibly of independent origin, suggesting phylogenetic conservation of editing between mollusks and insects. Based on this result, we predicted and experimentally verified two novel A-to-I editing sites in squid synaptotagmin I transcript. In addition, comparative analysis indicated that RNA editing usually occurred within highly conserved coding regions, but mostly altered less-conserved coding positions of these regions. Moreover, more than half of these edited amino acids are genomically encoded in the orthologs of other species; an example of a conversion model of the nonconservative edited site is addressed. Therefore, these data imply that RNA editing might play dual roles in evolution by extending protein diversity and maintaining phylogenetic conservation. PMID:18567816

Yang, Yun; Lv, Jianning; Gui, Bin; Yin, Heng; Wu, Xiaojie; Zhang, Yaozhou; Jin, Yongfeng

2008-01-01

103

Conservation of pericentromeric duplications of a 200-kb part of the human 21q22.1 region in primates  

Microsoft Academic Search

We analyzed the conservation of large paralogous regions (more than 200 kb) on human chromosome regions 21q22.1 and 21q11.2 and on pericentromeric regions of chromosomes 2, 13, and 18 in three nonhuman primate species. Orthologous regions were found by FISH analysis of metaphase chromosomes from Gorilla gorilla, Pan troglodytes, and Pongo pygmaeus. Only one orthologous region was detected in chromosomes

R. Orti; M. C. Potier; C. Maunoury; M. Prieur; N. Créau; J. M. Delabar

1998-01-01

104

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

SciTech Connect

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.

Angel, M.V.

1987-01-01

105

Precise detection of L. monocytogenes hitting its highly conserved region possessing several specific antibody binding sites.  

PubMed

Listeria monocytogenes, a facultative intracellular fast-growing Gram-positive food-borne pathogen, can infect immunocompromised individuals leading to meningitis, meningoencephalitis and septicaemias. From the pool of virulence factors of the organism, ActA, a membrane protein, has a critical role in the life cycle of L. monocytogenes. High mortality rate of listeriosis necessitates a sensitive and rapid diagnostic test for precise identification of L. monocytogenes. We used bioinformatic tools to locate a specific conserved region of ActA for designing and developing an antibody-antigen based diagnostic test for the detection of L. monocytogenes. A number of databases were looked for ActA related sequences. Sequences were analyzed with several online software to find an appropriate region for our purpose. ActA protein was found specific to Listeria species with no homologs in other organisms. We finally introduced a highly conserved region within ActA sequence that possess several antibody binding sites specific to L. monocytogenes. This protein sequence can serve as an antigen for designing a relatively cheap, sensitive, and specific diagnostic test for detection of L. monocytogenes. PMID:22575546

Jahangiri, Abolfazl; Rasooli, Iraj; Reza Rahbar, Mohammad; Khalili, Saeed; Amani, Jafar; Ahmadi Zanoos, Kobra

2012-07-21

106

A Conserved Stem Loop Motif in the 5?Untranslated Region Regulates Transforming Growth Factor-?1 Translation  

PubMed Central

Transforming growth factor-?1 (TGF-?1) regulates cellular proliferation, differentiation, migration, and survival. The human TGF-?1 transcript is inherently poorly translated, and translational activation has been documented in relation to several stimuli. In this paper, we have sought to identify in cis regulatory elements within the TGF-?1 5?Untranslated Region (5?UTR). In silico analysis predicted formation of stable secondary structure in a G/C-rich element between nucleotides +77 to +106, and demonstrated that this element is highly conserved across species. Circular dichroism spectroscopy confirmed the presence of secondary structure in this region. The proximal 5?UTR was inhibitory to translation in reporter gene experiments, and mutation of the secondary structure motif increased translational efficiency. Translational regulation of TGF-?1 mRNA is linked to altered binding of YB-1 protein to its 5?UTR. Immunoprecipitation-RT-qPCR demonstrated a high basal association of YB-1 with TGF-?1 mRNA. However, mutation of the secondary structure motif did not prevent interaction of YB-1 with the 5?UTR, suggesting that YB-1 binds to this region due to its G/C-rich composition, rather than a specific, sequence-dependent, binding site. These data identify a highly conserved element within the TGF-?1 5?UTR that forms stable secondary structure, and is responsible for the inherent low translation efficiency of this cytokine. PMID:20865036

Jenkins, Robert H.; Bennagi, Rasha; Martin, John; Phillips, Aled O.; Redman, James E.; Fraser, Donald J.

2010-01-01

107

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

NASA Astrophysics Data System (ADS)

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.

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

2010-12-01

108

Variable conservation of nucleolus organizer regions during karyotypic evolution in Microtidae.  

PubMed

The location of the nucleolus organizer regions (NORs) was studied in four species of Microtidae (Microtus nivalis, M. cabrerae, M. arvalis, and Arvicola sapidus). The comparative study of these locations shows that some NORs have been conserved despite the chromosome rearrangements that have occurred through karyotypic evolution, while others have been lost. In addition, there are many chromosomes in which NORs seem to have appeared or been lost without apparent relation to the chromosome rearrangements. Some hypotheses regarding these facts are discussed in the text. PMID:2185132

Sánchez, A; Burgos, M; Jiménez, R; Díaz de la Guardia, R

1990-02-01

109

Comparison of the conserved region in the dnaA gene from three mollicute species.  

PubMed

Polymerase chain reaction was carried out to amplify the conserved region (789 bp in the case of Mycoplasma capricolum) of the dnaA gene (1350 bp in the case of M. capricolum) of 15 representatives of the class Mollicutes using degenerate oligonucleotide primers. The dnaA gene fragments were amplified from M. mycoides subsp. capri, Spiroplasma apis and S. citri. The amino acid sequences deduced from the nucleotide sequences of the amplified fragments showed very low similarities to those of the corresponding regions of four walled bacteria. The values of similarity between any two of the three mollicute species were lower than those between any two of the four walled bacteria. PMID:8282191

Suzuki, K; Miyata, M; Fukumura, T

1993-12-01

110

Rearrangement of sapA homologs with conserved and variable regions in Campylobacter fetus.  

PubMed Central

The Campylobacter fetus surface-layer (S-layer) proteins mediate both complement resistance and antigenic variation in mammalian hosts. Wild-type strain 23D possesses the sapA gene, which encodes a 97-kDa S-layer protein, and several sapA homologs are present in both wild-type and mutant strains. Here we report that a cloned silent gene (sapA1) in C. fetus can express a functional full-length S-layer protein in Escherichia coli. Analysis of sapA and sapA1 and partial analysis of sapA2 indicate that a block of approximately 600 bp beginning upstream and continuing into the open reading frames is completely conserved, and then the sequences diverge completely, but immediately downstream of each gene is another conserved 50-bp sequence. Conservation of sapA1 among strains, the presence of a putative Chi (RecBCD recognition) site upstream of sapA, sapA1, and sapA2, and the sequence identities of the sapA genes suggest a system for homologous recombination. Comparison of the wild-type strain (23D) with a phenotypic variant (23D-11) indicates that variation is associated with removal of the divergent region of sapA from the expression locus and exchange with a corresponding region from a sapA homolog. We propose that site-specific reciprocal recombination between sapA homologs leads to expression of divergent S-layer proteins as one of the mechanisms that C. fetus uses for antigenic variation. Images Fig. 2 Fig. 3 Fig. 5 Fig. 6 PMID:8346244

Tummuru, M K; Blaser, M J

1993-01-01

111

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

SciTech Connect

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.

Wo, Jennifer Y. [Harvard Radiation Oncology Program, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Taghian, Alphonse G. [Massachusetts General Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Nguyen, Paul L. [Harvard Radiation Oncology Program, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Raad, Rita Abi [Massachusetts General Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Sreedhara, Meera B.A.; Bellon, Jennifer R.; Wong, Julia S. [Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Gadd, Michele A.; Smith, Barbara L. [Massachusetts General Hospital, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States); Harris, Jay R., E-mail: jharris@lroc.harvard.ed [Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, MA (United States)

2010-05-01

112

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

NASA Astrophysics Data System (ADS)

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.

Clerici, Nicola; Vogt, Peter

2013-04-01

113

Underreplicated regions in Drosophila melanogaster are enriched with fast-evolving genes and highly conserved noncoding sequences.  

PubMed

Many late replicating regions are underreplicated in polytene chromosomes of Drosophila melanogaster. These regions contain silenced chromatin and overlap long syntenic blocks of conserved gene order in drosophilids. In this report we show that in D. melanogaster the underreplicated regions are enriched with fast-evolving genes lacking homologs in distant species such as mosquito or human, indicating that the phylogenetic conservation of genes correlates with replication timing and chromatin status. Drosophila genes without human homologs located in the underreplicated regions have higher nonsynonymous substitution rate and tend to encode shorter proteins when compared with those in the adjacent regions. At the same time, the underreplicated regions are enriched with ultraconserved elements and highly conserved noncoding sequences, especially in introns of very long genes indicating the presence of an extensive regulatory network that may be responsible for the conservation of gene order in these regions. The regions have a modest preference for long noncoding RNAs but are depleted for small nucleolar RNAs, microRNAs, and transfer RNAs. Our results demonstrate that the underreplicated regions have a specific genic composition and distinct pattern of evolution. PMID:25062918

Makunin, Igor V; Kolesnikova, Tatyana D; Andreyenkova, Natalya G

2014-08-01

114

Underreplicated Regions in Drosophila melanogaster Are Enriched with Fast-Evolving Genes and Highly Conserved Noncoding Sequences  

PubMed Central

Many late replicating regions are underreplicated in polytene chromosomes of Drosophila melanogaster. These regions contain silenced chromatin and overlap long syntenic blocks of conserved gene order in drosophilids. In this report we show that in D. melanogaster the underreplicated regions are enriched with fast-evolving genes lacking homologs in distant species such as mosquito or human, indicating that the phylogenetic conservation of genes correlates with replication timing and chromatin status. Drosophila genes without human homologs located in the underreplicated regions have higher nonsynonymous substitution rate and tend to encode shorter proteins when compared with those in the adjacent regions. At the same time, the underreplicated regions are enriched with ultraconserved elements and highly conserved noncoding sequences, especially in introns of very long genes indicating the presence of an extensive regulatory network that may be responsible for the conservation of gene order in these regions. The regions have a modest preference for long noncoding RNAs but are depleted for small nucleolar RNAs, microRNAs, and transfer RNAs. Our results demonstrate that the underreplicated regions have a specific genic composition and distinct pattern of evolution. PMID:25062918

Makunin, Igor V.; Kolesnikova, Tatyana D.; Andreyenkova, Natalya G.

2014-01-01

115

Diversity and distribution of aquatic insects in Southern Brazil wetlands: implications for biodiversity conservation in a Neotropical region.  

PubMed

The selection of priority areas is an enormous challenge for biodiversity conservation. Some biogeographic methods have been used to identify the priority areas to conservation, and panbiogeography is one of them. This study aimed at the utilization of panbiogeographic tools, to identify the distribution patterns of aquatic insect genera, in wetland systems of an extensive area in the Neotropical region (approximately 280 000km2), and to compare the distribution of the biogeographic units identified by the aquatic insects, with the conservation units of Southern Brazil. We analyzed the distribution pattern of 82 genera distributed in four orders of aquatic insects (Diptera, Odonata, Ephemeroptera and Trichoptera) in Southern Brazil wetlands. Therefore, 32 biogeographic nodes corresponded to the priority areas for conservation of the aquatic insect diversity. Among this total, 13 were located in the Atlantic Rainforest, 16 in the Pampa and three amongst both biomes. The distribution of nodes showed that only 15% of the dispersion centers of insects were inserted in conservation units. The four priority areas pointed by node cluster criterion must be considered in further inclusions of areas for biodiversity conservation in Southern Brazil wetlands, since such areas present species from different ancestral biota. The inclusion of such areas into the conservation units would be a strong way to conserve the aquatic biodiversity in this region. PMID:22458224

Maltchik, Leonardo; Dalzochio, Marina Schmidt; Stenert, Cristina; Rolon, Ana Silvia

2012-03-01

116

Identification and characterization of deamidation sites in the conserved regions of human immunoglobulin gamma antibodies.  

PubMed

Deamidation of asparagine residues of biological pharmaceuticals is a major cause of chemical degradation if the compounds are not formulated and stored appropriately. The mechanism of this nonenzymatic chemical reaction has been studied in great detail; however, the identification of deamidation sites in a given protein remains a challenge. In this study, we identified and characterized all deamidation sites in the conserved region of a recombinant monoclonal antibody. The conserved region of this antibody is shared by all human IgGs with the exception of minor differences in the hinge region. Our high-performance liquid chromatography method could separate the succinimide, isoaspartic, and aspartic acid isoforms of peptide fragments generated using trypsin. Each of the isoforms was unambiguously identified using tandem mass spectrometry. Deamidation at the identified four sites was slow for the intact, folded antibody at accelerated degradation conditions (pH 7.5 and 37 degrees C). Deamidation was enhanced after reduction, alkylation, and tryptic digestion, indicating that the three-dimensional structure of the antibody reduced deamidation. Furthermore, after the reduction, alkylation, and tryptic digestion, only 4 of a possible 25 asparagine residues showed deamidation, demonstrating the effect of the primary amino acid sequence, especially the -1 and +1 amino acids flanking the deamidation site. For instance, the amino acid motifs SNG, ENN, LNG, and LNN were found to be more prone to deamidation, whereas the motifs GNT, TNY, YNP, WNS, SNF, CNV, SNT, WNS, FNW, HNA, FNS, SNK, GNV, HNH, SNY, LNW, SNL, NNF, DNA, GNS, and FNR showed no deamidation. Our findings should help predict deamidation sites in proteins and peptides and help develop deamidation-resistant biological therapeutics. PMID:16159134

Chelius, Dirk; Rehder, Douglas S; Bondarenko, Pavel V

2005-09-15

117

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

NASA Astrophysics Data System (ADS)

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.

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

2004-04-01

118

Conserved Regions of Gonococcal TbpB Are Critical for Surface Exposure and Transferrin Iron Utilization  

PubMed Central

The transferrin-binding proteins TbpA and TbpB enable Neisseria gonorrhoeae to obtain iron from human transferrin. The lipoprotein TbpB facilitates, but is not strictly required for, TbpA-mediated iron acquisition. The goal of the current study was to determine the contribution of two conserved regions within TbpB to the function of this protein. Using site-directed mutagenesis, the first mutation we constructed replaced the lipobox (LSAC) of TbpB with a signal I peptidase cleavage site (LAAA), while the second mutation deleted a conserved stretch of glycine residues immediately downstream of the lipobox. We then evaluated the resulting mutants for effects on TbpB expression, surface exposure, and transferrin iron utilization. Western blot analysis and palmitate labeling indicated that the lipobox, but not the glycine-rich motif, is required for lipidation of TbpB and tethering to the outer membrane. TbpB was released into the supernatant by the mutant that produces TbpB LSAC. Neither mutation disrupted the transport of TbpB across the bacterial cell envelope. When these mutant TbpB proteins were produced in a strain expressing a form of TbpA that requires TbpB for iron acquisition, growth on transferrin was either abrogated or dramatically diminished. We conclude that surface tethering of TbpB is required for optimal performance of the transferrin iron acquisition system, while the presence of the polyglycine stretch near the amino terminus of TbpB contributes significantly to transferrin iron transport function. Overall, these results provide important insights into the functional roles of two conserved motifs of TbpB, enhancing our understanding of this critical iron uptake system. PMID:23836816

Ostberg, Karen L.; DeRocco, Amanda J.; Mistry, Shreni D.; Dickinson, Mary Kathryne

2013-01-01

119

A Highly Conserved Region within H2B Is Important for FACT To Act on Nucleosomes  

PubMed Central

Histone N-terminal tails play crucial roles in chromatin-related processes. The tails of histones H3 and H4 are highly conserved and well characterized, but much less is known about the functions of the tails of histones H2A and H2B and their sequences are more divergent among eukaryotes. Here we characterized the function of the only highly conserved region in the H2B tail, the H2B repression (HBR) domain. Once thought to play a role only in repression, it also has an uncharacterized function in gene activation and DNA damage responses. We report that deletion of the HBR domain impairs the eviction of nucleosomes at the promoters and open reading frames of genes. A closer examination of the HBR domain mutants revealed that they displayed phenotypes similar to those of histone chaperone complex FACT mutants, including an increase in intragenic transcription and the accumulation of free histones in cells. Biochemical characterization of recombinant nucleosomes indicates that deletion of the HBR domain impairs FACT-dependent removal of H2A-H2B from nucleosomes, suggesting that the HBR domain plays an important role in allowing FACT to disrupt dimer-DNA interactions. We have uncovered a previously unappreciated role for the HBR domain in regulating chromatin structure and have provided insight into how FACT acts on nucleosomes. PMID:24248595

Zheng, Suting; Crickard, J. Brooks; Srikanth, Abhinaya

2014-01-01

120

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

PubMed Central

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

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

2013-01-01

121

Mutagenesis of apyrase conserved region 1 alters the nucleotide substrate specificity.  

PubMed

Two apyrases having different substrate specificity, MP67 and MpAPY2, are present in Mimosa pudica. The substrate specificity of MP67 is quite high against ADP, and is distinct from any other apyrase. This might be attributed to the nucleotide binding motif (DXG) in apyrase conserved region 1. We performed a single amino acid substitution at position X in the motif. The ratio of the velocity of ATP/ADP hydrolysis was higher (approximately 1) for the S63A-MP67 mutant than for wild type-MP67 (0.19). Binding affinity for ADP of A75S-MpAPY2 mutant was increased to a level higher than that of the wild type MpAPY2. Thus, the residue at position X in the DXG motif plays an important role in determining nucleotide preference. PMID:23470725

Okuhata, Riku; Otsuka, Yuki; Tsuchiya, Takahide; Kanzawa, Nobuyuki

2013-05-01

122

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

PubMed

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

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

2005-05-01

123

Mutagenesis of apyrase conserved region 1 alters the nucleotide substrate specificity  

PubMed Central

Two apyrases having different substrate specificity, MP67 and MpAPY2, are present in Mimosa pudica. The substrate specificity of MP67 is quite high against ADP, and is distinct from any other apyrase. This might be attributed to the nucleotide binding motif (DXG) in apyrase conserved region 1. We performed a single amino acid substitution at position X in the motif. The ratio of the velocity of ATP/ADP hydrolysis was higher (approximately 1) for the S63A-MP67 mutant than for wild type-MP67 (0.19). Binding affinity for ADP of A75S-MpAPY2 mutant was increased to a level higher than that of the wild type MpAPY2. Thus, the residue at position X in the DXG motif plays an important role in determining nucleotide preference. PMID:23470725

Okuhata, Riku; Otsuka, Yuki; Tsuchiya, Takahide; Kanzawa, Nobuyuki

2013-01-01

124

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

PubMed Central

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

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

1988-01-01

125

Human dimension of conservation planning: the case of Madagascar at national and regional scales  

E-print Network

and national parks?: social dilemmas and strategies in international conservation /conservation and development project (icdp) approach: observations from the ranomafana national parkconservation actions, about 64% of the PAs were under the IUCN categories II , a National Park,

Ramaharitra Tondrasoa, Tendro

2012-01-01

126

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

PubMed Central

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

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

127

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

USGS Publications Warehouse

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.

Kantrud, H.A.

1993-01-01

128

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

PubMed Central

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 conservation efforts. PMID:24937641

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

2014-01-01

129

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

PubMed

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 conservation efforts. PMID:24937641

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

2014-01-01

130

Evolutionary conservation of the AU-rich 3' untranslated region of messenger RNA.  

PubMed Central

AU-rich sequence motifs (specifically sequences containing reiterations of AUUUA) are found in the 3' untranslated region of mammalian mRNAs encoding cytokines, adhesion molecules, and protooncogenes. Because these AU-rich elements (3'AURE) have been observed to reduce the stability and translational efficiency of transcripts that contain them, and because many of these transcripts accumulate in cells exposed to inflammatory stimuli, we reasoned that mRNAs with 3'AURE may be highly conserved and that the AURE is a marker of mRNAs that are inducible by environmental stressors. To test this hypothesis, we developed a polymerase chain reaction (PCR) strategy to isolate specifically mRNAs with 3'AURE. We first validated the effectiveness of this approach by selectively amplifying two mRNAs containing 3'AURE from interleukin 1 (IL-1)-induced human endothelial cells, then used the same primers in reverse transcriptase-PCR of sea urchin RNA, and used the radiolabeled reaction products to screen a cDNA library prepared from endotoxin-exposed sea urchin coelomocytes. We identified 124 positive clones and isolated a 1608-base-pair fragment that contains an AU-rich consensus sequence upstream from a poly(A) tail. This sea urchin transcript hybridizes with immobilized poly(A)(+)-selected RNA prepared from living coelomocytes maintained in vitro for 8.5-13 h but not with RNA prepared from freshly harvested coelomocytes. Our results provide support for the growing body of evidence that 3' AURE are both conserved and functional and indicate further that isolation and short-term in vitro culture of sea urchin coelomocytes is sufficient to induce the expression of transcripts containing 3'AURE. Images PMID:8108409

Asson-Batres, M A; Spurgeon, S L; Diaz, J; DeLoughery, T G; Bagby, G C

1994-01-01

131

Autoantibodies from patients with primary biliary cirrhosis recognize a restricted region within the cytoplasmic tail of nuclear pore membrane glycoprotein Gp210  

PubMed Central

Patients with primary biliary cirrhosis (PBC) frequently have autoantibodies against a 210-kD integral glycoprotein of the nuclear envelope pore membrane. This protein, termed gp210, has a 1,783-amino acid amino-terminal domain located in the perinuclear space, a 20-amino acid transmembrane segment, and a 58-amino acid cytoplasmic carboxy- terminal tail. We now demonstrate that autoantibodies from 25 patients with PBC that recognize gp210 react with the cytoplasmic carboxy- terminal tail while none react with unmodified linear epitopes in the amino-terminal domain. The epitope(s) recognized by autoantibodies from all 25 patients is contained within a stretch of 15 amino acids. The recognized amino acid sequence is homologous to the protein products of the Escherichia coli mutY gene and Salmonella typhimurium mutB gene with an exact identity of six consecutive amino acids, suggesting that anti-gp210 antibodies may arise by molecular mimicry of bacterial antigenic determinants. PMID:7504063

1993-01-01

132

Automatic Identification of Highly Conserved Family Regions and Relationships in Genome Wide Datasets Including Remote Protein Sequences  

PubMed Central

Identifying shared sequence segments along amino acid sequences generally requires a collection of closely related proteins, most often curated manually from the sequence datasets to suit the purpose at hand. Currently developed statistical methods are strained, however, when the collection contains remote sequences with poor alignment to the rest, or sequences containing multiple domains. In this paper, we propose a completely unsupervised and automated method to identify the shared sequence segments observed in a diverse collection of protein sequences including those present in a smaller fraction of the sequences in the collection, using a combination of sequence alignment, residue conservation scoring and graph-theoretical approaches. Since shared sequence fragments often imply conserved functional or structural attributes, the method produces a table of associations between the sequences and the identified conserved regions that can reveal previously unknown protein families as well as new members to existing ones. We evaluated the biological relevance of the method by clustering the proteins in gold standard datasets and assessing the clustering performance in comparison with previous methods from the literature. We have then applied the proposed method to a genome wide dataset of 17793 human proteins and generated a global association map to each of the 4753 identified conserved regions. Investigations on the major conserved regions revealed that they corresponded strongly to annotated structural domains. This suggests that the method can be useful in predicting novel domains on protein sequences. PMID:24069417

Do?an, Tunca; Karaçal?, Bilge

2013-01-01

133

Structure-function relationship of bacterial prolipoprotein diacylglyceryl transferase: functionally significant conserved regions.  

PubMed Central

The structure-function relationship of bacterial prolipoprotein diacylgyceryl transferase (LGT) Has been investigated by a comparison of the primary structures of this enzyme in phylogenetically distant bacterial species, analysis of the sequences of mutant enzymes, and specific chemical modification of the Escherichia coli enzyme. A clone containing the gene for LGT, lgt, of the gram-positive species Staphylococcus aureus was isolated by complementation of the temperature-sensitive lgt mutant of E. coli (strain SK634) defective in LGT activity. In vivo and in vitro assays for prolipoprotein diacylglyceryl modification activity indicated that the complementing clone restored the prolipoprotein modification activity in the mutant strain. Sequence determination of the insert DNA revealed an open reading frame of 837 bp encoding a protein of 279 amino acids with a calculated molecular mass of 31.6 kDa. S. aureus LGT showed 24% identity and 47% similarity with E. coli, Salmonella typhimurium, and Haemophilus influenzae LGT.S. aureus LGT, while 12 amino acids shorter than the E. coli enzyme, had a hydropathic profile and a predicted pI (10.4) similar to those of the E. coli enzyme. Multiple sequence alignment among E. coli, S. typhimurium, H. influenzae, and S. aureus LGT proteins revealed regions of highly conserved amino acid sequences throughout the molecule. Three independent lgt mutant alleles from E. coli SK634, SK635, and SK636 and one lgt allele from S. typhimurium SE5221, all defective in LGT activity at the nonpermissive temperature, were cloned by PCR and sequenced. The mutant alleles were found to contain a single base alteration resulting in the substitution of a conserved amino acid. The longest set of identical amino acids without any gap was H-103-GGLIG-108 in LGT from these four microorganisms. In E. coli lgt mutant SK634, Gly-104 in this region was mutated to Ser, and the mutant organism was temperature sensitive in growth and exhibited low LGT activity in vitro. Diethylpyrocarbonate inactivated the E. coli LGT with a second-order rate constant of 18.6 M-1S-1, and the inactivation of LGT activity was reversed by hydroxylamine at pH 7. The inactivation kinetics were consistent with the modification of a single residue, His or Tyr, essential for LGT activity. PMID:7592473

Qi, H Y; Sankaran, K; Gan, K; Wu, H C

1995-01-01

134

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

USGS Publications Warehouse

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-equivalent scenarios; however, the cone-equivalent scenarios result in greater average water-level improvements within the area of the cone of depression because of focused conservation efforts within that area. Regardless of where conservation is located, the greatest average improvements in water level occur within the area of the cone of depression because of the corresponding large area of unsaturated aquifer material within the area of the cone of depression and the hydraulic gradient, which slopes from the periphery of the Delta towards the area of the cone of depression. Of the four conservation scenarios, the 25-percent cone-equivalent scenario resulted in the greatest increase in storage relative to the base scenario with a 32-percent improvement over the base scenario across the entire Delta and a 60-percent improvement within the area of the cone of depression. Overall, the results indicate that focusing conservation efforts within the area of the cone of depression, rather than distributing conservation efforts uniformly across the Delta, results in greater improvements in the amount of storage within the alluvial aquifer. Additionally, as the total amount of conservation increases (that is, from 5 to 25 percent), the difference in storage improvement between the Delta-wide and cone-equivalent scenarios also increases, resulting in greater gains in storage in the cone-equivalent scenario than in the Delta-wide scenario for the same amount of conservation.

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

2011-01-01

135

AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences  

Microsoft Academic Search

BACKGROUND: Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention.

Darío Guerrero; Rocío Bautista; David P Villalobos; Francisco R Cantón; M Gonzalo Claros

2010-01-01

136

Gravel–sand mulch for soil and water conservation in the semiarid loess region of northwest China  

Microsoft Academic Search

In the semiarid loess region of northwest China, the use of gravel and sand as mulch has been an indigenous farming technique for crop production for over 300 years. However, systematic studies concerning the effects of surface gravel–sand (mixed gravel and sand) covers on soil and water conservation are scarce. Based on previous studies, this study investigates the effects of

Xiao-Yan Li

2003-01-01

137

Agricultural Conservation Practices and Wetland Ecosystem Services in a Wetland-Dominated Landscape: The Piedmont-Coastal Plain Region  

Technology Transfer Automated Retrieval System (TEKTRAN)

In the wetlands-rich eastern Coastal Plain and Piedmont region, diverse inland wetlands (riverine, depressional, wet flats) have been impacted by or converted to agriculture. Farm Bill conservation practices that restore or enhance wetlands can return their ecological functions and services to the a...

138

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

SciTech Connect

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 7.5 mm across algorithms for scenarios I to III, respectively. The greatest accuracy was exhibited by the original Horn and Schunck optical flow algorithm. In this case, for scenario III (erased FMs not contributing to driving the DIR calculation), the mean error was half that of the modified demons algorithm (which exhibited the greatest error), across all deformations. Some algorithms failed to reproduce the geometry at all, while others accurately deformed high contrast features but not low-contrast regions—indicating poor interpolation between landmarks.Conclusions: The accuracy of DIR algorithms was quantitatively evaluated using a tissue equivalent, mass, and density conserving DEFGEL phantom. For the model studied, optical flow algorithms performed better than demons algorithms, with the original Horn and Schunck performing best. The degree of error is influenced more by the magnitude of displacement than the geometric complexity of the deformation. As might be expected, deformation is estimated less accurately for low-contrast regions than for high-contrast features, and the method presented here allows quantitative analysis of the differences. The evaluation of registration accuracy through observation of the same high contrast features that drive the DIR calculation is shown to be circular and hence misleading.

Yeo, U. J.; Supple, J. R.; Franich, R. D. [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000 (Australia)] [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000 (Australia); Taylor, M. L. [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000 (Australia) [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000 (Australia); Physical Sciences, Peter MacCallum Cancer Centre, East Melbourne 3002 (Australia); Medical Physics, William Buckland Radiotherapy Centre, The Alfred Hospital, Melbourne 3004 (Australia); Smith, R. [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000, Australia and Medical Physics, William Buckland Radiotherapy Centre, The Alfred Hospital, Melbourne 3004 (Australia)] [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000, Australia and Medical Physics, William Buckland Radiotherapy Centre, The Alfred Hospital, Melbourne 3004 (Australia); Kron, T. [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000, Australia and Physical Sciences, Peter MacCallum Cancer Centre, East Melbourne 3002 (Australia)] [School of Applied Sciences and Health Innovations Research Institute, RMIT University, Melbourne 3000, Australia and Physical Sciences, Peter MacCallum Cancer Centre, East Melbourne 3002 (Australia)

2013-10-15

139

Characterization of Conserved Region 2-Deficient Mutants of the Cytomegalovirus Egress Protein pM53  

PubMed Central

Dominant-negative (DN) mutants are powerful tools for studying essential protein-protein interactions. A systematic genetic screen of the essential murine cytomegalovirus (MCMV) protein pM53 identified the accumulation of inhibitory mutations within conserved region 2 (CR2) and CR4. The strong inhibitory potential of these CR4 mutants is characterized by a particular phenotype. The DN effect of the small insertion mutations in CR2 was too weak to analyze (M. Popa, Z. Ruzsics, M. Lötzerich, L. Dölken, C. Buser, P. Walther, and U. H. Koszinowski, J. Virol. 84:9035–9046, 2010); therefore, the present study describes the construction of M53 alleles lacking CR2 (either completely or partially) and subsequent examination of the DN effect on MCMV replication upon conditional expression. Overexpression of CR2-deficient pM53 inhibited virus production by about 10,000-fold. This was due to interference with capsid export from the nucleus and viral genome cleavage/packaging. In addition, the fate of the nuclear envelopment complex in the presence of DN pM53 overexpression was analyzed. The CR2 mutants were able to bind to pM50, albeit to a lesser extent than the wild-type protein, and relocalized the wild-type nuclear envelope complex in infected cells. Unlike the CR4 DN, the CR2 DN mutants did not affect the stability of pM50. PMID:22993161

Pogoda, Madlen; Bosse, Jens B.; Wagner, Felicia M.; Schauflinger, Martin; Walther, Paul; Koszinowski, Ulrich H.

2012-01-01

140

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

PubMed Central

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

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

2014-01-01

141

Comparative Genomics Identifies the Mouse Bmp3 Promoter and an Upstream Evolutionary Conserved Region (ECR) in Mammals  

PubMed Central

The Bone Morphogenetic Protein (BMP) pathway is a multi-member signaling cascade whose basic components are found in all animals. One member, BMP3, which arose more recently in evolution and is found only in deuterostomes, serves a unique role as an antagonist to both the canonical BMP and Activin pathways. However, the mechanisms that control BMP3 expression, and the cis-regulatory regions mediating this regulation, remain poorly defined. With this in mind, we sought to identify the Bmp3 promoter in mouse (M. musculus) through functional and comparative genomic analyses. We found that the minimal promoter required for expression in resides within 0.8 kb upstream of Bmp3 in a region that is highly conserved with rat (R. norvegicus). We also found that an upstream region abutting the minimal promoter acts as a repressor of the minimal promoter in HEK293T cells and osteoblasts. Strikingly, a portion of this region is conserved among all available eutherian mammal genomes (47/47), but not in any non-eutherian animal (0/136). We also identified multiple conserved transcription factor binding sites in the Bmp3 upstream ECR, suggesting that this region may preserve common cis-regulatory elements that govern Bmp3 expression across eutherian mammals. Since dysregulation of BMP signaling appears to play a role in human health and disease, our findings may have application in the development of novel therapeutics aimed at modulating BMP signaling in humans. PMID:23451274

Lowery, Jonathan W.; LaVigne, Anna W.; Kokabu, Shoichiro; Rosen, Vicki

2013-01-01

142

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

Microsoft Academic Search

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

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

1985-01-01

143

The Role of Prestressing in Establishing Regions of Instability for a Compound Column Under Conservative or Non-Conservative Load  

NASA Astrophysics Data System (ADS)

The influence of prestressing of a non-linear two-member column on its natural vibration and stability is studied. The perturbation method is used for solving the problem. Regions of divergence and flutter instabilities for a column has been determined on the basis of courses of eigencurves in relation to prestress rate. Discontinuities of the critical force have been observed for the border value of the prestress leading to the instability of the column without the external load. Although each prestress lowers the critical force, it can be used for passive vibration control.

PRZYBYLSKI, J.

2000-03-01

144

Structural and Functional Perturbation of Giardia lamblia Triosephosphate Isomerase by Modification of a Non-Catalytic, Non-Conserved Region  

PubMed Central

Background We have previously proposed triosephosphate isomerase of Giardia lamblia (GlTIM) as a target for rational drug design against giardiasis, one of the most common parasitic infections in humans. Since the enzyme exists in the parasite and the host, selective inhibition is a major challenge because essential regions that could be considered molecular targets are highly conserved. Previous biochemical evidence showed that chemical modification of the non-conserved non-catalytic cysteine 222 (C222) inactivates specifically GlTIM. The inactivation correlates with the physicochemical properties of the modifying agent: addition of a non-polar, small chemical group at C222 reduces the enzyme activity by one half, whereas negatively charged, large chemical groups cause full inactivation. Results In this work we used mutagenesis to extend our understanding of the functional and structural effects triggered by modification of C222. To this end, six GlTIM C222 mutants with side chains having diverse physicochemical characteristics were characterized. We found that the polarity, charge and volume of the side chain in the mutant amino acid differentially alter the activity, the affinity, the stability and the structure of the enzyme. The data show that mutagenesis of C222 mimics the effects of chemical modification. The crystallographic structure of C222D GlTIM shows the disruptive effects of introducing a negative charge at position 222: the mutation perturbs loop 7, a region of the enzyme whose interactions with the catalytic loop 6 are essential for TIM stability, ligand binding and catalysis. The amino acid sequence of TIM in phylogenetic diverse groups indicates that C222 and its surrounding residues are poorly conserved, supporting the proposal that this region is a good target for specific drug design. Conclusions The results demonstrate that it is possible to inhibit species-specifically a ubiquitous, structurally highly conserved enzyme by modification of a non-conserved, non-catalytic residue through long-range perturbation of essential regions. PMID:23894402

Hernández-Alcántara, Gloria; Torres-Larios, Alfredo; Enríquez-Flores, Sergio; García-Torres, Itzhel; Castillo-Villanueva, Adriana; Méndez, Sara T.; de la Mora-de la Mora, Ignacio; Gómez-Manzo, Saúl; Torres-Arroyo, Angélica; López-Velázquez, Gabriel; Reyes-Vivas, Horacio; Oria-Hernández, Jesús

2013-01-01

145

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

PubMed Central

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

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

2014-01-01

146

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

SciTech Connect

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.

Not Available

1985-03-29

147

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

PubMed Central

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

2011-01-01

148

The Capsid Gene of Feline Calicivirus Contains Linear B-Cell Epitopes in both Variable and Conserved Regions  

PubMed Central

In order to map linear B-cell (LBC) epitopes in the major capsid protein of feline calicivirus (FCV), an expression library containing random, short (100- to 200-bp) fragments of the FCV F9 capsid gene was constructed. Analysis of this library showed it to be representative of the region of the capsid gene that encodes the mature capsid protein. The library was screened by using polyclonal antisera from a cat that had been challenged experimentally with F9 to identify immunoreactive clones containing LBC epitopes. Twenty-six clones that reacted positively to feline antisera in immunoblots were identified. FCV-derived sequence from these clones mapped to a region of the capsid that spanned 126 amino acids and included variable regions C and E. An overlapping set of biotinylated peptides corresponding to this region was used to further map LBC epitopes by using F9 antisera. Four principal regions of reactivity were identified. Two fell within the hypervariable region at the 5? end of region E (amino acids [aa] 445 to 451 [antigenic site {ags} 2] and aa 451 to 457 [ags 3]). However, the other two were in conserved regions (aa 415 to 421 [ags 1; region D] and aa 475 to 479 [ags 4; central region E]). The reactivity of the peptide set with antisera from 11 other cats infected with a range of FCV isolates was also determined. Ten of 11 antisera reacted to conserved ags 4, suggesting that this region may be useful for future recombinant vaccine design. PMID:10482602

Radford, Alan D.; Willoughby, Kim; Dawson, Susan; McCracken, Christina; Gaskell, Rosalind M.

1999-01-01

149

Identification of Escherichia coli O157:H7 genomic regions conserved in strains with a genotype associated with human infection.  

PubMed

Beta-glucuronidase-negative, sorbitol-nonfermenting isolates of Shiga toxin-producing Escherichia coli O157 comprise part of a clone complex of related enterohemorrhagic E. coli isolates. High-resolution genotyping shows that the O157 populations have diverged into two different lineages that appear to have different ecologies. To identify genomic regions unique to the most common human-associated genotype, suppression subtractive hybridization was used to identify DNA sequences present in two clinical strains representing the human lineage I O157:H7 strains but absent from two bovine-derived lineage II strains. PCR assays were then used to test for the presence of these regions in 10 lineage I strains and 20 lineage II strains. Twelve conserved regions of genomic difference for lineage I (CRD(I)) were identified that were each present in at least seven of the lineage I strains but absent in most of the lineage II strains tested. The boundaries of the lineage I conserved regions were further delimited by PCR. Eleven of these CRD(I) were associated with E. coli Sakai S-loops 14, 16, 69, 72, 78, 82, 83, 91 to 93, 153, and 286, and the final CRD(I) was located on the pO157 virulence plasmid. Several potential virulence factors were identified within these regions, including a putative hemolysin-activating protein, an iron transport system, and several possible regulatory genes. Cluster analysis based on lineage I conserved regions showed that the presence/absence of these regions was congruent with the inferred phylogeny of the strains. PMID:17056689

Steele, Marina; Ziebell, Kim; Zhang, Yongxiang; Benson, Andrew; Konczy, Paulina; Johnson, Roger; Gannon, Victor

2007-01-01

150

Prediction of conserved regulatory elements in promoter regions of the cattle genome  

Technology Transfer Automated Retrieval System (TEKTRAN)

Cross-species DNA sequence comparison is the primary approach to discover regulatory elements by identifying highly conserved sequences due to evolutionary constraints. Previously, we reported that a systematic approach, combining position-specific weight matrixes (JASPAR) and phylogenetic footprint...

151

Systematic identification of conserved regulatory elements in upstream promoter regions of the cattle genome  

Technology Transfer Automated Retrieval System (TEKTRAN)

Cross-species DNA sequence comparison is the primary approach to discover regulatory elements by identifying highly conserved sequences due to evolutionary constraints. Previously, we reported that a systematic approach, combining position-specific weight matrixes (JASPAR) and phylogenetic footprint...

152

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...

153

Many voices, one wilderness : collaborative conservation in the greater Chicago region  

E-print Network

There has been a growing recognition in the conservation community that landscape-scale networks of preserves and habitat corridors are needed to adequately protect native biodiversity. While most of the efforts to protect ...

Bates, Justin (Justin Timothy)

2012-01-01

154

AlignMiner: a Web-based tool for detection of divergent regions in multiple sequence alignments of conserved sequences  

PubMed Central

Background Multiple sequence alignments are used to study gene or protein function, phylogenetic relations, genome evolution hypotheses and even gene polymorphisms. Virtually without exception, all available tools focus on conserved segments or residues. Small divergent regions, however, are biologically important for specific quantitative polymerase chain reaction, genotyping, molecular markers and preparation of specific antibodies, and yet have received little attention. As a consequence, they must be selected empirically by the researcher. AlignMiner has been developed to fill this gap in bioinformatic analyses. Results AlignMiner is a Web-based application for detection of conserved and divergent regions in alignments of conserved sequences, focusing particularly on divergence. It accepts alignments (protein or nucleic acid) obtained using any of a variety of algorithms, which does not appear to have a significant impact on the final results. AlignMiner uses different scoring methods for assessing conserved/divergent regions, Entropy being the method that provides the highest number of regions with the greatest length, and Weighted being the most restrictive. Conserved/divergent regions can be generated either with respect to the consensus sequence or to one master sequence. The resulting data are presented in a graphical interface developed in AJAX, which provides remarkable user interaction capabilities. Users do not need to wait until execution is complete and can.even inspect their results on a different computer. Data can be downloaded onto a user disk, in standard formats. In silico and experimental proof-of-concept cases have shown that AlignMiner can be successfully used to designing specific polymerase chain reaction primers as well as potential epitopes for antibodies. Primer design is assisted by a module that deploys several oligonucleotide parameters for designing primers "on the fly". Conclusions AlignMiner can be used to reliably detect divergent regions via several scoring methods that provide different levels of selectivity. Its predictions have been verified by experimental means. Hence, it is expected that its usage will save researchers' time and ensure an objective selection of the best-possible divergent region when closely related sequences are analysed. AlignMiner is freely available at http://www.scbi.uma.es/alignminer. PMID:20525162

2010-01-01

155

THE ECONOMICS OF BIODIVERSITY CONSERVATION-A STUDY IN A COFFEE GROWING REGION OF INDIA  

Microsoft Academic Search

This paper analyses the economics of biodiversity conservation in the context of a tropical ecosystem in India, where coffee is the main competitor for land use.Using primary data covering a cross section of coffee growers,the study notes that the opportunity costs of biodiversity conservation in terms of coffee benefits foregone are quite high.Even after including external costs due to wild

K. N. Ninan; Jyothis Sathyapalan

2003-01-01

156

Duck Nest Success on Conservation Reserve Program Land in the Prairie Pothole Region  

NSDL National Science Digital Library

The Northern Prairie Wildlife Research Center (NPWRC) continues to place scientific/ management resources online for general viewing. This resource, by H.A. Kantrud was originally published in 1993 in the Journal of Soil and Water Conservation [48(3):238-242] and examines nest success of dabbling ducks on Conservation Reserve Program (CRP) land. It may be browsed online or downloaded as a .zip file.

Kantrud, Harold A.

157

A unique genomic sequence in the Wolf-Hirschhorn syndrome [WHS] region of humans is conserved in the great apes  

Microsoft Academic Search

The Wolf-Hirschhorn syndrome (WHS) is caused by a partial deletion in the short arm of chromosome 4 band 16.3 (4p16.3). A unique-sequence human DNA probe (39 kb) localized within this region has been used to search for sequence homology in the apes' equivalent chromosome 3 by FISH-technique. The WHS loci are conserved in higher primates at the expected position. Nevertheless,

Sima T. Tarzami; Andrew M. Kringstein; Robert A. Conte; Ram S. Verma

1996-01-01

158

Geographical patterns in openland cover and hayfield mowing in the Upper Great Lakes region: implications for grassland bird conservation  

Microsoft Academic Search

Populations of many grassland bird species such as Grasshopper Sparrow (Ammodramus savannarum), Henslow’s Sparrow (A. henslowii), and Bobolink (Dolichonyx oryzivorus) have experienced considerable declines over the last century. To foster multi-species grassland bird conservation in the\\u000a Upper Great Lakes (UGL) states of Michigan, Minnesota, and Wisconsin, we quantified geographic patterns within three sub-regional\\u000a zones (e.g., North, Central, and South) of

R. Gregory Corace; David J. Flaspohler; Lindsey M. Shartell

2009-01-01

159

Identification of evolutionarily conserved, functional noncoding elements in the promoter region of the sodium channel gene SCN8A  

PubMed Central

SCN8A is a major neuronal sodium channel gene expressed throughout the central and peripheral nervous systems. Mutations of SCN8A result in movement disorders and impaired cognition. To investigate the basis for the tissue-specific expression of SCN8A, we located conserved, potentially regulatory sequences in the human, mouse, chicken, and fish genes by 5? RACE of brain RNA and genomic sequence comparison. A highly conserved 5? noncoding exon, exon 1c, is present in vertebrates from fish to mammals and appears to define the ancestral promoter region. The distance from exon 1c to the first coding exon increased tenfold during vertebrate evolution, largely by insertion of repetitive elements. The mammalian gene acquired three novel, mutually exclusive noncoding exons that are not represented in the lower vertebrates. Within the shared exon 1c, we identified four short sequence elements of 10-20 bp with an unusually high level of evolutionary conservation. The conserved elements are most similar to consensus sites for the transcription factors Pou6f1/Brn5, YY1, and REST/NRSF. Introduction of mutations into the predicted Pou6f1 and REST sites reduced promoter activity in transfected neuronal cells. A 470-bp promoter fragment containing all of the conserved elements directed brain-specific expression of the LacZ reporter in transgenic mice. Transgene expression was highest in hippocampal neurons and cerebellar Purkinje cells, consistent with the expression of the endogenous gene. The compact cluster of conserved regulatory elements in SCN8A provides a useful target for molecular analysis of neuronal gene expression. Electronic supplementary material The online version of this article (doi:10.1007/s00335-007-9059-8) contains supplementary material, which is available to authorized users. PMID:17924165

Drews, Valerie L.; Shi, Kehui; de Haan, Georgius

2007-01-01

160

Agents Recognizing Emergence  

E-print Network

Agents that recognize self organizing systems and their emergent properties have a competitive advantage. In this paper we introduce a classication of self-organizing systems based on phase transitions, macroscopic dynamic structures, evolution, self-regulation, and ultra-stability. Sometimes the agent can recognize the type of self-organizing system by observing its internal mechanisms such as feedback mechanisms or essential variables, but in general he has to interpret the system's behavior and in particular its relation with the environment. The agent therefore uses besides theories of self-organization also theories of cybernetics. 1 Introduction Autonomous agents and multi agent systems are active research areas in arti- cial intelligence. We are interested in cognitive agents that use models of their environment, including models of other agents. In agent-based software engineering it has been recognized that the major drawback of the agent perspective is that in exc...

161

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

PubMed

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. PMID:24555506

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

2014-05-01

162

Accomplishments of the Alaska Region's Habitat Conservation Division in Fiscal Year 2004  

E-print Network

Environmental Impact Statement NOAA Fisheries and the Council continued work in FY04 to develop an Environmental Impact Statement (EIS) to reexamine the identification of EFH in Alaska and the measures needed Conservation and Management Act, Fish and Wildlife Coordination Act, National Environmental Policy Act, Federal

163

Changes in twelve conserved soybean genomic regions following three rounds of polyploidy  

Technology Transfer Automated Retrieval System (TEKTRAN)

With the advent of high throughput sequencing, the availability of genomic sequence for comparative genomics is increasing exponentially. A set of highly conserved homoeologous segments would be valuable in the exploration of the retention and evolution of genes within gene families due to the evol...

164

Resources, Conservation and Recycling 51 (2007) 847869 Modeling obsolete computer stock under regional  

E-print Network

and recycling systems using GIS, and demonstrate the potential economic benefits from diverting electronicResources, Conservation and Recycling 51 (2007) 847­869 Modeling obsolete computer stock under buildings. © 2007 Elsevier B.V. All rights reserved. Keywords: Computer recycling; Product inventory

Illinois at Chicago, University of

2007-01-01

165

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

DOEpatents

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.

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

2013-05-28

166

Should recognizers have ears?  

Microsoft Academic Search

Recently, techniques motivated by human auditory perception are being applied in main-stream speech technology and there seems to be renewed interest in implementing more knowledge of human speech communication into a design of a speech recognizer. The paper discusses the author's experience with applying auditory knowledge to automatic recognition of speech. It advances the notion that the reason for applying

Hynek Hermansky

1998-01-01

167

Institutional Login Recognized as  

E-print Network

Institutional Login Recognized as: University of Texas at Austin (871-01-133) University of Texas, Argonne, IL 60439, USA (4) Department of Physics, University of Texas, Austin, TX 78712, USA Find more System (282-30-894) 641390 University of Texas 2007 (352-47-848) U Texas System (944-39-206) Welcome

Erskine, James L.

168

Recycling of ESCRTs by the AAA-ATPase Vps4 is regulated by a conserved VSL region in Vta1.  

PubMed

In eukaryotes, the multivesicular body (MVB) sorting pathway plays an essential role in regulating cell surface protein composition, thereby impacting numerous cellular functions. Vps4, an ATPase associated with a variety of cellular activities, is required late in the MVB sorting reaction to dissociate the endosomal sorting complex required for transport (ESCRT), a requisite for proper function of this pathway. However, regulation of Vps4 function is not understood. We characterize Vta1 as a positive regulator of Vps4 both in vivo and in vitro. Vta1 promotes proper assembly of Vps4 and stimulates its ATPase activity through the conserved Vta1/SBP1/LIP5 region present in Vta1 homologues across evolution, including human SBP1 and Arabidopsis thaliana LIP5. These results suggest an evolutionarily conserved mechanism through which the disassembly of the ESCRT proteins, and thereby MVB sorting, is regulated by the Vta1/SBP1/LIP5 proteins. PMID:16505166

Azmi, Ishara; Davies, Brian; Dimaano, Christian; Payne, Johanna; Eckert, Debra; Babst, Markus; Katzmann, David J

2006-02-27

169

Seroepidemiology of Toxoplasma in a coastal region of Haiti: multiplex bead assay detection of immunoglobulin G antibodies that recognize the SAG2A antigen.  

PubMed

Toxoplasma gondii is a globally distributed parasitic protozoan that infects most warm-blooded animals. We incorporated a bead coupled with recombinant SAG2A protein into our Neglected Tropical Disease (NTD) multiplex bead assay (MBA) panel and used it to determine Toxoplasma infection rates in two studies in Haiti. In a longitudinal cohort study of children aged 0-11 years, the infection rate varied with age reaching a maximum of 0·131 infections/year in children aged 3 years [95% confidence interval (CI) 0·065-0·204]. The median time to seroconversion was estimated to be 9·7 years (95% CI 7·6-?). In a cross-sectional, community-wide survey of residents of all ages, we determined an overall seroprevalence of 28·2%. The seroprevalence age curve from the cross-sectional study also suggested that the force of infection varied with age and peaked at 0·057 infections/year (95% CI 0·033-0·080) at age 2·6 years. Integration of the Toxoplasma MBA into NTD surveys may allow for better estimates of the potential burden of congenital toxoplasmosis in underserved regions. PMID:25600668

Priest, J W; Moss, D M; Arnold, B F; Hamlin, K; Jones, C C; Lammie, P J

2015-02-01

170

A Water Quality Model for Regional Stream Assessment and Conservation Strategy Development  

Microsoft Academic Search

Non-point-source (NPS) pollution remains the primary source of stream impairment in the United States. Many problems such\\u000a as eutrophication, sedimentation, and hypoxia are linked with NPS pollution which reduces the water quality for aquatic and\\u000a terrestrial organisms. Increasingly, NPS pollution models have been used for landscape-scale pollution assessment and conservation\\u000a strategy development. Our modeling approach functions at a scale between

Marcia S. Meixler; Mark B. Bain

2010-01-01

171

Molecular characterization of a newly recognized mouse parvovirus.  

PubMed Central

Mouse parvovirus (MPV), formerly known as orphan parvovirus, is a newly recognized rodent parvovirus distinct from both serotypes of minute virus of mice (MVM). Restriction analysis of the MPV genome indicated that many restriction sites in the capsid region were different from those of MVM, but most sites in the nonstructural (NS) region of the genome were conserved. MPV resembled MVM in genome size, replication intermediates, and NS proteins. Replication intermediates in infected cells were the same for MPV and MVM, including packaging of the 5-kb minus (V) strand. Furthermore, the MPV NS proteins were the same size as and present at the same ratio as the MVM(i) proteins in infected cells. Cloning and sequencing of the MPV genome revealed a genome organization closely resembling that of MVM, with conservation of open reading frames, promoter sequences, and splice sites. The left terminal hairpin was identical to that of MVM(i), but the right terminus was not conserved. Also, the MPV genome was unique in that it contained 1.8 copies of the terminal repeat sequence rather than the 1 or 2 copies found in other parvoviruses. The predicted amino acid sequence of the NS proteins of MPV and MVM(i) were nearly identical. In contrast, the predicted amino acid sequence of the capsid proteins of MPV was different from sequences of other parvoviruses. These results confirm that MPV is a distinct murine parvovirus and account for the antigenic differences between MPV and MVM. Images PMID:8083985

Ball-Goodrich, L J; Johnson, E

1994-01-01

172

Burnout: Recognize and Reverse.  

PubMed

Physician burnout may be underrecognized and can cause significant detrimental effects on personal health and job satisfaction. Burnout has been associated with medical errors, alcohol and drug abuse, and neglect and abandonment of career goals. With self-awareness, development of coping mechanisms, and the adoption of a strong social and professional support network, burnout can be combated. This article focuses on recognizing characteristics of burnout and providing strategies to cope to avoid reaching a high degree of burnout. PMID:24825874

Anne, Samantha

2014-05-13

173

Insertion of horizontally transferred genes within conserved syntenic regions of yeast genomes.  

PubMed

Horizontal gene transfer has been occasionally mentioned in eukaryotic genomes, but such events appear much less numerous than in prokaryotes, where they play important functional and evolutionary roles. In yeasts, few independent cases have been described, some of which corresponding to major metabolic functions, but no systematic screening of horizontally transferred genes has been attempted so far. Taking advantage of the synteny conservation among five newly sequenced and annotated genomes of Saccharomycetaceae, we carried out a systematic search for HGT candidates amidst genes present in only one species within conserved synteny blocks. Out of 255 species-specific genes, we discovered 11 candidates for HGT, based on their similarity with bacterial proteins and on reconstructed phylogenies. This corresponds to a minimum of six transfer events because some horizontally acquired genes appear to rapidly duplicate in yeast genomes (e.g. YwqG genes in Kluyveromyces thermotolerans and serine recombinase genes of the IS607 family in Saccharomyces kluyveri). We show that the resulting copies are submitted to a strong functional selective pressure. The mechanisms of DNA transfer and integration are discussed, in relation with the generally small size of HGT candidates. Our results on a limited set of species expand by 50% the number of previously published HGT cases in hemiascomycetous yeasts, suggesting that this type of event is more frequent than usually thought. Our restrictive method does not exclude the possibility that additional HGT events exist. Actually, ancestral events common to several yeast species must have been overlooked, and the absence of homologs in present databases leaves open the question of the origin of the 244 remaining species-specific genes inserted within conserved synteny blocks. PMID:19654869

Rolland, Thomas; Neuvéglise, Cécile; Sacerdot, Christine; Dujon, Bernard

2009-01-01

174

Cotton production potential and water conservation impact using the regional irrigation demand model of northern Texas  

Technology Transfer Automated Retrieval System (TEKTRAN)

Revised irrigation demands are calculated for the 21 northernmost counties in Texas, identified as Panhandle Region (also known as Region A), using the TAMA (Texas A&M–Amarillo) agricultural water use demand estimation model. Year 2000 demands are presented using the existing mixture of crops, aver...

175

The distribution and conservation of bats in the dry regions of Madagascar  

Microsoft Academic Search

We carried out extensive field surveys in the dry forest portions of Madagascar to document the species of bats occurring in these regions. These data combined with information in the literature and museum specimen records indicate that 28 species of Chiroptera occur in this region of the island, of which we documented 27 during our inventories. The community composition at

Steven M. Goodman; Daudet Andriafidison; Radosoa Andrianaivoarivelo; Scott G. Cardiff; Edina Ifticene; Richard K. B. Jenkins; Amyot Kofoky; Tsibara Mbohoahy; Daniel Rakotondravony; Julie Razafimanahaka; Fanja Ratrimomanarivo; Paul A. Racey

2005-01-01

176

Intergenic regions of Borrelia plasmids contain phylogenetically conserved RNA secondary structure motifs  

Microsoft Academic Search

BACKGROUND: Borrelia species are unusual in that they contain a large number of linear and circular plasmids. Many of these plasmids have long intergenic regions. These regions have many fragmented genes, repeated sequences and appear to be in a state of flux, but they may serve as reservoirs for evolutionary change and\\/or maintain stable motifs such as small RNA genes.

Nicholas Delihas

2009-01-01

177

REPRODUCTIVE ECOLOGY OF AMERICAN OYSTERCATCHERS IN THE CAPE ROMAIN REGION OF SOUTH CAROLINA: IMPLICATIONS FOR CONSERVATION  

E-print Network

REPRODUCTIVE ECOLOGY OF AMERICAN OYSTERCATCHERS IN THE CAPE ROMAIN REGION OF SOUTH CAROLINA;ii ABSTRACT The Cape Romain Region (CRR) is located along the coast of South Carolina and supports project on the coast of South Carolina and his guidance and support during my time here at Clemson

Jodice, Patrick

178

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

PubMed

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

Balemie, Kebu; Singh, Ranjay K

2012-09-01

179

Diversity, natural history and conservation of amphibians and reptiles from the San Vito Region, southwestern Costa Rica.  

PubMed

We present an inventory of the amphibians and reptiles of the San Vito de Coto Brus region, including the Las Cruces Biological Station, in southern Costa Rica, which is the result of a survey of the herpetofauna occurring in mountain forest fragments, pastures, coffee plantations, and other disturbed areas. We found 67 species, included 26 species of amphibians and of 41 of reptiles. We describe the distribution patterns of the community on the basis of the life zones, elevation, fragmentation, and degree of anthropogenic impact. We also provide some nouvelle data on the systematics of some select taxa, their geographical ranges, microhabitats, activity, and other relevant ecological and natural history features. Finally, we comment on the present conservation status of the herpetofauna in the region. Previous literature and collection records indicate a higher number of species occurring in this area, which suggests that some declines have occurred, especially of amphibians, in last decades. PMID:19256442

Santos-Barrera, Georgina; Pacheco, Jesus; Mendoza-Quijano, Fernando; Bolaños, Federico; Cháves, Gerardo; Daily, Gretchen C; Ehrlich, Paul R; Ceballos, Gerardo

2008-06-01

180

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

Federal Register 2010, 2011, 2012, 2013, 2014

...this NODA is to inform stakeholders of three possible approaches for enforcement of regional...solicit feedback from stakeholders on these approaches. Respondents are advised...referred to as Confidential Business Information...

2011-12-07

181

Immunoglobulin (Ig)G purified from human sera mirrors intravenous Ig human leucocyte antigen (HLA) reactivity and recognizes one's own HLA types, but may be masked by Fab complementarity-determining region peptide in the native sera.  

PubMed

Intravenous immunoglobulin (IVIg) reacted with a wide array of human leucocyte antigen (HLA) alleles, in contrast to normal sera, due possibly to the purification of IgG from the pooled plasma. The reactivity of IgG purified from normal sera was compared with that of native sera to determine whether any serum factors mask the HLA reactivity of anti-HLA IgG and whether IgG purified from sera can recognize the HLA types of the corresponding donors. The purified IgG, unlike native sera, mirrored IVIg reactivity to a wide array of HLA-I/-II alleles, indicating that anti-HLA IgG may be masked in normal sera - either by peptides derived from soluble HLA or by those from antibodies. A region (CDR) of the Fab region of IgG (but not the HLA peptides) masked HLA recognition by the purified IgG. Most importantly, some of the anti-HLA IgG purified from normal sera - and serum IgG from a few donors - indeed recognized the HLA types of the corresponding donors, confirming the presence of auto-HLA antibodies. Comparison of HLA types with the profile of HLA antibodies showed auto-HLA IgG to the donors' HLA antigens in this order of frequency: DPA (80%), DQA (71%), DRB345 (67%), DQB (57%), Cw (50%), DBP (43%), DRB1 (21%), A (14%) and B (7%). The auto-HLA antibodies, when unmasked in vivo, may perform immunoregulatory functions similar to those of therapeutic preparations of IVIg. PMID:25196542

Ravindranath, M H; Terasaki, P I; Maehara, C Y; Jucaud, V; Kawakita, S; Pham, T; Yamashita, W

2015-02-01

182

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

SciTech Connect

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.

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

2011-09-28

183

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

PubMed Central

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

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

1993-01-01

184

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 ...

185

METADATA FOR RESOURCE CONSERVATION RECOVERY ACT INFORMATION SYSTEM LOCATIONS - REGION 8  

EPA Science Inventory

The Region 8 data are located in the ARC/INFO coverage, R8RCR_PTS, which was derived from the Envirofacts point shapefile layer in the National Shapefile Repository. This Repository provides locations of EPA-regulated facilities from the Oracle table LRT_EF_COVERAGE_SRC, which is...

186

A national geographic framework for guiding conservation on a landscape scale  

USGS Publications Warehouse

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.

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

2012-01-01

187

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

PubMed

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

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

2014-06-01

188

A Phylogenetically Conserved Hairpin-Type 39 Untranslated Region Pseudoknot Functions in Coronavirus RNA Replication  

Microsoft Academic Search

Secondary and tertiary structures in the 3* untranslated region (UTR) of plus-strand RNA viruses have been postulated to function as control elements in RNA replication, transcription, and translation. Here we describe a 54-nucleotide (nt) hairpin-type pseudoknot within the 288-nt 3* UTR of the bovine coronavirus genome and show by mutational analysis of both stems that the pseudoknotted structure is required

GWYN D. WILLIAMS; RUEY-YI CHANG; DAVID A. BRIAN

1999-01-01

189

Conserved regions of the DMD 3' UTR regulate translation and mRNA abundance in cultured myotubes.  

PubMed

Duchenne muscular dystrophy (DMD), a severe muscle-wasting disease, is caused by mutations in the DMD gene, which encodes for the protein dystrophin. Its regulation is of therapeutic interest as even small changes in expression of functional dystrophin can significantly impact the severity of DMD. While tissue-specific distribution and transcriptional regulation of several DMD mRNA isoforms has been well characterized, the post-transcriptional regulation of dystrophin synthesis is not well understood. Here, we utilize qRTPCR and a quantitative dual-luciferase reporter assay to examine the effects of isoform specific DMD 5' UTRs and the highly conserved DMD 3' UTR on mRNA abundance and translational control of gene expression in C2C12 cells. The 5' UTRs were shown to initiate translation with low efficiency in both myoblasts and myotubes. Whereas, two large highly conserved elements in the 3' UTR, which overlap the previously described Lemaire A and D regions, increase mRNA levels and enhance translation upon differentiation of myoblasts into myotubes. The results presented here implicate an important role for DMD UTRs in dystrophin expression and delineate the cis-acting elements required for the myotube-specific regulation of steady-state mRNA levels and translational enhancer activity found in the DMD 3' UTR. PMID:24928536

Larsen, C Aaron; Howard, Michael T

2014-08-01

190

[Water and soil conservation function of typical plantation forest ecosystems in semi-arid region of Western Liaoning Province].  

PubMed

From the aspects of surface runoff and soil erosion, this paper quantitatively studied the water and soil conservation function of five plantation forest ecosystems in semi-arid region of Western Liaoning Province. The results showed that various types of test plantation forest ecosystems were all able to reduce surface runoff and soil erosion effectively. In June - September, the monthly mean surface runoff coefficient of Pinus tabulaeformis forest ecosystem, P. tabulaeformis - Hippophae rhamnoides forest ecosystem, H. rhamnoides forest ecosystem, P. simonii forest ecosystem, and P. simonii - H. rhamnoides forest ecosystem was 10.1%, 6.5%, 2.3%, 8.6% and 5.3% of that of barren hill, respectively, and the soil erosion quantity was 2.65%, 0.96%, 0.15%, 2.32% and 0.69% of that of barren hill, respectively. Among the five forest ecosystems, H. rhamnoides forest ecosystem had the least surface runoff and soil erosion, being the best in water and soil conservation function. PMID:18333474

Jiang, Ping; Guo, Fang; Luo, Yue-Chu; Wei, Jing; Sun, Xiao-Wei; Wu, Gang

2007-12-01

191

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

PubMed

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 PKC? (C1B?) and its W252Y variant. The W252Y mutation was previously shown to render C1B? 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 C1B? 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 C1B?-micelle interactions. In addition, we identified the C-terminal helix ?1 of C1B? as an interaction site with the head groups of phosphatidylserine, a known activator of PKC?. Taken together, our studies (i) reveal the identities of C1B? 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. PMID:25124034

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

2014-10-01

192

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

PubMed

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

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

2009-04-01

193

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

SciTech Connect

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.

Schwartz, F.; Eisenman, R.; Knoll, J.; Bruns, G. [Children`s Hospital and Department of Pediatrics, Boston, MA (United States)

1995-09-20

194

Functional analysis of a highly conserved abundant larval transcript-2 (alt-2) intron 2 repeat region of lymphatic filarial parasites.  

PubMed

The filarial-specific protein abundant larval transcript-2 (ALT-2) is expressed exclusively in the infective larval stage (L3) and is a crucial protein for establishing immunopathogenesis in human hosts. The alt-2 gene has a conserved minisatellite repeat (29 or 27bp) in intron 2 (IR2) whose significance within lymphatic filarial species is unknown. Here, we report the role of IR2 in the regulation of alt-2 gene expression using an in vitro model. Using electrophoretic mobility shift assays, we identified the presence of a putative nuclear protein binding region within IR2. Subsequent transient expression experiments in eukaryotic cell lines demonstrated that the IR2 downregulated the expression of a downstream luciferase reporter gene, which was further validated with RT-PCR. We therefore identify IR2 as a suppressor element that regulates L3 stage-specific expression of alt-2. PMID:24681262

Sakthidevi, Moorthy; Hoti, Sugeerappa Laxmanappa; Kaliraj, Perumal

2014-06-01

195

A gene from the human sex-determining region encodes a protein with homology to a conserved DNA-binding motif  

Microsoft Academic Search

A search of a 35-kilobase region of the human Y chromosome necessary for male sex determination has resulted in the identification of a new gene. This gene is conserved and Y-specific among a wide range of mammals, and encodes a testis-specific transcript. It shares homology with the mating-type protein, Mc, from the fission yeast Schizosaccharomyces pombe and a conserved DNA-binding

Andrew H. Sinclair; Philippe Berta; Mark S. Palmer; J. Ross Hawkins; Beatrice L. Griffiths; Matthijs J. Smith; Jamie W. Foster; Anna-Maria Frischauf; Robin Lovell-Badge; Peter N. Goodfellow

1990-01-01

196

Temporal variations in immune responses to conserved regions of Plasmodium falciparum merozoite surface proteins related to the severity of a prior malaria episode in Gabonese children  

Microsoft Academic Search

We measured cellular and humoral responses to conserved regions of Plasmodium falciparum merozoite surface proteins 1 and 2 (MSP-1 and MSP-2) at different times during and after acute infection in matched groups of Gabonese children who presented with either mild or severe malaria. We used an MSP-119 recombinant protein and peptides corresponding to conserved epitopes in MSP-1 and MSP-2 N-

Carsten Köhler; Anne E. Tebo; Beatrice Dubois; Philippe Deloron; Peter G. Kremsner; Adrian J. F. Luty

2003-01-01

197

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

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.

Boutrus, Rimoun; Abi-Raad, Rita; Niemierko, Andrzej [Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA (United States); Brachtel, Elena F. [Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA (United States); Rizk, Levi; Kelada, Alexandra [Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA (United States); Taghian, Alphonse G., E-mail: ataghian@partners.or [Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA (United States)

2010-11-01

198

Identification of conserved and variable regions in the envelope glycoprotein sequences of two feline immunodeficiency viruses isolated in Zurich, Switzerland.  

PubMed

The nucleotide sequences of the envelope (env) coding regions of two strains of the feline immunodeficiency virus isolated in Zurich, Switzerland (FIVZ1, FIVZ2) have been analysed. In addition, the complete sequence of the FIVZ1 isolate has been determined. Comparisons have been made with the previously published sequences of three North American isolates (PPR and the Petaluma strains FIV34TF10 and FIV14). The isolate FIVZ1 was very similar to the Petaluma strains of FIV and may represent a clonal derivative acquired by 'contamination'. Overall there are between 2.6% and 15.1% amino acid changes in the env gene products of the five isolates. Of the Zurich isolates, FIVZ2 exhibited the greatest divergence to the other viruses and based on its genotype, phenotype and origins probably represents a new isolate of FIV. Possibly the viruses diverged only recently from a common ancestor. Some 31 of the 33 cysteine residues and 17 of the 21 potential N-linked glycosylation sites of the FIV34TF10 env gene product were conserved among all five isolates. The open reading frame 3 (ORF3, or D) which overlaps the env gene (but is encoded in a different frame) has an ATG codon downstream of a potential splice acceptor site in all five isolates, supporting the view that it encodes a viral gene product. In ORF3 of FIVZ1 a stop codon was located 16 amino acids upstream of the stop codon of ORF3 of the other isolates. The ORF4 (or G) of isolate FIVZ2, thought to be the second coding exon of an FIV rev-like gene, contained a nucleotide deletion in amino acid 45 of ORF4, resulting in a--1 frameshift at this position. Comparison of the LTR sequences of the five isolates identified conserved promoter/enhancer elements. A potential stem-loop structure was identified in the R region of the LTRs of all the isolates, despite the heterogeneity of nucleotide sequences in that region. Such structures (TAR) are present in analogous regions of other lentiviruses and are responsible for tat-mediated trans-activation. PMID:1660215

Morikawa, S; Lutz, H; Aubert, A; Bishop, D H

1991-09-01

199

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

SciTech Connect

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)

Not Available

1980-01-01

200

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

PubMed

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

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

2012-06-01

201

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

USGS Publications Warehouse

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.

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

2012-01-01

202

The C-Terminal Domain from S. cerevisiae Pat1 Displays Two Conserved Regions Involved in Decapping Factor Recruitment  

PubMed Central

Eukaryotic mRNA decay is a highly regulated process allowing cells to rapidly modulate protein production in response to internal and environmental cues. Mature translatable eukaryotic mRNAs are protected from fast and uncontrolled degradation in the cytoplasm by two cis-acting stability determinants: a methylguanosine (m7G) cap and a poly(A) tail at their 5? and 3? extremities, respectively. The hydrolysis of the m7G cap structure, known as decapping, is performed by the complex composed of the Dcp2 catalytic subunit and its partner Dcp1. The Dcp1-Dcp2 decapping complex has a low intrinsic activity and requires accessory factors to be fully active. Among these factors, Pat1 is considered to be a central scaffolding protein involved in Dcp2 activation but also in inhibition of translation initiation. Here, we present the structural and functional study of the C-terminal domain from S. cerevisiae Pat1 protein. We have identified two conserved and functionally important regions located at both extremities of the domain. The first region is involved in binding to Lsm1-7 complex. The second patch is specific for fungal proteins and is responsible for Pat1 interaction with Edc3. These observations support the plasticity of the protein interaction network involved in mRNA decay and show that evolution has extended the C-terminal alpha-helical domain from fungal Pat1 proteins to generate a new binding platform for protein partners. PMID:24830408

Back, Régis; Keller, Jenny; Charenton, Clément; Taverniti, Valerio; Plesse, Claudine Gaudon; Lazar, Noureddine; Durand, Dominique; van Tilbeurgh, Herman; Séraphin, Bertrand; Graille, Marc

2014-01-01

203

Characterization of T-Cell Responses to Conserved Regions of the HIV-1 Proteome in BALB/c Mice  

PubMed Central

A likely requirement for a protective vaccine against human immunodeficiency virus type 1 (HIV-1)/AIDS is, in addition to eliciting antibody responses, induction of effective T cells. To tackle HIV-1 diversity by T-cell vaccines, we designed an immunogen, HIVconsv, derived from the most functionally conserved regions of the HIV-1 proteome and demonstrated its high immunogenicity in humans and rhesus macaques when delivered by regimens combining plasmid DNA, nonreplicating simian (chimpanzee) adenovirus ChAdV-63, and nonreplicating modified vaccinia virus Ankara (MVA) as vectors. Here, we aimed to increase the decision power for iterative improvements of this vaccine strategy in the BALB/c mouse model. First, we found that prolonging the period after the ChAdV63.HIVconsv prime up to 6 weeks increased the frequencies of HIV-1-specific, gamma interferon (IFN-?)-producing T cells induced by the MVA.HIVconsv boost. Induction of strong responses allowed us to map comprehensively the H-2d-restricted T-cell responses to these regions and identified 8 HIVconsv peptides, of which three did not contain a previously described epitope and were therefore considered novel. Induced effector T cells were oligofunctional and lysed sensitized targets in vitro. Our study therefore provides additional tools for studying and optimizing vaccine regimens in this commonly used small animal model, which will in turn guide vaccine improvements in more expensive nonhuman primate and human clinical trials. PMID:25230940

Ondondo, Beatrice; Abdul-Jawad, Sultan; Bridgeman, Anne

2014-01-01

204

How many kilowatts are in a negawatt? Verifying ex post estimates of utility conservation impacts at the regional level  

SciTech Connect

Restructuring of utilities raises questions about the future of conservation programs. One of the greatest obstacles has been the persistent uncertainity among utility planners regarding true resource effectiveness and cost-effectiveness of conservation relative to conventional generation. The authors use econometric techniques to examine the aggregate commercial and industrial conservation impacts reported. The paper shows that utility conservation programs have been effective in reducing electric loads and that utilities have reported accurately. 44 refs., 3 tabs.

Parfomak, P.W.; Lave, L.B. [Carnegie Mellon Univ., Pittsburgh, PA (United States)

1996-12-31

205

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

SciTech Connect

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.

Schaefer, F.V.; Calikoglu, A.S.; Whetsell, L.H. [H.A. Chapman Research Institute of Medical Genetics, Tulsa, OK (United States)

1994-09-01

206

Examples of geodiversity - biodiversity relationships from Brabant's sand regions, in nature conservation and restoration  

NASA Astrophysics Data System (ADS)

The Dutch province of Noord-Brabant is dominated by sand landscapes of aeolian and riverine origin dating from Pleistocene and Holocene times. Brabant's geological history is governed by its position on the fringe of a geological basin with re-activated faults and a Weichselian polar dune desert, a history that makes the region unique in Europe. Some areas have assemblages of geomorphology and soils that have remained relatively untouched up to the present day. In these more pristine areas, the morphological, geological and soil development is a governing factor for the small-scale vegetation differences and biodiversity. Examples of these relationships will be shown, such as loam forests, wetlands caused by 'wijst' - a feature that is special for Brabant, in which the higher grounds are wetter than the lower grounds - active drift sands, and dry and wet heathlands with 'vennen' - small ponds in different gradations of paludization. Many of these areas are Natura-2000 habitats. The geodiversity-biodiversity relationships will be part of the proposal for a European Geopark in Brabant. Measures to restore biodiversity are only sustainable if geodiversity is part of the nature restoration plan e.g. the history of the local landscape, geology, geomorphology and soils. Even if the areas have undergone a drastic transformation. Two examples will be given of nature restoration projects based on geodiversity-biodiversity relationships. The first example is the restoration of an active drift sand, such as still occur in The Netherlands but are extremely rare in the rest of Europe. Over the last decades they have also stabilized in The Netherlands due to high nitrogen deposition. The other example concerns a nature restoration project in a stream valley. These stream valleys originally had a high and small-scale geodiversity that was completely destroyed by stream regulation for agriculture production. This was the first project to study the former and present-day geo-dynamics and use these to restore the stream habitats and optimize geo-biodiversity relationships.

van den Ancker, Hanneke; Heskes, Erik; Jungerius, Pieter Dirk; Maes, Bert; Harthoorn, Jaap

2014-05-01

207

Evidence on How a Conserved Glycine in the Hinge Region of HapR Regulates Its DNA Binding Ability  

PubMed Central

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. PMID:21383015

Dongre, Mitesh; Singh, Naorem Santa; Dureja, Chetna; Peddada, Nagesh; Solanki, Ashish K.; Ashish; Raychaudhuri, Saumya

2011-01-01

208

7 CFR 636.21 - Environmental services credits for conservation improvements.  

Code of Federal Regulations, 2013 CFR

... Environmental services credits for conservation improvements. 636.21 Section...Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE... Environmental services credits for conservation improvements. USDA recognizes...

2013-01-01

209

7 CFR 636.21 - Environmental services credits for conservation improvements.  

Code of Federal Regulations, 2012 CFR

... Environmental services credits for conservation improvements. 636.21 Section...Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE... Environmental services credits for conservation improvements. USDA recognizes...

2012-01-01

210

7 CFR 636.21 - Environmental services credits for conservation improvements.  

Code of Federal Regulations, 2014 CFR

... Environmental services credits for conservation improvements. 636.21 Section...Agriculture (Continued) NATURAL RESOURCES CONSERVATION SERVICE, DEPARTMENT OF AGRICULTURE... Environmental services credits for conservation improvements. USDA recognizes...

2014-01-01

211

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

USGS Publications Warehouse

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.

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

2005-01-01

212

Conservation status of the White-Bellied Sea-Eagle Haliaeetus leucogaster in Australia determined using mtDNA control region sequence data  

Microsoft Academic Search

Considered to have a declining world population, concern has been expressed in recent years over the conservation status of the White-bellied Sea-Eagle Haliaeetus leucogaster (Gmelin, 1788) within Australia. We used mitochondrial (mtDNA) control region sequence data to investigate the current distribution of genetic variation in this species at the continental level and within and between specified regional units. We were

Jill M. Shephard; Jane M. Hughes; Carla P. Catterall; Penny D. Olsen

2005-01-01

213

Ground beetles (Coleoptera, Carabidae)on set-aside fields in the Campine region and their importance for nature conservation in Flanders (Belgium)  

Microsoft Academic Search

Three set-aside fields of arable land on sandy soil in the Campine region of Flanders (Belgium), differently managed for nature conservation purposes, were sampled for their carabid beetle fauna during a complete year cycle by means of pitfall traps. About 3650 ground beetles belonging to 53 species were obtained. Besides this remarkably high diversity, no less than 11 Red data

Konjev Desender; Robert Bosmans

1998-01-01

214

The Isolation of Conserved DNA Sequences Related the Human Sex-Determining Region Y Gene from the Lesser Black-Backed Gull (Larus fuscus)  

Microsoft Academic Search

The sex-determining region gene (SRY) is a recently discovered candidate for the mammalian testis determining factor (TDF). The gene appears to form part of a family with several autosomal representatives. I have investigated the occurrence of SRY-related sequences in birds. The polymerase chain reaction was used to isolate six homologues of the conserved motif of the SRY gene from the

Richard Griffiths

1991-01-01

215

Cloning of a negative transcription factor that binds to the upstream conserved region of Moloney murine leukemia virus.  

PubMed Central

The long terminal repeat of Moloney murine leukemia virus (MuLV) contains the upstream conserved region (UCR). The UCR core sequence, CGCCATTTT, binds a ubiquitous nuclear factor and mediates negative regulation of MuLV promoter activity. We have isolated murine cDNA clones encoding a protein, referred to as UCRBP, that binds specifically to the UCR core sequence. Gel mobility shift assays demonstrate that the UCRBP fusion protein expressed in bacteria binds the UCR core with specificity identical to that of the UCR-binding factor in the nucleus of murine and human cells. Analysis of full-length UCRBP cDNA reveals that it has a putative zinc finger domain composed of four C2H2 zinc fingers of the GLI subgroup and an N-terminal region containing alternating charges, including a stretch of 12 histidine residues. The 2.4-kb UCRBP message is expressed in all cell lines examined (teratocarcinoma, B- and T-cell, macrophage, fibroblast, and myocyte), consistent with the ubiquitous expression of the UCR-binding factor. Transient transfection of an expressible UCRBP cDNA into fibroblasts results in down-regulation of MuLV promoter activity, in agreement with previous functional analysis of the UCR. Recently three groups have independently isolated human and mouse UCRBP. These studies show that UCRBP binds to various target motifs that are distinct from the UCR motif: the adeno-associated virus P5 promoter and elements in the immunoglobulin light- and heavy-chain genes, as well as elements in ribosomal protein genes. These results indicate that UCRBP has unusually diverse DNA-binding specificity and as such is likely to regulate expression of many different genes. Images PMID:1309593

Flanagan, J R; Becker, K G; Ennist, D L; Gleason, S L; Driggers, P H; Levi, B Z; Appella, E; Ozato, K

1992-01-01

216

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

PubMed

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. PMID:25223007

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

2014-06-01

217

Osmostress Induces Autophosphorylation of Hog1 via a C-Terminal Regulatory Region That Is Conserved in p38?  

PubMed Central

Many protein kinases require phosphorylation at their activation loop for induction of catalysis. Mitogen-activated protein kinases (MAPKs) are activated by a unique mode of phosphorylation, on neighboring Tyrosine and Threonine residues. Whereas many kinases obtain their activation via autophosphorylation, MAPKs are usually phosphorylated by specific, dedicated, MAPK kinases (MAP2Ks). Here we show however, that the yeast MAPK Hog1, known to be activated by the MAP2K Pbs2, is activated in pbs2? cells via an autophosphorylation activity that is induced by osmotic pressure. We mapped a novel domain at the Hog1 C-terminal region that inhibits this activity. Removal of this domain provides a Hog1 protein that is partially independent of MAP2K, namely, partially rescues osmostress sensitivity of pbs2? cells. We further mapped a short domain (7 amino acid residues long) that is critical for induction of autophosphorylation. Its removal abolishes autophosphorylation, but maintains Pbs2-mediated phosphorylation. This 7 amino acids stretch is conserved in the human p38?. Similar to the case of Hog1, it’s removal from p38? abolishes p38?’s autophosphorylation capability, but maintains, although reduces, its activation by MKK6. This study joins a few recent reports to suggest that, like many protein kinases, MAPKs are also regulated via induced autoactivation. PMID:22984552

Maayan, Inbal; Beenstock, Jonah; Marbach, Irit; Tabachnick, Shira; Livnah, Oded; Engelberg, David

2012-01-01

218

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

PubMed Central

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 CIDR1? domains bind CD36. Here we describe the CD36-binding portion of a CIDR1? domain, MC179, as a bundle of three ?-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 CIDR1? 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 CIDR1? 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 DBL1? domains are approximately 100 residues larger and that CIDR1? 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 molecular basis of cytoadherence. PMID:18773118

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

2008-01-01

219

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

PubMed

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

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

2013-07-01

220

NIH Recognizes 2015 FARE Winners  

Cancer.gov

The NIH Fellows Award for Research Excellence (FARE) recognizes scientific research by intramural postdoctoral fellows and by predoctoral fellows conducting their doctoral dissertation research at NIH. Winners receive a $1,000 travel stipend to attend

221

Recognizing actions using embodiment & empathy  

E-print Network

Here I demonstrate the power of using embodied artificial intelligence to attack the action recognition problem, which is the challenge of recognizing actions performed by a creature given limited data about the creature's ...

McIntyre, Robert Louis

2014-01-01

222

A virtual vocabulary speech recognizer  

E-print Network

A system for the automatic recognition of human speech is described. A commercially available speech recognizer sees its recognition vocabulary increased through the use of virtual memory management techniques. central to ...

Pathe, Peter D

1983-01-01

223

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

USGS Publications Warehouse

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.

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

2010-01-01

224

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

PubMed

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. PMID:25032268

Glass, Jennifer; Levchak, Philip

2014-01-01

225

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

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.

Watson, J.M.; Spencer, J.A.; Graves, J.A.M. (La Trobe Univ., Bundoora, Victoria (Australia)); Riggs, A.D. (Beckman Inst., Duarte, CA (USA))

1990-09-01

226

Statistical evidence for conserved, local secondary structure in the coding regions of eukaryotic mRNAs and pre-mRNAs  

Microsoft Academic Search

Owing to the degeneracy of the genetic code, protein-coding regions of mRNA sequences can harbour more than only amino acid information. We search the mRNA sequences of 11 human protein-coding genes for evolutionarily conserved secondary structure elements using RNA-Decoder, a comparative secondary structure prediction pro- gram that is capable of explicitly taking the known protein-coding context of the mRNA sequences

Irmtraud M. Meyer; Istvan Miklos

2005-01-01

227

Variation in life-cycle between three rare and endangered floodplain violets in two regions: implications for population viability and conservation  

Microsoft Academic Search

We studied the demography of Viola elatior, V. pumila, and V. stagnina, three rare and endangered Central European floodplain species, to (i) analyse variation in life-cycles among congeners and\\u000a between regions (Dyje-Morava floodplains, Czech Republic; Upper Rhine, Germany), (ii) to define sensitive stages in the life-cycles,\\u000a and (iii) to identify possible threats for population viability and species conservation.\\u000a \\u000a Matrix models

Rolf Lutz Eckstein; Ji?í Danihelka; Annette Otte

2009-01-01

228

Phylogenetic analysis of a highly conserved region of the polymerase gene from 11 coronaviruses and development of a consensus polymerase chain reaction assay  

Microsoft Academic Search

Viruses in the genus Coronavirus are currently placed in three groups based on antigenic cross-reactivity and sequence analysis of structural protein genes. Consensus polymerase chain reaction (PCR) primers were used to obtain cDNA, then cloned and sequenced a highly conserved 922 nucleotide region in open reading frame (ORF) 1b of the polymerase (pol) gene from eight coronaviruses. These sequences were

Charles B. Stephensen; Donald B. Casebolt; Nupur N. Gangopadhyay

1999-01-01

229

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  

Microsoft Academic Search

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 5 210) collected from patients with clinically defined Lyme disease at

FANG TING LIANG; ALLEN C. STEERE; ADRIANA R. MARQUES; BARBARA J. B. JOHNSON; JAMES N. MILLER; MARIO T. PHILIPP

1999-01-01

230

An evolutionary conserved region (ECR) in the human dopamine receptor D4 gene supports reporter gene expression in primary cultures derived from the rat cortex  

PubMed Central

Background Detecting functional variants contributing to diversity of behaviour is crucial for dissecting genetics of complex behaviours. At a molecular level, characterisation of variation in exons has been studied as they are easily identified in the current genome annotation although the functional consequences are less well understood; however, it has been difficult to prioritise regions of non-coding DNA in which genetic variation could also have significant functional consequences. Comparison of multiple vertebrate genomes has allowed the identification of non-coding evolutionary conserved regions (ECRs), in which the degree of conservation can be comparable with exonic regions suggesting functional significance. Results We identified ECRs at the dopamine receptor D4 gene locus, an important gene for human behaviours. The most conserved non-coding ECR (D4ECR1) supported high reporter gene expression in primary cultures derived from neonate rat frontal cortex. Computer aided analysis of the sequence of the D4ECR1 indicated the potential transcription factors that could modulate its function. D4ECR1 contained multiple consensus sequences for binding the transcription factor Sp1, a factor previously implicated in DRD4 expression. Co-transfection experiments demonstrated that overexpression of Sp1 significantly decreased the activity of the D4ECR1 in vitro. Conclusion Bioinformatic analysis complemented by functional analysis of the DRD4 gene locus has identified a) a strong enhancer that functions in neurons and b) a transcription factor that may modulate the function of that enhancer. PMID:21599953

2011-01-01

231

Genetic organization of the Escherichia coli K10 capsule gene cluster: identification and characterization of two conserved regions in group III capsule gene clusters encoding polysaccharide transport functions.  

PubMed

Analysis of the Escherichia coli K10 capsule gene cluster identified two regions, regions 1 and 3, conserved between different group III capsule gene clusters. Region 1 encodes homologues of KpsD, KpsM, KpsT, and KpsE proteins, and region 3 encodes homologues of the KpsC and KpsS proteins. An rfaH mutation abolished K10 capsule production, suggesting that expression of the K10 capsule was regulated by RfaH in a manner analogous to group II capsule gene clusters. An IS3 element and a phiR73-like prophage, both of which may have played a role in the acquisition of group III capsule gene clusters, were detected flanking the K10 capsule genes. PMID:10094710

Clarke, B R; Pearce, R; Roberts, I S

1999-04-01

232

Comparative architectural aspects of regions of conserved synteny on human chromosome 11p15.3 and mouse chromosome 7 (including genes WEE1 and LMO1).  

PubMed

Human chromosome 11p15.3 is associated with chromosome aberrations in the Beckwith Wiedemann Syndrome and implicated in the pathogenesis of different tumor types including lung cancer and leukemias. To date, only single tumor-relevant genes with linkage to this region (e.g. LMO1) have been found suggesting that this region may harbor additional potential disease associated genes. Although this genomic area has been studied for years, the exact order of genes/chromosome markers between D11S572 and the WEE1 gene locus remained unclear. Using the FISH technique and PAC clones of the flanking markers we determined the order of the genomic markers. Based on these clones we established a PAC contig of the respective region. To analyse the chromosome area in detail the synteny of the orthologous region on distal mouse chromosome 7 was determined and a corresponding mouse clone contig established, proving the conserved order of the genes and markers in both species: "cen-WEE1-D11S2043-ZNF143-RANBP7-CEGF1- ST5-D11S932-LMO1-D11S572-TUB-tel", with inverted order of the murine genes with respect to the telomere/centromere orientation. The region covered by these contigs comprises roughly 1.6 MB in human as well as in mouse. The genomic sequence of the two subregions (around WEE1 and LMO1) in both species was determined using a shotgun sequencing strategy. Comparative sequence analysis techniques demonstrate that the content of repetitive elements seems to decline from centromere to telomere (52.6% to 34.5%) in human and in the corresponding murine region from telomere to centromere (41.87% to 27.82%). Genomic organisation of the regions around WEE1 and LMO1 was conserved, although the length of gene regions varied between the species in an unpredictable ratio. CpG islands were found conserved in putative promoter regions of the known genes but also in regions which so far have not been described as harboring expressed sequences. PMID:11528126

Cichutek, A; Brueckmann, T; Seipel, B; Hauser, H; Schlaubitz, S; Prawitt, D; Hankeln, T; Schmidt, E R; Winterpacht, A; Zabel, B U

2001-01-01

233

Antibodies and PMBC from EIAV infected carrier horses recognize gp45 and p26 synthetic peptides.  

PubMed

Equine infectious anemia virus (EIAV) is a lentivirus causing a persistent infection in horses characterized by recurrent febrile episodes and high levels of viremia associated with a novel antigenic strain of the virus. The virus contains two envelope glycoproteins, gp90 and gp45, and four internal proteins, p26, p15, p11 and p9. Considering that the most infected horses are able to restrict EIAV replication to very low levels and that gp45 and p26 contain highly conserved epitopes among lentiviruses, it would be necessary to identify those conserved epitopes stimulating cellular and humoral responses. The aims of this study were to determine if the synthetic peptides identified as gp45 (aa 523-547) and p26 (aa 318-346) representing two highly conserved and immunodominant regions of EIA virus are recognized by PBMC and antibodies to EIAV adult mixed-breed naturally infected carrier horses, and if these peptides are able to induce immune responses in mice. Antibodies from 100% of carrier horses, evaluated by ELISA, recognized both peptides; PBMC from 80% of carrier horses, evaluated by lymphoproliferation assay, recognized, at least, one peptide. Furthermore, immunization with 100 microg of each peptide elicited humoral and cellular responses in BALB/c mice, antibodies appeared at 48 or 63 days of immunization with gp45 or p26, respectively. Although the kinetics of gp45- and p26-specific antibody responses were similar, percentage of positivity was higher for gp45. The lymphoproliferation assay, evaluated by BrdU uptake, was higher in mice immunized with gp45 or p26 than in the control group (P<0.05). Based on our findings, we consider that both peptides could be included in an effective vaccine design to induce long-term immunological memory. PMID:16105689

Soutullo, A; García, M I; Bailat, A; Racca, A; Tonarelli, G; Malan Borel, I

2005-12-15

234

Reciprocal Chromosome Painting Reveals Detailed Regions of Conserved Synteny between the Karyotypes of the Domestic Dog ( Canis familiaris) and Human  

Microsoft Academic Search

The domestic dog is increasingly being recognized as a useful model for human disease. The aim of this study was to conduct the first detailed whole-genome comparison of human and dog using bidirectional heterologous chromosome painting (reciprocal Zoo-FISH) analysis. We used whole-chromosome paint probes produced from degenerate oligonucleotide-primed PCR amplification of high-resolution bivariate flow-sorted human and dog chromosomes. No fewer

Matthew Breen; Rachael Thomas; Matthew M. Binns; Nigel P. Carter; Cordelia F. Langford

1999-01-01

235

Biotelemetry and biologging in endangered species research and animal conservation: relevance to regional, national, and IUCN Red List threat assessments  

Microsoft Academic Search

The current biodiversity crisis is characterized by the decline and extinction of numer- ous animal populations and species world-wide. To aid in understanding the threats and causes of population decline and the assessment of endangerment status of a species, conservation scientists and practitioners are increasingly relying on remote assessments using biotelemetry (radio telemetry, acoustic telemetry, satellite tracking) and biologging (archival

Steven J. Cooke

2008-01-01

236

Identification of broadly recognized, T helper 1 lymphocyte epitopes in an equine lentivirus.  

PubMed

Equine infectious anaemia virus (EIAV) is a horse lentivirus causing lifelong, persistent infection. During acute infection, CD8(+) cytotoxic T lymphocytes (CTL) are probably involved in terminating plasma viraemia. However, only a few EIAV CTL epitopes, restricted to fewer horse major histocompatibility complex (MHC) class I alleles, are known. As interferon-gamma (IFN-gamma)-secreting CD4(+), T helper 1 (Th1) lymphocytes promote CTL activity and help maintain memory CTL, identifying broadly recognized EIAV Th1 epitopes would contribute significantly to vaccine strategies seeking to promote strong CTL responses among horses with varying class I haplotypes. To this end, peripheral blood mononuclear cells (PBMC) from 10 MHC disparate, EIAV-infected horses were tested in T-lymphocyte proliferation assays for recognition of peptides from the Gag p26 capsid region and a portion of Pol. Both regions are highly conserved among EIAV isolates, and this Pol region is 51-63% homologous to other lentiviral Pol proteins. Seven of 10 horses recognized peptide Gag 221-245, and peptides Gag 242-261 and Pol 323-344 were recognized by five and four horses, respectively. Furthermore, the Gag peptides were recognized by two additional horses after resolving their initial plasma viraemia, indicating that these two peptides can be immunodominant early in infection. Gag peptide-responsive PBMC produced only IFN-gamma, indicating a Th1 response, while Pol 323-344-responsive PBMC produced IFN-gamma both with and without interleukin-4. PBMC from uninfected horses failed to either proliferate or secrete cytokines in response to peptide stimulation. Finally, CD4(+) T lymphocytes were required for proliferation responses, as shown by assays using CD4- versus CD8-depleted PBMC. PMID:11918691

Fraser, Darrilyn G; Oaks, J Lindsay; Brown, Wendy C; McGuire, Travis C

2002-03-01

237

Identification of broadly recognized, T helper 1 lymphocyte epitopes in an equine lentivirus  

PubMed Central

Equine infectious anaemia virus (EIAV) is a horse lentivirus causing lifelong, persistent infection. During acute infection, CD8+ cytotoxic T lymphocytes (CTL) are probably involved in terminating plasma viraemia. However, only a few EIAV CTL epitopes, restricted to fewer horse major histocompatibility complex (MHC) class I alleles, are known. As interferon-? (IFN-?)-secreting CD4+, T helper 1 (Th1) lymphocytes promote CTL activity and help maintain memory CTL, identifying broadly recognized EIAV Th1 epitopes would contribute significantly to vaccine strategies seeking to promote strong CTL responses among horses with varying class I haplotypes. To this end, peripheral blood mononuclear cells (PBMC) from 10 MHC disparate, EIAV-infected horses were tested in T-lymphocyte proliferation assays for recognition of peptides from the Gag p26 capsid region and a portion of Pol. Both regions are highly conserved among EIAV isolates, and this Pol region is 51–63% homologueous to other lentiviral Pol proteins. Seven of 10 horses recognized peptide Gag 221–245, and peptides Gag 242–261 and Pol 323–344 were recognized by five and four horses, respectively. Furthermore, the Gag peptides were recognized by two additional horses after resolving their initial plasma viraemia, indicating that these two peptides can be immunodominant early in infection. Gag peptide-responsive PBMC produced only IFN-?, indicating a Th1 response, while Pol 323–344-responsive PBMC produced IFN-? both with and without interleukin-4. PBMC from uninfected horses failed to either proliferate or secrete cytokines in response to peptide stimulation. Finally, CD4+ T lymphocytes were required for proliferation responses, as shown by assays using CD4- versus CD8-depleted PBMC. PMID:11918691

Fraser, Darrilyn G; Oaks, J Lindsay; Brown, Wendy C; McGuire, Travis C

2002-01-01

238

Recognizing Wetlands An Informational Pamphlet  

E-print Network

Recognizing Wetlands An Informational Pamphlet What is a Wetland? The US Army Corps of Engineers(Corps) and the US Environmental Protection Agency define wetlands as follows: Those areas that are inundated conditions. Wetlands generally include swamps, marshes, bogs, and similar areas. Wetlands are areas

US Army Corps of Engineers

239

Recognizing and Managing Interpersonal Conflict.  

ERIC Educational Resources Information Center

Practical advice is offered, to managers and supervisors at any level, on recognizing and analyzing interpersonal conflicts, managing such conflicts and making them productive, and ensuring that performance reviews result in progress for both supervisor and employee. Conflict is seen as inevitable, an opportunity to take action, and manageable.…

Deane, Nancy; Hovland, Michael

1993-01-01

240

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

PubMed Central

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

De Pablos, Luis M.

2012-01-01

241

Conservation Conservation ResourcesConservation Resources  

E-print Network

Northwest Power and Conservation Council Conservation ResourcesConservation Resources in thein the Draft 5Draft 5thth Northwest Power PlanNorthwest Power Plan Tom EckmanTom Eckman Manager, Conservation ResourcesManager, Conservation Resources Northwest Power and Conservation CouncilNorthwest Power

242

Mammalian mitochondrial D-loop region structural analysis: identification of new conserved sequences and their functional and evolutionary implications  

Microsoft Academic Search

This paper reports the first comprehensive analysis of Displacement loop (D-loop) region sequences from ten different mammalian orders. It represents a systematic evolutionary study at the molecular level on regulatory homologous regions in organisms belonging to a well defined class, mammalia, which radiated about 150 million years ago (Mya). We have aligned and analyzed 26 complete D-loop region sequences available

Elisabetta Sbisà; Filomena Tanzariello; Aurelio Reyes; Graziano Pesole; Cecilia Saccone

1997-01-01

243

War and Biodiversity Conservation: The Role of Warfare Ecology  

Microsoft Academic Search

\\u000a The environmental impacts of war are widely recognized but poorly understood, leading to calls for a dedicated subfield known\\u000a as warfare ecology. Recent research establishes the relevance of warfare ecology to biodiversity conservation. Studies show\\u000a that war is exceedingly prevalent in the world’s most biodiverse regions and that both overt and secondary impacts of conflict\\u000a can be well documented. Additionally,

Thor Hanson

244

Beyond biology: understanding regional, multi-species habitat conservation plans from an ecological, economic, and sociopolitical perspective  

E-print Network

Conservation Plan BCCP: Status ? ITP issued 5/96; Location? Travis Co. , TX; Duration ? 30 yrs. ; Size ? 561, 000 acres with a 30, 000 acre reserve; Species covered ? golden cheeked warbler (Dendroica chrysoparia), black-capped Vireo (Vireo arricapillus), 6... gnatcatcher (Polioptila californica californi ca), peregrine falcon (Falco pereg ri nus), Riverside fairy shrimp (Strptocephalus woottoni), southwestern arroyo toad (Bufo mi croscaphus californicus), least Bell's vireo (Vireo belfli pusillus), southwestern...

Schmidt, Jennifer

2013-02-22

245

Global Conservation Priorities for Marine Turtles  

PubMed Central

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 widespread, long-lived taxa. PMID:21969858

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

246

Global conservation priorities for marine turtles.  

PubMed

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 widespread, long-lived taxa. PMID:21969858

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

247

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

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.

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. (Baylor College of Medicine, Houston, TX (USA))

1989-07-01

248

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 ...

249

Systematic conservation planning  

Microsoft Academic Search

The realization of conservation goals requires strategies for managing whole landscapes including areas allocated to both production and protection. Reserves alone are not adequate for nature conservation but they are the cornerstone on which regional strategies are built. Reserves have two main roles. They should sample or represent the biodiversity of each region and they should separate this biodiversity from

C. R. Margules; R. L. Pressey

2000-01-01

250

Energy Conservation Simplified  

ERIC Educational Resources Information Center

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…

Hecht, Eugene

2008-01-01

251

Human antibodies to the conserved region of the M protein: opsonization of heterologous strains of group A streptococci  

Microsoft Academic Search

A 20-mer peptide (p145) in the carboxyl-terminal region of the M protein of group A streptococci (GAS) has previously been defined as the target of bactericidal antibodies. Sequence analysis of seven field isolates from indigenous Australians living in an area highly endemic for GAS and five laboratory reference strains (encompassing nine unique serotypes plus three nontypeables) demonstrates that this region

Evelyn R. Brandt; Wendy A. Hayman; Bart Currie; Sumalee Pruksakorn; Michael F. Good

1997-01-01

252

The Sequence Organization of Yp\\/Proximal Xq Homologous Regions of the Human Sex Chromosomes Is Highly Conserved  

Microsoft Academic Search

Detailed deletion analysis of patients with breakpoints in Yp has allowed the definition of two distinct intervals on the Y chromosome short arm outside the pseudoautosomal region that are homologous to Xq21.3. Detailed YAC contigs have been developed over these regions on both the X and Y chromosomes, and the relative order of markers has been compared to assess whether

Carole A. Sargent; Hayley Briggs; Isabel J. Chalmers; Bronwen Lambson; Elizabeth Walker; Nabeel A. Affara

1996-01-01

253

Sequence Conservation of the Region Targeted by the Abbott RealTime HBV Viral Load Assay in Clinical Specimens  

PubMed Central

The Abbott RealTime HBV assay targets the N-terminal region of the S gene. Here we analyzed the sequence variability of the assay target region from >2,100 clinical specimens. Thermodynamic modeling of the percentage of bound primer/probe at the assay annealing temperature was performed to assess the potential effect of sequence variability. PMID:23345287

Rhoads, James; Young, Thomas P.; Parkin, Neil T.; Holzmayer, Vera; Yuen, Lilly; Mullen, Carolyn

2013-01-01

254

Sequence conservation of the region targeted by the Abbott RealTime HBV viral load assay in clinical specimens.  

PubMed

The Abbott RealTime HBV assay targets the N-terminal region of the S gene. Here we analyzed the sequence variability of the assay target region from >2,100 clinical specimens. Thermodynamic modeling of the percentage of bound primer/probe at the assay annealing temperature was performed to assess the potential effect of sequence variability. PMID:23345287

Cloherty, Gavin A; Rhoads, James; Young, Thomas P; Parkin, Neil T; Holzmayer, Vera; Yuen, Lilly; Mullen, Carolyn

2013-04-01

255

Animal conservation, carbon and sustainability  

Microsoft Academic Search

International conventions to reduce carbon dioxide levels focus on ecosystems and do not specifically recognize the need to conserve species. However, species are the build- ing blocks of ecosystems, they are more widely understood among the public, and they provide means of capturing market values from ecosystems. Achieving successful conservation globally will require ensuring that the systems under which species

N. Leader-Williams

2002-01-01

256

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

USGS Publications Warehouse

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.

Castelblanco-Martínez, D.N.; Padilla-Saldivar, J.; Hernández-Arana, H.A.; Slone, D.H.; Reid, J.P.; Morales-Vela, B.

2013-01-01

257

Building an optical pattern recognizer  

NASA Astrophysics Data System (ADS)

The present portable solid-optics correlator for real-time pattern recognition uses pixelated spatial light modulators and phase-only filters, and will operate on sensor information extracted from any sensor system. Prospective operations of such a rugged and portable optical pattern recognizer include smart weapon midcourse guidance and navigation, target recognition, aim-point selection, and precise terminal homing. An account is given of the testing procedure being used by the U.S. Army missile command for a missile-guidance appligation of this optical correlator.

Lindberg, Perry C.; Gregory, Don A.

1991-08-01

258

Position and sequence conservation in Amniota of polymorphic enhancer HS1.2 within the palindrome of IgH 3'Regulatory Region  

PubMed Central

Background The Immunoglobulin heavy chain (IgH) 3' Regulatory Region (3'RR), located at the 3' of the constant alpha gene, plays a crucial role in immunoglobulin production. In humans, there are 2 copies of the 3'RR, each composed of 4 main elements: 3 enhancers and a 20 bp tandem repeat. The single mouse 3'RR differs from the two human ones for the presence of 4 more regulative elements with the double copy of one enhancer at the border of a palindromic region. Results We compared the 3'RR organization in genomes of vertebrates to depict the evolutionary history of the region and highlight its shared features. We found that in the 8 species in which the whole region was included in a fully assembled contig (mouse, rat, dog, rabbit, panda, orangutan, chimpanzee, and human), the shared elements showed synteny and a highly conserved sequence, thus suggesting a strong evolutionary constraint. In these species, the wide 3'RR (~30 kb in human) bears a large palindromic sequence, consisting in two ~3 kb complementary branches spaced by a ~3 kb sequence always including the HS1.2 enhancer. In mouse and rat, HS3 is involved by the palindrome so that one copy of the enhancer is present on each side. A second relevant feature of our present work concerns human polymorphism of the HS1.2 enhancer, associated to immune diseases in our species. We detected a similar polymorphism in all the studied Catarrhini (a primate parvorder). The polymorphism consists of multiple copies of a 40 bp element up to 12 in chimpanzees, 8 in baboons, 6 in macaque, 5 in gibbons, 4 in humans and orangutan, separated by stretches of Cytosine. We show specific binding of this element to nuclear factors. Conclusions The nucleotide sequence of the palindrome is not conserved among evolutionary distant species, suggesting pressures for the maintenance of two self-matching regions driving a three-dimensional structure despite of the inter-specific divergence at sequence level. The information about the conservation of the palindromic structure and the settling in primates of the polymorphic feature of HS1.2 show the relevance of these structures in the control and modulation of the Ig production through the formation of possible three-dimensional structures. PMID:21406099

2011-01-01

259

Mapping of the gene for the tyrosine kinase Itk to a region of conserved synteny between mouse chromosome 11 and human chromosome 5q  

SciTech Connect

The protein-tyrosine kinase gene Itk is expressed preferentially in T lymphoid cells of the mouse and is induced by IL-2. A related gene, Btk, is expressed in the murine B lymphoid and myeloid lineages. Because mutations in Btk and the corresponding human gene are associated with X-linked immunodeficiency syndromes, it was of interest to map Itk and its human counterpart. By Southern blot analysis of DNA from the progeny of two multilocus crosses, murine Itk was mapped to chromosome 11. By fluorescence in situ hybridization, human ITK was mapped to 5q32-q33. Murine Itk and its human homologue lie within regions of conserved synteny that includes several growth factor and growth factor receptor genes. This region in humans is frequently deleted in the myelodysplastic syndrome, suggesting possible involvement of ITK in this disorder. 20 refs., 2 figs.

Janis, E.M.; Siliciano, J.D.; Isaac, D.D.

1994-09-01

260

An operator associated with autoregulation of the repressor gene in actinophage phiC31 is found in highly conserved copies in intergenic regions in the phage genome.  

PubMed Central

Previous reports have suggested that the repressor gene, c, of phiC31 is autoregulated and that likely operators are conserved inverted repeat sequences (CIRs1&2) located just upstream of the promoters, cp1 and cp2. Evidence is now presented that the CIRs 1&2 are indeed binding sites for one of the three inframe, N-terminally different protein isoforms of 42, 54 and 74 kDa produced by the c gene. A cp1-aphII fusion was repressed in a Streptomyces coelicolor A3(2) phiC31 lysogen and characterisation of an operator-constitutive (Oc) mutant showed a single mutation in CIR-1. CIR-1 containing fragments were retarded in electrophoresis gels by the 42 kDa repressor protein isoform and this retardation was inhibited by the addition of competing DNA fragments containing either CIR-1 or CIR-2. Using a combination of Southern blotting and analysis of available DNA sequence we also show that at least 18 copies of the CIRs are present throughout the phiC31 genome. Alignment of 9 CIR sequences showed that 8 contained a perfectly conserved 17 bp core whilst the exception had a single mismatch. The core includes a 16 bp inverted repeat (IR), and is usually part of a more extensive and less highly conserved palindrome. When superimposed on a previously derived transcription map of the early region, the CIRs lie in intergenic regions associated with transcription initiation and/or termination. Images PMID:8139924

Ingham, C J; Owen, C E; Wilson, S E; Hunter, I S; Smith, M C

1994-01-01

261

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

PubMed Central

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

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

2014-01-01

262

Conservation Strategy for Sable Island  

E-print Network

Towards a Conservation Strategy for Sable Island Environment Canada, Canadian Wildlife Service, Atlantic Region #12;SABLE ISLAND CONSERVATION STRATEGY page - i March, 1998 A CONSERVATION STRATEGY FOR SABLE ISLAND PREPARED BY This Conservation Strategy for Sable Island was prepared for Environment Canada

Jones, Ian L.

263

Conservation physiology  

Microsoft Academic Search

Conservation biologists increasingly face the need to provide legislators, courts and conservation managers with data on causal mechanisms underlying conservation problems such as species decline. To develop and monitor solutions, conservation biologists are progressively using more techniques that are physiological. Here, we review the emerging discipline of conservation physiology and suggest that, for conservation strategies to be successful, it is

Martin Wikelski; Steven J. Cooke

2006-01-01

264

Conservation tillage issues: cover crop-based organic rotational no-till grain production in the mid-atlantic region  

Technology Transfer Automated Retrieval System (TEKTRAN)

Organic producers in the mid-Atlantic region are interested in reducing tillage, labor, and time requirements for grain production. Cover crop-based organic rotational no-till grain production is one approach to accomplishing these goals. Advancements in a system for planting crops into a mat of cov...

265

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

PubMed

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

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

2014-07-01

266

Pub1p C-Terminal RRM Domain Interacts with Tif4631p through a Conserved Region Neighbouring the Pab1p Binding Site  

PubMed Central

Pub1p, a highly abundant poly(A)+ mRNA binding protein in Saccharomyces cerevisiae, influences the stability and translational control of many cellular transcripts, particularly under some types of environmental stresses. We have studied the structure, RNA and protein recognition modes of different Pub1p constructs by NMR spectroscopy. The structure of the C-terminal RRM domain (RRM3) shows a non-canonical N-terminal helix that packs against the canonical RRM fold in an original fashion. This structural trait is conserved in Pub1p metazoan homologues, the TIA-1 family, defining a new class of RRM-type domains that we propose to name TRRM (TIA-1 C-terminal domain-like RRM). Pub1p TRRM and the N-terminal RRM1-RRM2 tandem bind RNA with high selectivity for U-rich sequences, with TRRM showing additional preference for UA-rich ones. RNA-mediated chemical shift changes map to ?-sheet and protein loops in the three RRMs. Additionally, NMR titration and biochemical in vitro cross-linking experiments determined that Pub1p TRRM interacts specifically with the N-terminal region (1–402) of yeast eIF4G1 (Tif4631p), very likely through the conserved Box1, a short sequence motif neighbouring the Pab1p binding site in Tif4631p. The interaction involves conserved residues of Pub1p TRRM, which define a protein interface that mirrors the Pab1p-Tif4631p binding mode. Neither protein nor RNA recognition involves the novel N-terminal helix, whose functional role remains unclear. By integrating these new results with the current knowledge about Pub1p, we proposed different mechanisms of Pub1p recruitment to the mRNPs and Pub1p-mediated mRNA stabilization in which the Pub1p/Tif4631p interaction would play an important role. PMID:21931728

Rico-Lastres, Palma; Pérez-Cañadillas, José Manuel

2011-01-01

267

Sequence conservation in the rRNA first internal transcribed spacer region of Babesia gibsoni genotype Asia isolates.  

PubMed

Babesia gibsoni genotype Asia is a small, tick-transmitted intraerythrocytic protozoan that parasitizes dogs. Reports suggest that it is increasingly diagnosed in the United States. The clinical outcome of infection with this piroplasm is often variable, leading us to hypothesize that the different clinical outcomes resulting from B. gibsoni genotype Asia infection are due to genetically distinguishable strains that differ in virulence. As a first step to assess the genetic variability of B. gibsoni isolates originating from the southeastern United States, we sequenced the rRNA first internal transcribed spacer region of recent isolates from Georgia and Alabama, and compared these sequences with isolates originating from Japan and Australia. All isolates examined proved to be genetically identical at the first internal transcribed spacer region, although this region differed distinctly from other Babesia species and closely related apicomplexan species. Although negating our hypothesis, this information gives us insight into the recent evolutionary history and spread of B. gibsoni genotype Asia in dogs in the U.S. Our research suggests that the gradual rise in prevalence of canine babesiosis due to B. gibsoni genotype Asia in the United States may be a result of clonal expansion of a single strain within a susceptible host population. PMID:18207327

Bostrom, B; Wolf, C; Greene, C; Peterson, D S

2008-03-25

268

Conserved cis-regulatory regions in a large genomic landscape control SHH and BMP-regulated Gremlin1 expression in mouse limb buds  

PubMed Central

Background Mouse limb bud is a prime model to study the regulatory interactions that control vertebrate organogenesis. Major aspects of limb bud development are controlled by feedback loops that define a self-regulatory signalling system. The SHH/GREM1/AER-FGF feedback loop forms the core of this signalling system that operates between the posterior mesenchymal organiser and the ectodermal signalling centre. The BMP antagonist Gremlin1 (GREM1) is a critical node in this system, whose dynamic expression is controlled by BMP, SHH, and FGF signalling and key to normal progression of limb bud development. Previous analysis identified a distant cis-regulatory landscape within the neighbouring Formin1 (Fmn1) locus that is required for Grem1 expression, reminiscent of the genomic landscapes controlling HoxD and Shh expression in limb buds. Results Three highly conserved regions (HMCO1-3) were identified within the previously defined critical genomic region and tested for their ability to regulate Grem1 expression in mouse limb buds. Using a combination of BAC and conventional transgenic approaches, a 9?kb region located ~70?kb downstream of the Grem1 transcription unit was identified. This region, termed Grem1 Regulatory Sequence 1 (GRS1), is able to recapitulate major aspects of Grem1 expression, as it drives expression of a LacZ reporter into the posterior and, to a lesser extent, in the distal-anterior mesenchyme. Crossing the GRS1 transgene into embryos with alterations in the SHH and BMP pathways established that GRS1 depends on SHH and is modulated by BMP signalling, i.e. integrates inputs from these pathways. Chromatin immunoprecipitation revealed interaction of endogenous GLI3 proteins with the core cis-regulatory elements in the GRS1 region. As GLI3 is a mediator of SHH signal transduction, these results indicated that SHH directly controls Grem1 expression through the GRS1 region. Finally, all cis-regulatory regions within the Grem1 genomic landscape locate to the DNAse I hypersensitive sites identified in this genomic region by the ENCODE consortium. Conclusions This study establishes that distant cis-regulatory regions scattered through a larger genomic landscape control the highly dynamic expression of Grem1, which is key to normal progression of mouse limb bud development. PMID:22888807

2012-01-01

269

The TAF9 C-Terminal Conserved Region Domain Is Required for SAGA and TFIID Promoter Occupancy To Promote Transcriptional Activation  

PubMed Central

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 (spt20?) 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. PMID:24550006

Saint, Malika; Sawhney, Sonal; Sinha, Ishani; Singh, Rana Pratap; Dahiya, Rashmi; Thakur, Anushikha; Siddharthan, Rahul

2014-01-01

270

Understanding the distribution of marine megafauna in the English channel region: identifying key habitats for conservation within the busiest seaway on earth.  

PubMed

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

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

271

A conserved proline residue in the leucine zipper region of AtbZIP34 and AtbZIP61 in Arabidopsis thaliana interferes with the formation of homodimer  

SciTech Connect

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.

Shen Huaishun [College of Life Sciences, Beijing Normal University, Beijing 100875 (China); State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433 (China); Cao Kaiming [State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433 (China); Wang Xiping [College of Life Sciences, Beijing Normal University, Beijing 100875 (China); State Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200433 (China)], E-mail: xipingwang@hotmail.com

2007-10-19

272

Understanding the Distribution of Marine Megafauna in the English Channel Region: Identifying Key Habitats for Conservation within the Busiest Seaway on Earth  

PubMed Central

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

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

273

The isolation of conserved DNA sequences related to the human sex-determining region Y gene from the lesser black-backed gull (Larus fuscus).  

PubMed

The sex-determining region gene (SRY) is a recently discovered candidate for the mammalian testis determining factor (TDF). The gene appears to form part of a family with several autosomal representatives. I have investigated the occurrence of SRY-related sequences in birds. The polymerase chain reaction was used to isolate six homologues of the conserved motif of the SRY gene from the lesser black-backed gull (Larus fuscus). Female unique copies of the motif are apparently absent. Sequence similarity and phylogenetic parsimony methods suggest that, irrespective of avian or mammalian origin, SRY-type sequences fall into two subfamilies. This is consistent with the presence of two archetypal genes in an ancestor common to both taxonomic classes. PMID:1679546

Griffiths, R

1991-05-22

274

ROCC, a conserved region in cohesin's Mcd1 subunit, is essential for the proper regulation of the maintenance of cohesion and establishment of condensation  

PubMed Central

Cohesin helps orchestrate higher-order chromosome structure, thereby promoting sister chromatid cohesion, chromosome condensation, DNA repair, and transcriptional regulation. To elucidate how cohesin facilitates these diverse processes, we mutagenized Mcd1p, the kleisin regulatory subunit of budding yeast cohesin. In the linker region of Mcd1p, we identified a novel evolutionarily conserved 10–amino acid cluster, termed the regulation of cohesion and condensation (ROCC) box. We show that ROCC promotes cohesion maintenance by protecting a second activity of cohesin that is distinct from its stable binding to chromosomes. The existence of this second activity is incompatible with the simple embrace mechanism of cohesion. In addition, we show that the ROCC box is required for the establishment of condensation. We provide evidence that ROCC controls cohesion maintenance and condensation establishment through differential functional interactions with Pds5p and Wpl1p. PMID:24966169

Eng, Thomas; Guacci, Vincent; Koshland, Doug

2014-01-01

275

Promoters recognized by forkhead proteins exist for individual 21U-RNAs.  

PubMed

C. elegans 21U-RNAs are equivalent to the piRNAs discovered in other metazoans and have important roles in gametogenesis and transposon control. The biogenesis and molecular function of 21U-RNAs and piRNAs are poorly understood. Here, we demonstrate that transcription of each 21U-RNA is regulated separately through a conserved upstream DNA motif. We use genomic analysis to show that this motif is associated with low nucleosome occupancy, a characteristic of many promoters that drive expression of protein-coding genes, and that RNA polymerase II is localized to this nucleosome-depleted region. We establish that the most conserved 8-mer sequence in the upstream region of 21U-RNAs, CTGTTTCA, is absolutely required for their individual expression. Furthermore, we demonstrate that the 8-mer is specifically recognized by Forkhead family (FKH) transcription factors and that 21U-RNA expression is diminished in several FKH mutants. Our results suggest that thousands of small noncoding transcription units are regulated by FKH proteins. PMID:22819322

Cecere, Germano; Zheng, Grace X Y; Mansisidor, Andres R; Klymko, Katherine E; Grishok, Alla

2012-09-14

276

Promoters Recognized by Forkhead Proteins Exist for Individual 21U-RNAs  

PubMed Central

Summary C. elegans 21U-RNAs are equivalent to the piRNAs discovered in other metazoans and have important roles in gametogenesis and transposon control. The biogenesis and molecular function of 21U-RNAs and piRNAs are poorly understood. Here, we demonstrate that transcription of each 21U-RNA is regulated separately through a conserved upstream DNA motif. We use genomic analysis to show that this motif is associated with low nucleosome occupancy, a characteristic of many promoters that drive expression of protein-coding genes, and that RNA polymerase II is localized to this nucleosome-depleted region. We establish that the most conserved 8-mer sequence in the upstream region of 21U-RNAs, CTGTTTCA, is absolutely required for their individual expression. Furthermore, we demonstrate that the 8-mer is specifically recognized by Forkhead family (FKH) transcription factors and that 21U-RNA expression is diminished in several FKH mutants. Our results suggest that thousands of small non-coding transcription units are regulated by FKH proteins. PMID:22819322

Cecere, Germano; Zheng, Grace X.Y.; Mansisidor, Andres R.; Klymko, Katherine E.; Grishok, Alla

2012-01-01

277

Adenovirus Delivered Short Hairpin RNA Targeting a Conserved Site in the 5? Non-Translated Region Inhibits All Four Serotypes of Dengue Viruses  

PubMed Central

Background Dengue is a mosquito-borne viral disease caused by four closely related serotypes of Dengue viruses (DENVs). This disease whose symptoms range from mild fever to potentially fatal haemorrhagic fever and hypovolemic shock, threatens nearly half the global population. There is neither a preventive vaccine nor an effective antiviral therapy against dengue disease. The difference between severe and mild disease appears to be dependent on the viral load. Early diagnosis may enable timely therapeutic intervention to blunt disease severity by reducing the viral load. Harnessing the therapeutic potential of RNA interference (RNAi) to attenuate DENV replication may offer one approach to dengue therapy. Methodology/Principal Findings We screened the non-translated regions (NTRs) of the RNA genomes of representative members of the four DENV serotypes for putative siRNA targets mapping to known transcription/translation regulatory elements. We identified a target site in the 5? NTR that maps to the 5? upstream AUG region, a highly conserved cis-acting element essential for viral replication. We used a replication-defective human adenovirus type 5 (AdV5) vector to deliver a short-hairpin RNA (shRNA) targeting this site into cells. We show that this shRNA matures to the cognate siRNA and is able to inhibit effectively antigen secretion, viral RNA replication and infectious virus production by all four DENV serotypes. Conclusion/Significance The data demonstrate the feasibility of using AdV5-mediated delivery of shRNAs targeting conserved sites in the viral genome to achieve inhibition of all four DENV serotypes. This paves the way towards exploration of RNAi as a possible therapeutic strategy to curtail DENV infection. PMID:22848770

Korrapati, Anil Babu; Swaminathan, Gokul; Singh, Aarti; Khanna, Navin; Swaminathan, Sathyamangalam

2012-01-01

278

A comparison among root soil-conservation effects for nine herbs at the cold region highway in north-eastern China  

NASA Astrophysics Data System (ADS)

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.

Xu, W.; Wang, X.; Zhang, Y.; Liu, Y.

2014-12-01

279

Biodiversity funds and conservation needs in the EU under climate change  

PubMed Central

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

Lung, Tobias; Meller, Laura; van Teeffelen, Astrid J.A.; Thuiller, Wilfried; Cabeza, Mar

2014-01-01

280

Recognizing child maltreatment in Bangladesh.  

PubMed

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. PMID:9280385

Khan, N Z; Lynch, M A

1997-08-01

281

A Conservation Practices for Conserving  

E-print Network

A Conservation Catalog Practices for Conserving Pennsylvania's Natural Resources #12;#12;A Conservation Catalog 1 Introduction P ennsylvania is a land of great natural resources and Pennsylvania. The Pennsylvania Conservation Catalog is a cooperative effort of the Pennsylvania Conservation Partnership which

Kaye, Jason P.

282

Delta-associated molluscan life and death assemblages in the northern Adriatic Sea: Implications for paleoecology, regional diversity and conservation  

PubMed Central

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. More samples would be necessary to account for the diversity of living molluscs in the study area, which is, however, well recorded in the death assemblages. There is no indication of a major environmental change over the last decades in this area, but due to the long history of anthropogenic pressure here, such a potential impact might be preserved in historical layers of the deeper sedimentary record. PMID:23407873

Weber, Kristina; Zuschin, Martin

2013-01-01

283

Arabic word recognizer for mobile applications  

NASA Astrophysics Data System (ADS)

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.

Khanna, Nitin; Abdollahian, Golnaz; Brame, Ben; Boutin, Mireille; Delp, Edward J.

2011-03-01

284

A model assessing the conservation threats to freshwater turtles of Sub-Saharan Africa predicts urgent need for continental conservation planning  

Microsoft Academic Search

Global assessment of conservation threats to several taxonomic groups are urgently needed for species living in regions of\\u000a the world where field research is curtailed by logistic or economic constraints. For instance, it is now widely recognized\\u000a that freshwater turtles represent one of the most endangered groups of vertebrates in the world. This situation has been particularly\\u000a evident with Asian

Luca Luiselli

2009-01-01

285

The phylogeographical pattern and conservation of the Chinese cobra (Naja atra) across its range based on mitochondrial control region sequences.  

PubMed

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 (?st?=?0.76, P<0.0001) with high haplotype diversity (h?=?1.00) and low nucleotide diversity (??=?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

Lin, Long-Hui; Hua, Lei; Qu, Yan-Fu; Gao, Jian-Fang; Ji, Xiang

2014-01-01

286

Highly conserved HIV-1 gp120 glycans proximal to CD4-binding region affect viral infectivity and neutralizing antibody induction.  

PubMed

Glycosylation plays important roles in gp120 structure and HIV-1 immune evasion. In the current study, we introduced deglycosylations into the 24 N-linked glycosylation sites of a R5 env MWS2 cloned from semen and systematically analyzed the impact on infectivity, antigenicity, immunogenicity and sensitivity to entry inhibitors. We found that mutants N156-T158A, N197-S199A, N262-S264A and N410-T412A conferred decreased infectivity and enhanced sensitivity to a series of antibodies and entry inhibitors. When mice were immunized with the DNA of wild-type or mutated gp160, gp140 or gp120; N156-T158A, N262-S264A and N410-T412A were more effective in inducing neutralizing activity against wild-type MWS2 as well as heterologous IIIB and CH811 Envs. In general, gp160 and gp140 induced higher neutralizing activity compared with gp120. Our study demonstrates for the first time that removal of individual glycan N156, N262 or N410 proximal to CD4-binding region impairs viral infectivity and results in enhanced capability to induce neutralizing activity. PMID:22192629

Huang, Xin; Jin, Wei; Hu, Kai; Luo, Sukun; Du, Tao; Griffin, George E; Shattock, Robin J; Hu, Qinxue

2012-02-01

287

The Phylogeographical Pattern and Conservation of the Chinese Cobra (Naja atra) across Its Range Based on Mitochondrial Control Region Sequences  

PubMed Central

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 (?st?=?0.76, P<0.0001) with high haplotype diversity (h?=?1.00) and low nucleotide diversity (??=?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

Lin, Long-Hui; Hua, Lei; Qu, Yan-Fu; Gao, Jian-Fang; Ji, Xiang

2014-01-01

288

A conserved phenylalanine as a relay between the ?5 helix and the GDP binding region of heterotrimeric Gi protein ? subunit.  

PubMed

G protein activation by G protein-coupled receptors is one of the critical steps for many cellular signal transduction pathways. Previously, we and other groups reported that the ?5 helix in the G protein ? subunit plays a major role during this activation process. However, the precise signaling pathway between the ?5 helix and the guanosine diphosphate (GDP) binding pocket remains elusive. Here, using structural, biochemical, and computational techniques, we probed different residues around the ?5 helix for their role in signaling. Our data showed that perturbing the Phe-336 residue disturbs hydrophobic interactions with the ?2-?3 strands and ?1 helix, leading to high basal nucleotide exchange. However, mutations in ? strands ?5 and ?6 do not perturb G protein activation. We have highlighted critical residues that leverage Phe-336 as a relay. Conformational changes are transmitted starting from Phe-336 via ?2-?3/?1 to Switch I and the phosphate binding loop, decreasing the stability of the GDP binding pocket and triggering nucleotide release. When the ?1 and ?5 helices were cross-linked, inhibiting the receptor-mediated displacement of the C-terminal ?5 helix, mutation of Phe-336 still leads to high basal exchange rates. This suggests that unlike receptor-mediated activation, helix 5 rotation and translocation are not necessary for GDP release from the ? subunit. Rather, destabilization of the backdoor region of the G? subunit is sufficient for triggering the activation process. PMID:25037222

Kaya, Ali I; Lokits, Alyssa D; Gilbert, James A; Iverson, Tina M; Meiler, Jens; Hamm, Heidi E

2014-08-29

289

Prioritizing global conservation efforts.  

PubMed

One of the most pressing issues facing the global conservation community is how to distribute limited resources between regions identified as priorities for biodiversity conservation. Approaches such as biodiversity hotspots, endemic bird areas and ecoregions are used by international organizations to prioritize conservation efforts globally. Although identifying priority regions is an important first step in solving this problem, it does not indicate how limited resources should be allocated between regions. Here we formulate how to allocate optimally conservation resources between regions identified as priorities for conservation--the 'conservation resource allocation problem'. Stochastic dynamic programming is used to find the optimal schedule of resource allocation for small problems but is intractable for large problems owing to the "curse of dimensionality". We identify two easy-to-use and easy-to-interpret heuristics that closely approximate the optimal solution. We also show the importance of both correctly formulating the problem and using information on how investment returns change through time. Our conservation resource allocation approach can be applied at any spatial scale. We demonstrate the approach with an example of optimal resource allocation among five priority regions in Wallacea and Sundaland, the transition zone between Asia and Australasia. PMID:16541073

Wilson, Kerrie A; McBride, Marissa F; Bode, Michael; Possingham, Hugh P

2006-03-16

290

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...

291

Site-directed mutations in a highly conserved region of Bacillus thuringiensis delta-endotoxin affect inhibition of short circuit current across Bombyx mori midguts.  

PubMed Central

Bacillus thuringiensis delta-endotoxins (Cry toxins) are insecticidal proteins of approximately 65 kDa in the proteolytically processed and active form. The structure of one of these toxins, CryIIIA, has been determined by Li et al. [Li, J., Carroll, J. & Ellar, D. J. (1991) Nature (London) 353, 815-821] and contains three domains. It is believed that other delta-endotoxins adopt similar three-dimensional structure. Li et al. proposed that the first domain is the membrane pore-forming domain. Previous work from our laboratory has shown that the second domain is the receptor binding domain, but the function of the third domain is unclear. Site-directed mutagenesis was used to convert the "arginine face" of one of five highly conserved regions, QRYRVRIRYAS of CryIAa (residues 525-535), to selected other residues. This sequence corresponds to the beta-sheet 17 of CryIIIA in the third domain. Mutations in the second and third arginine positions resulted in structural alterations in the protein and were poorly expressed in Escherichia coli. Toxins from genes mutated to replace lysine for the first and fourth arginines were unaltered in expression and structure, as measured by trypsin activation, CD spectra, and receptor binding, but were substantially reduced in their insecticidal properties and inhibition of short circuit current across Bombyx mori midguts. It is proposed that this region plays a role in toxin function as an ion channel. PMID:8415651

Chen, X J; Lee, M K; Dean, D H

1993-01-01

292

The Structure of the Hantavirus Zinc Finger Domain is Conserved and Represents the Only Natively Folded Region of the Gn Cytoplasmic Tail  

PubMed Central

Hantaviruses, of the family Bunyaviridae, are present throughout the world and cause a variety of infections ranging from the asymptomatic to mild and severe hemorrhagic fevers. Hantaviruses are enveloped anti-sense RNA viruses that contain three genomic segments that encode for a nucleocapsid protein, two membrane glycoproteins (Gn and Gc), and an RNA polymerase. Recently, the pathogenicity of hantaviruses has been mapped to the carboxyl end of the 150 residue Gn cytoplasmic tail. The Gn tail has also been shown to play a role in binding the ribonucleoprotein (RNP), a step critical for virus assembly. In this study, we use NMR spectroscopy to compare the structure of a Gn tail zinc finger domain of both a pathogenic (Andes) and a non-pathogenic (Prospect Hill) hantavirus. We demonstrate that despite a stark difference in the virulence of both of these viruses, the structure of the Gn core zinc finger domain is largely conserved in both strains. We also use NMR backbone relaxation studies to demonstrate that the regions of the Andes virus Gn tail immediately outside the zinc finger domain, sites known to bind the RNP, are disordered and flexible, thus intimating that the zinc finger domain is the only structured region of the Gn tail. These structural observations provide further insight into the role of the Gn tail during viral assembly as well as its role in pathogenesis. PMID:22203819

Estrada, D. Fernando; Conner, Michael; Jeor, Stephen C.; Guzman, Roberto N. De

2011-01-01

293

A light-regulated DNA-binding activity interacts with a conserved region of a Lemna gibba rbcS promoter.  

PubMed Central

We have characterized a DNA-binding activity, designated light-regulated nuclear factor (LRF-1), which interacted with a specific sequence located 150 nucleotides upstream from the transcription start site of a phytochrome-regulated Lemna gibba rbcS gene (SSU5B). There was a higher level of LRF-1 activity recovered from nuclei of light-grown plants than from dark-treated plants. In light-grown plants given a 1-day dark treatment, either white light or a single 2-min red illumination caused a rapid twofold to threefold increase in this activity, suggesting that the phytochrome system is probably involved in its regulation. The nuclear extracts also contained an activity that bound specifically to Box II sequences from a pea rbcS gene [Green, P.J., Yong, M.H., Cuozzo, M., Kano-Murakami, Y., Silverstein, P., and Chua, N.-H. (1988). EMBO J. 7, 4035-4044], but this activity was not higher in the light-grown compared with the dark-treated plants. Comparison of about 700 base pairs upstream from the SSU5B transcription start site with the upstream sequences of two other Lemna rbcS genes revealed several conserved regions. One of these regions is found upstream of rbcS genes in other species and is contained in the sequence which was shown to interact with LRF-1. PMID:2152129

Buzby, J S; Yamada, T; Tobin, E M

1990-01-01

294

A Conserved Virulence Plasmidic Region Contributes to the Virulence of the Multiresistant Escherichia coli Meningitis Strain S286 Belonging to Phylogenetic Group C  

PubMed Central

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

Caro, Valérie; Diancourt, Laure; Bingen, Edouard; Bidet, Philippe; Bonacorsi, Stéphane

2013-01-01

295

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

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 HNF1? expression was downregulated with small interfering RNA. Following HNF1? overexpression in Huh7 cells, the intron 1 ECR increased SV40 promoter activity by 11-fold and OCT1 promoter activity by 6-fold. Without HNF1? 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

O’Brien, Valerie P.; Bokelmann, Kristin; Ramírez, Jacqueline; Jobst, Karoline; Ratain, Mark J.; Brockmöller, Jürgen

2013-01-01

296

Evidence on How a Conserved Glycine in the Hinge Region of HapR Regulates Its DNA Binding Ability: LESSONS FROM A NATURAL VARIANT.  

SciTech Connect

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.

M Dongre; N Singh; C Dureja; N Peddada; A Solanki; F Ashish; S Raychaudhuri

2011-12-31

297

A performance comparison of two handwriting recognizers  

Microsoft Academic Search

An experiment is described comparing two commercial handwriting recognizers with discrete hand-printed characters. Each recognizer was tested at two levels of constraint, one using lowercase letters (which were the only symbols included in the input text) and the other using both uppercase and lowercase letters. Two factors—recognizer and constraint—with two levels each, resulted in four test conditions. A total of

I. Scott Mackenzie; Larry Chang

1999-01-01

298

Conserving Energy  

NSDL National Science Digital Library

In this project you will learn what energy is, how energy is used , and how to conserve it What are new ways of protecting the environment to conserve energy? Use your 4- column chart to record information about the questions i ask and you learn about. Begin by seeing what energy isEnergy Quest Tells different ways of conserving energy. List what you learn. What are simple ways to conserve energy everyday? How are vehicle manufactures inventing ways to conserve ...

Mr. Y

2009-10-21

299

Invariant NKT cells recognize glycolipids from pathogenic Gram-positive bacteria  

PubMed Central

Natural killer T (NKT) cells recognize glycolipid antigens presented by CD1d. These cells express an evolutionarily conserved, invariant T cell receptor (TCR), but the forces driving TCR conservation have remained uncertain. Here we show that NKT cells recognize diacylglycerol-containing glycolipids from Streptococcus pneumoniae, the leading cause of community-acquired pneumonia, and group B Streptococcus, which causes neonatal sepsis and meningitis. Furthermore, CD1d-dependent responses by NKT cells are required for activation and host protection. The glycolipid response was dependent on vaccenic acid, which is found at a low level in mammalian cells. Our results show how microbial lipids position the sugar for recognition by the invariant TCR, and most important, they extend the range of microbes recognized by this conserved TCR to several clinically important bacteria. PMID:21892173

Kinjo, Yuki; Illarionov, Petr; Vela, José Luis; Pei, Bo; Girardi, Enrico; Li, Xiangming; Li, Yali; Imamura, Masakazu; Kaneko, Yukihiro; Okawara, Akiko; Miyazaki, Yoshitsugu; Gómez-Velasco, Anaximandro; Rogers, Paul; Dahesh, Samira; Uchiyama, Satoshi; Khurana, Archana; Kawahara, Kazuyoshi; Yesilkaya, Hasan; Andrew, Peter W.; Wong, Chi-Huey; Kawakami, Kazuyoshi; Nizet, Victor; Besra, Gurdyal S.; Tsuji, Moriya; Zajonc, Dirk M.; Kronenberg, Mitchell

2011-01-01

300

Shrubland Lepidoptera of southern New England and southeastern New York: ecology, conservation, and management  

Microsoft Academic Search

Sandplain and ridgetop pitch pine (Pinus rigida)–scrub oak (Quercus ilicifolia) barrens and other shrub-dominated natural communities (e.g., heathlands and maritime shrublands) are important habitats for rare Lepidoptera (moths and butterflies) in southern New England and southeastern New York. Fifty-six species of conservation concern representing 11 families of Lepidoptera are recognized as dependent on shrubland habitats in this region, including 23%

David L. Wagner; Michael W. Nelson; Dale F. Schweitzer

2003-01-01

301

Energy Conservation Simplified  

NASA Astrophysics Data System (ADS)

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 principle developed. The final conservation law, although rich in specificity, is fairly involved. More significantly, it obscures a fundamental underlying simplicity, which could only be appreciated post-relativity (1905). Energy is the scalar measure of physical change. Using the special theory it will be shown that there are only two all-encompassing classifications of energy—energy of rest and energy of motion—and that we can apply the idea of conservation of energy to all physical processes using only these two energy types as quantified by mass and KE.

Hecht, Eugene

2008-02-01

302

Structure of the mitochondrial control region of the Eurasian otter (Lutra lutra; Carnivora, Mustelidae): patterns of genetic heterogeneity and implications for conservation of the species in Italy.  

PubMed

In this study we determined the complete sequence of the mitochondrial DNA (mtDNA) control region of the Eurasian otter (Lutra lutra). We then compared these new sequences with orthologues of nine carnivores belonging to six families (Mustelidae, Mephitidae, Canidae, Hyaenidae, Ursidae, and Felidae). The comparative analyses identified all the conserved regions previously found in mammals. The Eurasian otter and seven other species have a single location with tandem repeats in the right domain, while the spotted hyena (Hyaenidae) and the tiger (Felidae) have repeated sequences in both the right and left domains. To assess the degree of genetic heterogeneity of the Eurasian otter in Italy we sequenced two fragments of the gene and analyzed length polymorphisms of repeated sequences and heteroplasmy in 32 specimens. The study includes 23 museum specimens collected in northern, central, and southern Italy; most of these specimens are from extinct populations, while the southern Italian samples belong to the sole extant Italian population of the Eurasian otter. The study also includes all the captive-reared animals living in the colony "Centro Lontra, Caramanico Terme" (Pescara, central Italy). The colony is maintained for reintroduction of the species. We found a low level of genetic polymorphism; a single haplotype is dominant, but our data indicate the presence in central and southern Italy of two slightly divergent haplotypes. One haplotype belongs to an extinct population, the other is present in the single extant Italian population. Analyses of length polymorphisms and heteroplasmy indicate that the autochthonous Italian samples are characterized by a distinct array of repeated sequences from captive-reared animals. PMID:15731216

Ketmaier, V; Bernardini, C

2005-01-01

303

Synthetic peptides from conserved regions of the Plasmodium falciparum early transcribed membrane and ring exported proteins bind specifically to red blood cell proteins.  

PubMed

Severe malaria pathology is directly associated with cytoadherence of infected red blood cells (iRBCs) to healthy RBCs and/or endothelial cells occurring during the intraerythrocytic development of Plasmodium falciparum. We synthesized, as 20-mer long peptides, the members of the ring exported (REX) protein family encoded in chromosome 9, as well as the early transcribed membrane proteins (E-TRAMP) 10.2 and 4, to identify specific RBC binding regions in these proteins. Twelve binding peptides were identified (designated as HABPs): three were identified in REX1, two in REX2, one in REX3, two in REX4 and four in E-TRAMP 10.2. The majority of these HABPs was conserved among different P. falciparum strains, according to sequence analysis. No HABPs were found in E-TRAMP 4. Bindings of HABPs were saturable and sensitive to the enzymatic treatment of RBCs and HABPs had different structural features, according to circular dichroism studies. Our results suggest that the REX and E-TRAMP families participate in relevant interactions with RBC membrane proteins, which highlight these proteins as potential targets for the development of fully effective immunoprophylactic methods. PMID:19755146

Garcia, Jeison; Curtidor, Hernando; Obando-Martinez, Ana Z; Vizcaíno, Carolina; Pinto, Martha; Martinez, Nora L; Patarroyo, Manuel A; Patarroyo, Manuel E

2009-11-16

304

Use of an intron length polymorphism to localize the tropoelastin gene to mouse Chromosome 5 in a region of linkage conservation with human Chromosome 7  

SciTech Connect

The complete coding sequence for mouse tropoelastin was obtained from overlapping reverse transcriptase polymerase chain reaction (PCR) amplimers. These cDNA fragments were derived from mouse tropoelastin mRNA using PCR oligomers complementary to conserved domains within rat tropoelastin mRNA. A comparison of coding domains of mouse and rat tropoelastin mRNA revealed a greater than 93% homology at the nucleotide level and over 96% similarity in the predicted amino acid sequence. PCR primers complementary to regions of the mouse tropoelastin mRNA were used to define a novel intron length polymorphism (ILP) within intron 8 of the mouse tropoelastin gene (Eln). This ILP proved to be informative in an intraspecific backcross in which genomic DNA samples from 75 backcross mice were used to map the tropoelastin gene to a position in the distal half of mouse chromosome 5. The linkage and genetic distances between Eln and the closest molecular markers used in this study are centromere-D5Mit95, D5Mit96-6.7 cM-Gus, Eln-4.0 cM-Zp3-telomere.

Wydner, K.S.; Passmore, H.C. [Rutgers Univ., Piscataway, NJ (United States)] [Rutgers Univ., Piscataway, NJ (United States); Sechler, J.L.; Boyd, C.D. [UMDNJ-Robert Wood Johnson Medical School, New Brunswick, NJ (United States)] [UMDNJ-Robert Wood Johnson Medical School, New Brunswick, NJ (United States)

1994-09-01

305

Residues in three conserved regions of the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase are required for quaternary structure  

SciTech Connect

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.

Fitchen, J.H.; McIntosh, L. (Michigan State Univ., East Lansing (USA)); Knight, S.; Andersson, I.; Branden, C.I. (Uppsala Biomedical Center (Sweden))

1990-08-01

306

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

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. PMID:24375401

Crespin, Silvio J; García-Villalta, Jorge E

2014-10-01

307

Higher-Order Neural Networks Recognize Patterns  

NASA Technical Reports Server (NTRS)

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.

Reid, Max B.; Spirkovska, Lilly; Ochoa, Ellen

1996-01-01

308

Teaching Students to Recognize Irony  

ERIC Educational Resources Information Center

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.…

Milner, Joseph O.; Hawkins, Robin H.; Milner, Lucy M.

2014-01-01

309

Conserved regions of the Plasmodium falciparum rhoptry-associated protein 3 mediate specific host-pathogen interactions during invasion of red blood cells.  

PubMed

Invasion of red blood cells (RBCs) by the Plasmodium falciparum malaria merozoite is mediated by parasite surface molecules and proteins contained within apical organelles that are capable of recognizing receptors on the membrane of RBCs. The identification and characterization of these P. falciparum invasion-associated proteins is the first step for unveiling potential new drug and vaccine target molecules to eradicate this deadly disease. Among the exclusive set of malarial vaccine candidates, the members of the rhoptry-associated protein (RAP) family have been associated with the parasite's binding to and invasion of RBCs. Remarkably, the third member of this family (named RAP-3) has been recently detected on the surface of non-infected RBCs exposed to free merozoites, therefore suggesting the participation of this protein during RBC infection. In this study, the sequence of RAP-3 was finely mapped using synthetic peptides in order to identify which are the specific binding regions involved in RAP3-RBC interactions. Two high-activity binding peptides (HABPs) established high affinity interactions with RBC surface molecules of about 27-90 kDa, which were differentially affected by different enzymatic treatments. RAP-1 and RAP-2 HABPs inhibited binding of RAP-3 HABPs to different extents, thus suggesting the recognition of similar binding sites on RBC membrane, as well as ability of RAP-3 HABPs to inhibit P. falciparum infection in vitro. Altogether, these functional analyses of RAP-3 HABPs strongly suggest a potential role for this protein in RBC invasion, and highlight its HABPs as potential targets to develop a fully protective minimal subunit-based malarial vaccine. PMID:20833215

García, Jeison; Curtidor, Hernando; Vanegas, Magnolia; Arévalo-Pinzon, Gabriela; Patarroyo, Manuel A; Patarroyo, Manuel E

2010-12-01

310

Part I: International and Regional Management Arrangements Western Hemisphere Inter-American Convention (IAC) for the Protection and Conservation of Sea Turtles  

E-print Network

to the most endangered sea turtle species, such as Leatherbacks and Hawksbills, as well as calling-American Convention (IAC) for the Protection and Conservation of Sea Turtles Basic Instrument Inter-American Convention for the Protection and Conservation of Sea Turtles Member Nations Argentina, Belize, Brazil, Chile

311

Collections Conservation.  

ERIC Educational Resources Information Center

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

DeCandido, Robert

312

Conservative logic  

Microsoft Academic Search

Conservative logic is a comprehensive model of computation which explicitly reflects a number of fundamental principles of physics, such as the reversibility of the dynamical laws and the conservation of certainadditive quantities (among which energy plays a distinguished role). Because it more closely mirrors physics than traditional models of computation, conservative logic is in a better position to provide indications

Edward Fredkin; Tommaso Toffoli

1982-01-01

313

Conservation of wading birds  

USGS Publications Warehouse

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.

Kushlan, J.A.

1996-01-01

314

Transgenically mediated shRNAs targeting conserved regions of foot-and-mouth disease virus provide heritable resistance in porcine cell lines and suckling mice  

PubMed Central

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

2013-01-01

315

Point mutations in a conserved region (TonB box) of Escherichia coli outer membrane protein BtuB affect vitamin B12 transport.  

PubMed Central

Uptake of cobalamins and iron chelates in Escherichia coli K-12 is dependent on specific outer membrane transport proteins and the energy-coupling function provided by the TonB protein. The btuB product is the outer membrane receptor for cobalamins, bacteriophage BF23, and the E colicins. A short sequence near the amino terminus of mature BtuB, previously called the TonB box, is conserved in all tonB-dependent receptors and colicins and is the site of the btuB451 mutation (Leu-8----Pro), which prevents energy-coupled cobalamin uptake. This phenotype is partially suppressed by certain mutations in tonB. To examine the role of individual amino acids in the TonB box of BtuB, more than 30 amino acid substitutions in residues 6 to 13 were generated by doped oligonucleotide-directed mutagenesis. Many of the mutations affecting each amino acid did not impair transport activity, although some substitutions reduced cobalamin uptake and the Leu-8----Pro and Val-10----Gly alleles were completely inactive. To test whether the btuB451 mutation affects only cobalamin transport, a hybrid gene was constructed which encodes the signal sequence and first 39 residues of BtuB fused to the bulk of the ferrienterobactin receptor FepA (residues 26 to 723). This hybrid protein conferred all FepA functions but no BtuB functions. The presence of the btuB451 mutation in this fusion gene eliminated all of its tonB-coupled reactions, showing that the TonB box of FepA could be replaced by that from BtuB. These results suggest that the TonB-box region of BtuB is involved in active transport in a manner dependent not on the identity of specific side chains but on the local secondary structure. PMID:2687240

Gudmundsdottir, A; Bell, P E; Lundrigan, M D; Bradbeer, C; Kadner, R J

1989-01-01

316

Recognizing scene viewpoint using panoramic place representation  

E-print Network

We introduce the problem of scene viewpoint recognition, the goal of which is to classify the type of place shown in a photo, and also recognize the observer's viewpoint within that category of place. We construct a database ...

Xiao, Jianxiong

317

Identification of autoantigens recognized by the 2F5 and 4E10 broadly neutralizing HIV-1 antibodies  

PubMed Central

Many human monoclonal antibodies that neutralize multiple clades of HIV-1 are polyreactive and bind avidly to mammalian autoantigens. Indeed, the generation of neutralizing antibodies to the 2F5 and 4E10 epitopes of HIV-1 gp41 in man may be proscribed by immune tolerance because mice expressing the VH and VL regions of 2F5 have a block in B cell development that is characteristic of central tolerance. This developmental blockade implies the presence of tolerizing autoantigens that are mimicked by the membrane-proximal external region of HIV-1 gp41. We identify human kynureninase (KYNU) and splicing factor 3b subunit 3 (SF3B3) as the primary conserved, vertebrate self-antigens recognized by the 2F5 and 4E10 antibodies, respectively. 2F5 binds the H4 domain of KYNU which contains the complete 2F5 linear epitope (ELDKWA). 4E10 recognizes an epitope of SF3B3 that is strongly dependent on hydrophobic interactions. Opossums carry a rare KYNU H4 domain that abolishes 2F5 binding, but they retain the SF3B3 4E10 epitope. Immunization of opossums with HIV-1 gp140 induced extraordinary titers of serum antibody to the 2F5 ELDKWA epitope but little or nothing to the 4E10 determinant. Identification of structural motifs shared by vertebrates and HIV-1 provides direct evidence that immunological tolerance can impair humoral responses to HIV-1. PMID:23359068

Yang, Guang; Holl, T. Matt; Liu, Yang; Li, Yi; Lu, Xiaozhi; Nicely, Nathan I.; Kepler, Thomas B.; Alam, S. Munir; Liao, Hua-Xin; Cain, Derek W.; Spicer, Leonard; VandeBerg, John L.; Haynes, Barton F.

2013-01-01

318

Islamic Headdress Influences How Emotion is Recognized from the Eyes  

PubMed Central

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 niq?b 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 niq?b 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

Kret, Mariska Esther; de Gelder, Beatrice

2012-01-01

319

Conservation Online  

NSDL National Science Digital Library

Started as a germ of an idea back in 1987 (on a real, live bulletin board, as opposed to an electronic one), Conservation Online (CoOL) has been providing online resources for conservation professionals since 1993. As its website announces, it is a "full text library of conservation information," covering a wide array of topics ranging from digital imaging to reprographics, and quite a bit of material in between. By clicking on any given topic, visitors will receive a brief overview of the subject, its terminology, and then a list of general online resources for consideration. Another nice feature of the site is the mailing list archive, which contain the archives of various queries submitted to different professional conservation groups, such as the Association of Moving Image Archivists, the Textiles Conservation Discussion List, and the Conservation Framer's Mailing List. The site is rounded out by a timeline that traces the CoOL's history from the summer of 1987 to July 2003.

320

Highly Conserved Protective Epitopes on Influenza B Viruses  

PubMed Central

Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and ‘universal’ vaccines for influenza. However, a significant part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here we report human monoclonal antibodies, CR8033, CR8071 and CR9114, which protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses. PMID:22878502

Dreyfus, Cyrille; Laursen, Nick S.; Kwaks, Ted; Zuijdgeest, David; Khayat, Reza; Ekiert, Damian C.; Lee, Jeong Hyun; Metlagel, Zoltan; Bujny, Miriam V.; Jongeneelen, Mandy; van der Vlugt, Remko; Lamrani, Mohammed; Korse, Hans J.W.M.; Geelen, Eric; Sahin, Özcan; Sieuwerts, Martijn; Brakenhoff, Just P.J.; Vogels, Ronald; Li, Olive T.W.; Poon, Leo L. M.; Peiris, Malik; Koudstaal, Wouter; Ward, Andrew B.; Wilson, Ian A.; Goudsmit, Jaap; Friesen, Robert H.E.

2012-01-01

321

Highly conserved protective epitopes on influenza B viruses.  

PubMed

Identification of broadly neutralizing antibodies against influenza A viruses has raised hopes for the development of monoclonal antibody-based immunotherapy and "universal" vaccines for influenza. However, a substantial part of the annual flu burden is caused by two cocirculating, antigenically distinct lineages of influenza B viruses. Here, we report human monoclonal antibodies, CR8033, CR8071, and CR9114, that protect mice against lethal challenge from both lineages. Antibodies CR8033 and CR8071 recognize distinct conserved epitopes in the head region of the influenza B hemagglutinin (HA), whereas CR9114 binds a conserved epitope in the HA stem and protects against lethal challenge with influenza A and B viruses. These antibodies may inform on development of monoclonal antibody-based treatments and a universal flu vaccine for all influenza A and B viruses. PMID:22878502

Dreyfus, Cyrille; Laursen, Nick S; Kwaks, Ted; Zuijdgeest, David; Khayat, Reza; Ekiert, Damian C; Lee, Jeong Hyun; Metlagel, Zoltan; Bujny, Miriam V; Jongeneelen, Mandy; van der Vlugt, Remko; Lamrani, Mohammed; Korse, Hans J W M; Geelen, Eric; Sahin, Özcan; Sieuwerts, Martijn; Brakenhoff, Just P J; Vogels, Ronald; Li, Olive T W; Poon, Leo L M; Peiris, Malik; Koudstaal, Wouter; Ward, Andrew B; Wilson, Ian A; Goudsmit, Jaap; Friesen, Robert H E

2012-09-14

322

Global versus Local Conservation Focus of U.S. State Agency Endangered Bird Species Lists  

PubMed Central

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. PMID:20062538

Wells, Jeffrey V.; Robertson, Bruce; Rosenberg, Kenneth V.; Mehlman, David W.

2010-01-01

323

Global versus local conservation focus of U.S. state agency endangered bird species lists.  

PubMed

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. PMID:20062538

Wells, Jeffrey V; Robertson, Bruce; Rosenberg, Kenneth V; Mehlman, David W

2010-01-01

324

MPhil Textile Conservation MPhil Textile Conservation  

E-print Network

MPhil Textile Conservation #12;MPhil Textile Conservation Textile conservation is a multi skills necessary to carry out conservation treatments. The two-year programme provides a comprehensive to its preservation and interpretation. The programme is housed in new conservation laboratories

Guo, Zaoyang

325

Conservation Biology Institute  

NSDL National Science Digital Library

The Conservation Biology Institute (CBI), a non-profit organization founded in 1997, is active in three primary areas related to conservation biology - applied research, education, and professional services. Through its research - alone or in collaboration with others - CBI actively seeks to develop new conservation tools, techniques, and analyses that can be used to better address a wide range of ecological concerns from endangered species protection to regional conservation planning. Based on a combination of field-based biology and computer mapping technologies (i.e., remote sensing and geographic information systems), CBIs primary research areas include: forest, aquatic, and watershed assessments, local and regional conservation planning, endangered species research and management, ecosystem monitoring, and carnivore conservation. Their formal education program, still in development, currently consists of five basic subdivisions (or program areas) including internships/ fellowships, education materials, college courses, short courses, and workshops/guest lectures. CBIs professional services are conducted alone or in collaboration with outside organizations and include: biological surveys and consulting, geographical information system (GIS) mapping services, as well as scientific reviews and white papers.

326

Design Alternatives for Evaluating the Impact of Conservation Projects  

ERIC Educational Resources Information Center

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…

Margoluis, Richard; Stem, Caroline; Salafsky, Nick; Brown, Marcia

2009-01-01

327

Conservation businesses and conservation planning in a biological diversity hotspot.  

PubMed

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

Di Minin, Enrico; Macmillan, Douglas Craig; Goodman, Peter Styan; Escott, Boyd; Slotow, Rob; Moilanen, Atte

2013-08-01

328

Federally-Recognized Tribes of the Columbia-Snake Basin.  

SciTech Connect

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.

United States. Bonneville Power Administration

1997-11-01

329

Recognizing environmental risks in oil and gas property acquisitions  

SciTech Connect

Within the last 20 yr, our society has become increasingly sensitive to environmental concerns. These concerns have been recognized by Congress through the passage of federal laws addressing numerous environmental issues. With the passage of the Comprehensive Environmental Response, Compensation, and Liability Act (CERCLA) in 1980, the business community suddenly was thrust into a new arena of environmental cleanup costs can become the responsibility of the unfortunate party who has possession of the property when the contamination is discovered, regardless of who caused the environmental damage. The financial and industrial community recognizes these concerns as civil liability risks. Sophisticated financial institutions and industrial firms have required environmental due diligence assessments on major financial transactions involving real estate for several years. The oil and gas industry is not immune from the environmental and financial risks associated with acquisitions of potentially contaminated properties. The Resource Conservation and Recovery Act (RCRA) currently exempts drilling fluids, produced waters, and associated wastes from hazardous waste regulation. However, several products used at exploration and production facilities are not exempt wastes when disposed of and, therefore, are subject to RCRA regulations. Cleanup of RCRA hazardous waters are subject to provisions of CERCLA. Futhermore, state agencies have authority to require cleanup of RCRA-exempt wastes (e.g., crude oil spills) that have contaminated soil or groundwater. The risk associated with acquiring cleanup (and financial) responsibility at contaminated producing facilities or other acquisitions can be reduced through the environmental assessment process.

Mundt, W.J. (R.W. Beck and Associates, Denver, CO (United States))

1993-09-01

330

Maintaining Maintainability = Recognizing Reachability Tim Menzies  

E-print Network

Maintaining Maintainability = Recognizing Reachability Tim Menzies NASA/WVU IV&V Facility 100 University Drive, Fairmont WV 26554, USA tim@menzies.com;http://www.tim.menzies.com Bojan Cukic Dept an operational profile). White-box (WB) testing costs more than black-box to define: analysts must reflect over

Menzies, Tim

331

HOW TO RECOGNIZE AND USE CALENDAR DATES  

Technology Transfer Automated Retrieval System (TEKTRAN)

A frequent concern of beginning SAS programmers is how to make a SAS program recognize calendar dates in various formats. For example, Sept., SEP, 9, 09, /9, /09, and even $9 are all valid representations for the month of September. Although a program may currently read a date correctly, a new chall...

332

RECOGNIZING AND PARAMETRIZING CURVES WITHOUT AFFINE SINGULARITIES  

E-print Network

Kong RGC-CERG grant. 1 #12;2 CHI-MING LAM, VLADIMIR SHPILRAIN, AND JIE-TAI YU The purposeRECOGNIZING AND PARAMETRIZING CURVES WITHOUT AFFINE SINGULARITIES CHI-MING LAM, VLADIMIR SHPILRAIN, AND JIE-TAI YU Abstract. Some time ago, Shpilrain and Yu reported an algorithm for deciding whether

Shpilrain, Vladimir

333

Great Apes' Capacities to Recognize Relational Similarity  

ERIC Educational Resources Information Center

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…

Haun, Daniel B. M.; Call, Josep

2009-01-01

334

Recognizing Digressive Questions During Interactive Generation  

Microsoft Academic Search

In expository discourse, people sometimes ask ques- tions that digress from the purpose of the discussion. A system that provides interactive explanations and advice must be able to distinguish pertinent questions from questions that digress. It must also be able .to recognize questions that are incoherent. These types of questions require different treatment. Pertinent ques- tions must be answered to

Susan M. Hailer

335

Learning to Recognize Volcanoes on Venus  

Microsoft Academic Search

.Dramatic improvements in sensor and image acquisition technology have createda demand for automated tools that can aid in the analysis of large image databases.We describe the development of JARtool, a trainable software system that learnsto recognize volcanoes in a large data set of Venusian imagery. A machine learningapproach is used because it is much easier for geologists to identify examples

Michael C. Burl; Lars Asker; Padhraic Smyth; Usama M. Fayyad; Pietro Perona; Larry Crumpler; Jayne Aubele

1998-01-01

336

How Should a Speech Recognizer Work?  

ERIC Educational Resources Information Center

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…

Scharenborg, Odette; Norris, Dennis; ten Bosch, Louis; McQueen, James M.

2005-01-01

337

Image Complexity Metrics for Automatic Target Recognizers  

Microsoft Academic Search

Designers of automatic target recognizers (ATR) need measures of image complexity to compare the performance of dierent ATRs. An image complexity metric should provide an ap rioriestimate of the diculty of locating a true target in an image. An ideal image metric is a mapping from the set of all images to a nite real interval. The extrema of the

Richard Alan Peters II; Robin N. Strickland

1990-01-01

338

METHOD AND MEANS FOR RECOGNIZING COMPLEX PATTERNS  

Microsoft Academic Search

This patent relates to a method and means for recognizing a complex ; pattern in a picture. The picture is divided into framelets, each framelet being ; sized so that any segment of the complex pattern therewithin is essentially a ; straight line. Each framelet is scanned to produce an electrical pulse for each ; point scanned on the segment

P. Hough; P. V. C

1962-01-01

339

Recognizing Human Actions: A Local SVM Approach  

Microsoft Academic Search

Local space-time features capture local events in video and can be adapted to the size, the frequency and the veloc- ity of moving patterns. In this paper we demonstrate how such features can be used for recognizing complex motion patterns. We construct video representations in terms of lo- cal space-time features and integrate such representations with SVM classification schemes for

Christian Schüldt; Ivan Laptev; Barbara Caputo

2004-01-01

340

Recognizing Action Units for Facial Expression Analysis  

Microsoft Academic Search

Most automatic expression analysis systems attempt to recognize a small set of prototypic expressions, such as happiness, anger, surprise, and fear. Such pro- totypic 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

Ying-li Tian; Takeo Kanade; Jeffrey F. Cohn

2001-01-01

341

Recognizing 3-D Objects Using Surface Descriptions  

Microsoft Academic Search

The authors provide a complete method for describing and recognizing 3-D objects, using surface information. Their system takes as input dense range date and automatically produces a symbolic description of the objects in the scene in terms of their visible surface patches. This segmented representation may be viewed as a graph whose nodes capture information about the individual surface patches

Ting-jun Fan; Gérard G. Medioni; Ramakant Nevatia

1989-01-01

342

Evaluating Local Benefits from Conservation in Nepal's Annapurna Conservation Area  

NASA Astrophysics Data System (ADS)

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.

Spiteri, Arian; Nepal, Sanjay K.

2008-09-01

343

Evaluating local benefits from conservation in Nepal's Annapurna Conservation Area.  

PubMed

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. PMID:18458999

Spiteri, Arian; Nepal, Sanjay K

2008-09-01

344

C. elegans RNA-binding protein GLD-1 recognizes its multiple targets using sequence, context, and structural information to repress translation  

PubMed Central

Caenorhabditis elegans GLD-1, a maxi-KH motif containing RNA-binding protein, has various functions mainly during female germ cell development, suggesting that it likely controls the expression of a selective group of maternal mRNAs. To gain an insight into how GLD-1 specifically recognizes these mRNA targets, we identified 38 biochemically proven GLD-1 binding regions from multiple mRNA targets that are among over 100 putative targets co-immunoprecipitated with GLD-1. The sequence information of these regions revealed three over-represented and phylogenetically conserved sequence motifs. We found that two of the motifs, one of which is novel, are important for GLD-1 binding in several GLD-1 binding regions but not in other regions. Further analyses indicate that the importance of one of the sequence motifs is dependent on two aspects: (1) surrounding sequence information, likely acting as an accessory feature for GLD-1 to efficiently select the sequence motif and (2) RNA secondary structural environment where the sequence motif resides, which likely provides “binding-site accessibility” for GLD-1 to effectively recognize its targets. Our data suggest some mRNAs recruit GLD-1 by a distinct mechanism, which involves more than one sequence motif that needs to be embedded in the correct context and structural environment. PMID:24744981

Doh, Jung H; Jung, Yuchae; Reinke, Valerie; Lee, Min-Ho

2013-01-01

345

Positive impacts in soil and water conservation in an Andean region of South America: Case scenarios from a USAID multidisciplinary cooperative project  

Technology Transfer Automated Retrieval System (TEKTRAN)

The USAID-SANREM-Virginia Polytechnic Institute project has made and continues to make an excellent impact, specifically showcasing the positive results of soil and water conservation (Barrera et al. 2010a; 2010b). This project has strong international cooperation between the USA, Ecuador and Bolivi...

346

Characterization of New Mutations in Pyrazinamide-Resistant Strains of Mycobacterium tuberculosis and Identification of Conserved Regions Important for the Catalytic Activity of the Pyrazinamidase PncA  

Microsoft Academic Search

Recently, the gene pncA, encoding the pyrazinamidase (PZase) of Mycobacterium tuberculosis, was identified (8); mu- tations in pncA have been shown to be associated with pyra- zinamide (PZA) resistance (1, 5, 9, 10). However, the muta- tions found in the amino acid sequence of the PZase from M. tuberculosis have not been investigated with respect to their locations in conserved

NADINE LEMAITRE; WLADIMIR SOUGAKOFF; CHANTAL TRUFFOT-PERNOT; VINCENT JARLIER

1999-01-01

347

Conservation in Conflict  

NSDL National Science Digital Library

What happens when war occurs in areas where there is war? Ecologist Peter Zahler who has worked in Afghanistan since 2002, talks about how conserving biodiversity may bring peace to the war-torn region. You can read more about Zahler's work in the article Nurturing Wildlife in War-Torn Afghanistan that appeared in the New Yorker Times in December, 2011.

Wildlife Conservation Society

348

CONSERVATION VOICES GRAVITY RULES  

E-print Network

CONSERVATION VOICES GRAVITY RULES By David R. Montgomery When it comes to runoff and erosion of life that we value today in this region, and pass them on to future generations, we need to not only headwater environments from degradation through wilderness and Wild & Scenic Rivers protection is a prudent

Montgomery, David R.

349

50 CFR 665.208 - Protected species conservation.  

Code of Federal Regulations, 2013 CFR

...2013-10-01 false Protected species conservation. 665.208 Section 665...Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC...665.208 Protected species conservation. The Regional...

2013-10-01

350

50 CFR 665.208 - Protected species conservation.  

Code of Federal Regulations, 2010 CFR

...2010-10-01 false Protected species conservation. 665.208 Section 665...Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC...665.208 Protected species conservation. The Regional...

2010-10-01

351

50 CFR 665.208 - Protected species conservation.  

Code of Federal Regulations, 2014 CFR

...2014-10-01 false Protected species conservation. 665.208 Section 665...Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL OCEANIC...665.208 Protected species conservation. The Regional...

2014-10-01

352

Water Conservation  

NSDL National Science Digital Library

This activity was developed to get students thinking about the many ways that people use freshwater and how we can conserve this precious and fundamental natural resource. Students will watch a short documentary describing issues related to clean water availability, analyze water-use data and start to think about how they consume and can conserve water. This background knowledge will lead to students collecting data about their own water use and finding areas in their lives to conserve water. This activity uses the 5E instructional model and is part of the "Survivor Earth" series of one-hour lessons.

353

Semiarid soil and water conservation  

Microsoft Academic Search

This book provides an overview of soil and water conservation and emphasizes practical control measures. Contents include surface hydrology, analysis of the erosion process, and practical control measures through: correct land use; crop rotations; shifting cultivation; contour farming; and strip cropping; Water harvesting, recently developed systems now in use, and rangeland management for soil and water conservation in semi-arid regions

1986-01-01

354

Energy Conservation  

ERIC Educational Resources Information Center

Comments on The Potential for Energy Conservation,'' a study by the Office of Emergency Preparedness, emphasizing the coming dependence on foreign oil, and presses for government influence to encourage development of more efficient cars. (AL)

Abelson, Philip H.

1972-01-01

355

Conservation Ecology  

NSDL National Science Digital Library

Conservation Ecology is a new, exclusively electronic, peer-reviewed scientific journal of the Resilience Alliance, with content ranging from the applied to the theoretical. Topics covered by the journal include: "the conservation of ecosystems, landscapes, species, populations, and genetic diversity; the restoration of ecosystems and habitats; and the management of resources." This site includes the full text version of the articles (including past issues), as well as instructions on how to submit papers and how to subscribe. Subscriptions to Conservation Ecology are free of charge and all materials are available for browsing without cost. Edited by ecosystem ecology expert, Dr. C. S. Holling, Conservation Ecology breaks new ground in an important, emerging science.

1997-01-01

356

Conservation Presentation.  

ERIC Educational Resources Information Center

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)

Friday, Gerald

2001-01-01

357

Energy Conservation  

NSDL National Science Digital Library

Students are introduced to the idea that energy use impacts the environment and our wallets. They discuss different types of renewable and nonrenewable energy sources, as well as the impacts of energy consumption. Through a series of activities, students understand how they use energy and how it is transformed from one type to another. They learn innovative ways engineers conserve energy and how energy can be conserved in their homes.

Integrated Teaching and Learning Program,

358

Methods for Assessing the Conservation Value of Rivers  

NASA Astrophysics Data System (ADS)

Assessments of rivers for conservation value in the US and the UK have built on concepts of recognizing biological representation, distinctiveness and conservation status, to support the goals of maximizing protection of biodiversity. In the UK, the System for Evaluating Rivers for Conservation (SERCON) scores attributes related to physical diversity, naturalness, representativeness (of aquatic macrophyte communities), importance to rare species, occurrence of special features, and human impacts. SERCON is designed to facilitate repeatable and comparable assessments of river reaches (generally 10 to 30 km in length). In the US, high diversity, endemism and rates of decline in riverine biota have led to a greater emphasis on protecting imperiled species (based on species occurrence data, expert opinion, and the occurrence of habitat elements considered essential to species persistence) as well as protecting the full range of habitat or community types occurring in a given region. Assessing value with respect to representing biodiversity is an evolving science, utilizing methods for habitat and community classification, and probabilistic models of assemblage richness. Methods for assessing the value of a particular river reach with respect to ecological processes that maintain lotic communities are particularly needed for conservation planning at local scales.

Freeman, M. C.; Boon, P. J.

2005-05-01

359

SNF11, a New Component of the Yeast SNF-SWI Complex That Interacts with a Conserved Region of SNF2  

Microsoft Academic Search

The yeast SNF-SWI complex is required for transcriptional activation of diverse genes and has been shown to alter chromatin structure. The complex has at least 10 components, including SNF2\\/SWI2, SNF5, SNF6, SWI1\\/ADR6, and SWI3, and has been widely conserved in eukaryotes. Here we report the characterization of a new component. We identified proteins that interact in the two-hybrid system with

ISABELLE TREICH; BRADLEY R. CAIRNS; TERESA DE LOSSANTOS

360

Complete Currarino Syndrome Recognized in Adulthood  

PubMed Central

Currarino syndrome is a hereditary pathology that is characterized by sacrococcygeal bone defect, presacral mass, and anorectal malformation. Sacrococcygeal bone defect is almost always a part of the syndrome. The complete form of this entity displays all three abnormalities and is very uncommon. In this report, we present the magnetic resonance imaging findings of a case with complete form of Currarino syndrome recognized in adulthood.

Akay, Sinan; Battal, Bilal; Karaman, Bulent; Bozkurt, Yalcin

2015-01-01

361

Recognizing Materials using Perceptually Inspired Features  

PubMed Central

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

Sharan, Lavanya; Liu, Ce; Rosenholtz, Ruth; Adelson, Edward H.

2013-01-01

362

Recognizing Action Units for Facial Expression Analysis  

PubMed Central

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. PMID:25210210

Tian, Ying-li; Kanade, Takeo; Cohn, Jeffrey F.

2010-01-01

363

Gag protein epitopes recognized by CD4(+) T-helper lymphocytes from equine infectious anemia virus-infected carrier horses.  

PubMed

Antigen-specific T-helper (Th) lymphocytes are critical for the development of antiviral humoral responses and the expansion of cytotoxic T lymphocytes (CTL). Identification of relevant Th lymphocyte epitopes remains an important step in the development of an efficacious subunit peptide vaccine against equine infectious anemia virus (EIAV), a naturally occurring lentivirus of horses. This study describes Th lymphocyte reactivity in EIAV carrier horses to two proteins, p26 and p15, encoded by the relatively conserved EIAV gag gene. Using partially overlapping peptides, multideterminant and possibly promiscuous epitopes were identified within p26. One peptide was identified which reacted with peripheral blood mononuclear cells (PBMC) from all five EIAV-infected horses, and three other peptides were identified which reacted with PBMC from four of five EIAV-infected horses. Four additional peptides containing both CTL and Th lymphocyte epitopes were also identified. Multiple epitopes were recognized in a region corresponding to the major homology region of the human immunodeficiency virus, a region with significant sequence similarity to other lentiviruses including simian immunodeficiency virus, puma lentivirus, feline immunodeficiency virus, Jembrana disease virus, visna virus, and caprine arthritis encephalitis virus. PBMC reactivity to p15 peptides from EIAV carrier horses also occurred. Multiple p15 peptides were shown to be reactive, but not all infected horses had Th lymphocytes recognizing p15 epitopes. The identification of peptides reactive with PBMC from outbred horses, some of which encoded both CTL and Th lymphocyte epitopes, should contribute to the design of synthetic peptide or recombinant vector vaccines for EIAV. PMID:10196322

Lonning, S M; Zhang, W; McGuire, T C

1999-05-01

364

CTL from EIAV carrier horses with diverse MHC class I alleles recognize epitope clusters in Gag matrix and capsid proteins  

PubMed Central

Cytotoxic T lymphocytes (CTL) are important for controlling equine infectious anemia virus (EIAV). Because Gag matrix (MA) and capsid (CA) are the most frequently recognized proteins, the hypothesis that CTL from EIAV-infected horses with diverse MHC class I alleles recognize epitope clusters (EC) in these proteins was tested. Four EC were identified by CTL from 15 horses and 8 of these horses had diverse MHC class I alleles. Two of the eight had CTL to EC1, six to EC2, five to EC3, and four to EC4. Because EC2–4 were recognized by CTL from >50% of horses with diverse alleles, the hypothesis was accepted. EC1 and EC3 were the most conserved EC and these more conserved broadly recognized EC may be most useful for CTL induction, helping overcome MHC class I polymorphism and antigenic variation. PMID:15327905

Chung, Chungwon; Mealey, Robert H.; McGuire, Travis C.

2012-01-01

365

A Recognized Leader in Marine & Atmospheric  

E-print Network

Health · Tropical Marine Ecosystem · Weather, Climate and Society · Weather Forecasting Ph for Ecosystem Science and Policy · National Resource Center of Aplysia · R.J. Dunlap Marine Conservation Program Ten Major Cities of the Future Master of Professional Science (MPS) The MPS program is dedicated

Miami, University of

366

Virus-neutralizing monoclonal antibody to a conserved epitope on the duck hepatitis B virus pre-S protein.  

PubMed Central

In this study we used duck hepatitis B virus (DHBV)-infected Pekin ducks and heron hepatitis B virus (HHBV)-infected heron tissue to search for epitopes responsible for virus neutralization on pre-S proteins. Monoclonal antibodies were produced by immunizing mice with purified DHBV particles. Of 10 anti-DHBV specific hybridomas obtained, 1 was selected for this study. This monoclonal antibody recognized in both DHBV-infected livers and viremic sera a major (36-kilodalton) protein and several minor pre-S proteins in all seven virus strains used. In contrast, pre-S proteins of HHBV-infected tissue or viremic sera did not react. Thus, the monoclonal antibody recognizes a highly conserved DHBV pre-S epitope. For mapping of the epitope, polypeptides from different regions of the DHBV pre-S/S gene were expressed in Escherichia coli and used as the substrate for immunoblotting. The epitope was delimited to a sequence of approximately 23 amino acids within the pre-S region, which is highly conserved in four cloned DHBV isolates and coincides with the main antigenic domain as predicted by computer algorithms. In in vitro neutralization assays performed with primary duck hepatocyte cultures, the antibody reduced DHBV infectivity by approximately 75%. These data demonstrate a conserved epitope of the DHBV pre-S protein which is located on the surface of the viral envelope and is recognized by virus-neutralizing antibodies. Images PMID:1689393

Lambert, V; Fernholz, D; Sprengel, R; Fourel, I; Deléage, G; Wildner, G; Peyret, C; Trépo, C; Cova, L; Will, H

1990-01-01

367

Selective advantage for conservative viruses  

NASA Astrophysics Data System (ADS)

In this article we study the full semiconservative treatment of a model for the coevolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semiconservatively replicating viruses interacting with a realistic semiconservatively replicating immune system. The conservative virus is found to have a selective advantage in the form of an ability to survive in regions with a wider range of mutation rates than its semiconservative counterpart, as well as an increased replication rate where both species can survive. This may help explain the existence of a rich range of viruses with conservatively replicating genomes, a trait that is found nowhere else in nature.

Brumer, Yisroel; Shakhnovich, Eugene I.

2005-03-01

368

Recognizing Age-Separated Face Images: Humans and Machines  

PubMed Central

Humans utilize facial appearance, gender, expression, aging pattern, and other ancillary information to recognize individuals. It is interesting to observe how humans perceive facial age. Analyzing these properties can help in understanding the phenomenon of facial aging and incorporating the findings can help in designing effective algorithms. Such a study has two components - facial age estimation and age-separated face recognition. Age estimation involves predicting the age of an individual given his/her facial image. On the other hand, age-separated face recognition consists of recognizing an individual given his/her age-separated images. In this research, we investigate which facial cues are utilized by humans for estimating the age of people belonging to various age groups along with analyzing the effect of one's gender, age, and ethnicity on age estimation skills. We also analyze how various facial regions such as binocular and mouth regions influence age estimation and recognition capabilities. Finally, we propose an age-invariant face recognition algorithm that incorporates the knowledge learned from these observations. Key observations of our research are: (1) the age group of newborns and toddlers is easiest to estimate, (2) gender and ethnicity do not affect the judgment of age group estimation, (3) face as a global feature, is essential to achieve good performance in age-separated face recognition, and (4) the proposed algorithm yields improved recognition performance compared to existing algorithms and also outperforms a commercial system in the young image as probe scenario. PMID:25474200

Yadav, Daksha; Singh, Richa; Vatsa, Mayank; Noore, Afzel

2014-01-01

369

The helicase-binding domain of Escherichia coli DnaG primase interacts with the highly conserved C-terminal region of single-stranded DNA-binding protein  

PubMed Central

During bacterial DNA replication, DnaG primase and the ? 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. PMID:23430154

Naue, Natalie; Beerbaum, Monika; Bogutzki, Andrea; Schmieder, Peter; Curth, Ute

2013-01-01

370

Beyond Bags of Features: Spatial Pyramid Matching for Recognizing Natural Scene Categories  

Microsoft Academic Search

This paper presents a method for recognizing scene cat- egories based on approximate global geometric correspon- dence. This technique works by partitioning the image into increasingly fine sub-regions and computing histograms of local features found inside each sub-region. The result- ing \\

Svetlana Lazebnik; Cordelia Schmid; Jean Ponce

2006-01-01

371

Massachusetts Conservation  

NSDL National Science Digital Library

Massachusetts has long been a leader in the conservation and preservation movements. From early attempts to create an Emerald Necklace around Boston to the battle to save the Old State House, the commonwealth has rich, fascinating tales and experiences. This wonderful travel itinerary was created by the National Park Service's Heritage Education Services in partnership with the Massachusetts Historical Commission and the National Conference of State Historic Preservation Officers. On the site, visitors can look over essays, a list of sites, maps, and external websites. The powerful essays include "Conservation and Landscape Planning in Massachusetts" and "American Conservation in the Twentieth Century." Checking out the List of Sites area, visitors can read a complete list of all the places mentioned in the itinerary (complete with details and photos) such as the Boston Public Garden, the Lynn Woods Historic District, and the Fruitlands Museums Historic District.

372

Local Responses to Participatory Conservation in Annapurna Conservation Area, Nepal  

NASA Astrophysics Data System (ADS)

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.

Khadka, Damodar; Nepal, Sanjay K.

2010-02-01

373

Recognizing and responding to a suicide crisis.  

PubMed

Data from therapists who were treating 26 patients when they committed suicide were utilized to identify signs that warned of a suicide crisis. Three factors were identified as markers of the suicide crisis: a precipitating event; one or more intense affective stats other than depression; and at least one of three behavioral patterns: speech or actions suggesting suicide, deterioration in social or occupational functioning, and increased substance abuse. Problems in communication between patient and therapist, often originating in therapeutic anxiety over the patient's possible suicide, were identified as factors interfering with crisis recognition. Evaluation of the identified affects and behaviors may help therapists recognize a suicide crisis. PMID:11411185

Hendin, H; Maltsberger, J T; Lipschitz, A; Haas, A P; Kyle, J

2001-04-01

374

Recognizing Patterns In Log-Polar Coordinates  

NASA Technical Reports Server (NTRS)

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.

Weiman, Carl F. R.

1992-01-01

375

Recognizing women in the archaeological record  

SciTech Connect

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.

Bumsted, M.P.

1987-01-01

376

Water Conservation  

NSDL National Science Digital Library

In this lesson, students study the availability of water on Earth and discuss methods that can be used to purify and conserve this critical resource. Using multimedia interactives, video, and classroom activities, they will identify sources of fresh water available for consumption, understand the need for water conservation, and compare the benefits and drawbacks of different water management techniques. They will also assess how much water they and their families typically use, and think about ways to reduce their water usage. Finally, students explore different techniques being employed for water management around the world, including the use of dams to create reservoirs.

2005-01-01

377

Mutational analysis of conserved regions harboring catalytic triad residues of the levansucrase protein encoded by the lsc-3 gene (lsc3) of Pseudomonas syringae pv. tomato DC3000.  

PubMed

Levansucrase encoded by the lsc-3 (lsc3) gene at genomic locus PSPTOA0032 of Pseudomonas syringae pv. tomato DC3000 was mutationally analyzed. Altogether, 18 single-amino-acid mutants of 13 positions of Lsc3 were studied for catalytic properties, including production of fructooligosaccharides (FOS). Asp62, Asp219, and Glu303 were proved as members of the catalytic triad. Respective alanine replacement mutants were practically inactive with their kcat values reduced up to ?130,000 times. Additionally, the requirements of Trp61, Gln301, and Arg304, located in conserved sequence blocks around the catalytic triad positions for the catalysis were shown. The catalytic significance of the position equivalent to Arg304 was shown for levansucrases for the first time. Replacement of Gln301 specifically affected the polymerizing ability of Lsc3. The Gln301Ala mutant was largely hydrolytic and produced 31 times less FOS than the wild type. Despite high conservation grades, Leu66, Pro220, Asp225, and His306 tolerated replacement well. Quantification of produced FOS showed a high biotechnological potential of Lsc3. Using 1 mg of Lsc3 protein, 15.4 g of FOS with a degree of polymerization from 3 to 7 can be synthesized in a 20 H reaction with 1,200 mM sucrose. Our expression system allowed us to produce up to 30 mg of Lsc3 protein from 1 L of induced culture of recombinant Escherichia coli. PMID:23725335

Mardo, Karin; Visnapuu, Triinu; Vija, Heiki; Elmi, Triin; Alamäe, Tiina

2014-01-01

378

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

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. PMID:25642223

López-Fuentes, Eunice; Torres-Tejerizo, Gonzalo; Cervantes, Laura; Brom, Susana

2015-01-01

379

Recognizing connotative meaning in military chat communications  

NASA Astrophysics Data System (ADS)

Over the last five to seven years the use of chat in military contexts has expanded quite significantly, in some cases becoming a primary means of communicating time-sensitive data to decision makers and operators. For example, during humanitarian operations with Joint Task Force-Katrina, chat was used extensively to plan, task, and coordinate predeployment and ongoing operations. The informal nature of chat communications allows the relay of far more information than the technical content of messages. Unlike formal documents such as newspapers, chat is often emotive. "Reading between the lines" to understand the connotative meaning of communication exchanges is now feasible, and often important. Understanding the connotative meaning of text is necessary to enable more useful automatic intelligence exploitation. The research project described in this paper was directed at recognizing user connotations of uncertainty and urgency. The project built a matrix of speech features indicative of these categories of meaning, developed data mining software to recognize them, and evaluated the results.

Budlong, Emily R.; Walter, Sharon M.; Yilmazel, Ozgur

2009-05-01

380

Ants recognize foes and not friends  

PubMed Central

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

Guerrieri, Fernando J.; Nehring, Volker; Jørgensen, Charlotte G.; Nielsen, John; Galizia, C. Giovanni; d'Ettorre, Patrizia

2009-01-01

381

Protein Conservation: an View into Proteomics  

NSDL National Science Digital Library

Students review aspects of protein structure and folding and then move to 3D molecules, evaluating the consequences of both conservative and non-conservative substitutions in protein sequences. The activity culminates in a comparison of human, rat and bacterial enzymes; students discuss why it is be important for some regions to be conserved. Students will be able to:Explain the basic forces at work in protein folding; differentiate conservative and non-conservative substitutions in mutations; compare human, rat and bacterial enzymes and discuss why it is be important for some to be conserved.

Molecular Literacy Project

382

Comparative architectural aspects of regions of conserved synteny on human chromosome 11p15.3 and mouse chromosome 7 (including genes WEE1 and LMO1)  

Microsoft Academic Search

Human chromosome 11p15.3 is associated with chromosome aberrations in the Beckwith Wiedemann Syndrome and implicated in the pathogenesis of different tumor types including lung cancer and leukemias. To date, only single tumor-relevant genes with linkage to this region (e.g. LMO1) have been found suggesting that this region may harbor additional potential disease associated genes. Although this genomic area has been

A. Cichutek; T. Brueckmann; B. Seipel; H. Hauser; S. Schlaubitz; D. Prawitt; T. Hankeln; E. R. Schmidt; A. Winterpacht; B. U. Zabel

2001-01-01

383

conservation perspective  

E-print Network

sharks can be sus- tainably harvested. In two recent papers, Baum et al. (2003) and Baum and Myers (2004conservation perspective Introduction Sharks are generally regarded to exhibit slow growth, late. 2000a). Although our knowledge of the demography and population dynamics of sharks has been slow

Hawai'i at Manoa, University of

384

Marketing Conservation.  

ERIC Educational Resources Information Center

In 1986, Northeast Utilities began helping shool administrators combat school building energy wastage through a program called Energy Alliance. The typical school can reduce its energy bill by 30 percent by adopting a wide range of conservation measures, including cogeneration, relamping, and energy audits. (MLH)

Ellis, William B.

1987-01-01

385

Wildlife Conservation  

Microsoft Academic Search

Ecotourism has been proposed as a viable economic activity that can minimiz e negative human impacts on wildlife habitat and provide an incentive to preserv e natural areas. The potential of ecotourism as a wildlife conservation strategy is lim - ited by its inability to insure the long-term protection of environmental assets and by its tendency to contribute directly to

Jack Coburn

1969-01-01

386

Colorful Conservation  

ERIC Educational Resources Information Center

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…

Skophammer, Karen

2011-01-01

387

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)

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-percent and 42-percent of groundwater for cotton, corn and soybeans, respectively. Even in extreme drought years such as 2007, cotton, corn and soybeans produced under the 97.5:2.5 management strategy could conserve 32-percent, 46-percent and 38-percent of groundwater, respectively.

Thornton, Robert Frank

388

Optimal Conservation of Migratory Species  

PubMed Central

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 connectivity and the correct statement of the conservation problem. Our framework can be used to identify efficient conservation strategies for migratory taxa worldwide, including insects, birds, mammals, and marine organisms. PMID:17710150

Martin, Tara G.; Chadès, Iadine; Arcese, Peter; Marra, Peter P.; Possingham, Hugh P.; Norris, D. Ryan

2007-01-01

389

Mapping of Epitopes Recognized by Antibodies Induced by Immunization of Mice with PspA and PspC  

PubMed Central

Pneumococcal surface protein A (PspA) and pneumococcal surface protein C (PspC) are important candidates for an alternative vaccine against pneumococcal infections. Since these antigens show variability, the use of variants that do not afford broad protection may lead to the selection of vaccine escape bacteria. Epitopes capable of inducing antibodies with broad cross-reactivities should thus be the preferred antigens. In this work, experiments using peptide arrays show that most linear epitopes recognized by antibodies induced in mice against different PspAs were located at the initial 44 amino acids of the mature protein and that antibodies against these linear epitopes did not confer protection against a lethal challenge. Conversely, linear epitopes recognized by antibodies to PspC included the consensus sequences involved in the interaction with human factor H and secretory immunoglobulin A (sIgA). Since linear epitopes of PspA were not protective, larger overlapping fragments containing 100 amino acids of PspA of strain Rx1 were constructed (fragments 1 to 7, numbered from the N terminus) to permit the mapping of antibodies with conformational epitopes not represented in the peptide arrays. Antibodies from mice immunized with fragments 1, 2, 4, and 5 were capable of binding onto the surface of pneumococci and mediating protection against a lethal challenge. The fact that immunization of mice with 100-amino-acid fragments located at the more conserved N-terminal region of PspA (fragments 1 and 2) induced protection against a pneumococcal challenge indicates that the induction of antibodies against conformational epitopes present at this region may be important in strategies for inducing broad protection against pneumococci. PMID:24807052

Vadesilho, Cintia F. M.; Ferreira, Daniela M.; Gordon, Stephen B.; Briles, David E.; Moreno, Adriana T.; Oliveira, Maria Leonor S.; Ho, Paulo L.

2014-01-01

390

Setting practical conservation priorities for birds in the Western andes of Colombia.  

PubMed

We aspired to set conservation priorities in ways that lead to direct conservation actions. Very large-scale strategic mapping leads to familiar conservation priorities exemplified by biodiversity hotspots. In contrast, tactical conservation actions unfold on much smaller geographical extents and they need to reflect the habitat loss and fragmentation that have sharply restricted where species now live. Our aspirations for direct, practical actions were demanding. First, we identified the global, strategic conservation priorities and then downscaled to practical local actions within the selected priorities. In doing this, we recognized the limitations of incomplete information. We started such a process in Colombia and used the results presented here to implement reforestation of degraded land to prevent the isolation of a large area of cloud forest. We used existing range maps of 171 bird species to identify priority conservation areas that would conserve the greatest number of species at risk in Colombia. By at risk species, we mean those that are endemic and have small ranges. The Western Andes had the highest concentrations of such species-100 in total-but the lowest densities of national parks. We then adjusted the priorities for this region by refining these species ranges by selecting only areas of suitable elevation and remaining habitat. The estimated ranges of these species shrank by 18-100% after accounting for habitat and suitable elevation. Setting conservation priorities on the basis of currently available range maps excluded priority areas in the Western Andes and, by extension, likely elsewhere and for other taxa. By incorporating detailed maps of remaining natural habitats, we made practical recommendations for conservation actions. One recommendation was to restore forest connections to a patch of cloud forest about to become isolated from the main Andes. PMID:25065287

Ocampo-Peñuela, Natalia; Pimm, Stuart L

2014-10-01

391

CONSERVATION m Diversity, Distribution, and Conservation Status of the Native Freshwater Fishes of the Southern United States  

E-print Network

The Southeastern Fishes Council Technical Advisory Committee reviewed the diversity, distribution, and status of all native freshwater and diadromous fishes across 51 major drainage units of the southern United States. The southern United States supports more native fishes than any area of comparable size on the North American continent north of Mexico, but also has a high proportion of its fishes in need of conservation action. The review included 662 native freshwater and diadromous fishes and 24 marine fishes that are significant components of freshwater ecosystems. Of this total, 560 described, freshwater fish species are documented, and 49 undescribed species are included provisionally pending formal description. Described subspecies (86) are recognized within 43 species, 6 fishes have undescribed subspecies, and 9 others are recognized as complexes of undescribed taxa. Extinct, endangered, threatened, or vulnerable status is recognized for 28 % (187 taxa) of southern freshwater and diadromous fishes. To date, 3 southern fishes are known to be extinct throughout their ranges, 2 are extirpated from the study region, and 2 others may be extinct. Of the extant southern fishes, 41 (6%) are regarded as endangered, 46 (7%) are regarded as threatened, and 101 (15%) are regarded as vulnerable. Five marine fishes that frequent fresh water are regarded as vulnerable. Our assessment represents a 75 % increase in jeopardized

L. Warren; Brooks M. Burr; Stephen J. Walsh; Henry L. Bart; Robert C; David A. Etnier; Byron J. Freeman; Bernard R. Kuhajda; Richard L. Mayden; Henry W. Robison; Stephen T. Ross; Wayne C. Starnes

392

Simon 1.0 Pattern Recognizer  

E-print Network

Shrivastava, Sarah Welch #12;Overview · Background information -transcription, translation -basic toggle witch · Current Progress #12;DNA transcription ·DNA is transcribed to RNA by RNA polymerase, a protein complex ·Transcription starts at the promoter region ·The operator region affects transcription #12;mRNA translation ·m

Petta, Jason

393

Phylogeography and conservation of impala and greater kudu.  

PubMed

The phylogeography of the bush habituated African bovid species impala (Aepyceros melampus) and greater kudu (Tragelaphus strepsiceros) is investigated using mitochondrial DNA (mtDNA) markers. Combined analysis of individual lineages, relationships and population genetics suggest a colonization process from Southern Africa toward Eastern regions in the greater kudu. Results are less clear for the impala, although remaining consistent with a similar pattern of historical dispersion. The study reveals a similar pattern, that is a marked divergence of lineages from South-western Africa relative to other regions. This pattern is opposed to previously published findings in other African bovid species. In the impala, the genetically isolated region is consistent with morphology because it is recognized as the subspecies A. m. petersi, the black-faced impala. In contrast, the similar split of South-western mitochondrial lineages was not expected in the greater kudu on the basis of morphology. Both species show a significant population genetic differentiation. Beyond their phylogeographical value, our results should raise conservation concerns about South-western populations of both species. The black-faced impala is categorized as vulnerable and our data show indications of hybridization with common impala A. m. melampus. The previously unrecognized genetic status of the South-western kudus could also imply conservation regulations. PMID:11298982

Nersting, L G; Arctander, P

2001-03-01

394

Chaotic itinerancy in coupled dynamical recognizers  

NASA Astrophysics Data System (ADS)

We argue that chaotic itinerancy in interaction between humans originates in the fluctuation of predictions provided by the nonconvergent nature of learning dynamics. A simple simulation model called the coupled dynamical recognizer is proposed to study this phenomenon. Daily cognitive phenomena provide many examples of chaotic itinerancy, such as turn taking in conversation. It is therefore an interesting problem to bridge two chaotic itinerant phenomena. A clue to solving this is the fluctuation of prediction, which can be translated as "hot prediction" in the context of cognitive theory. Hot prediction is simply defined as a prediction based on an unstable model. If this approach is correct, the present simulation will reveal some dynamic characteristics of cognitive interactions.

Ikegami, Takashi; Morimoto, Gentaro

2003-09-01

395

How proteins recognize the TATA box.  

PubMed

The crystal structure of a complex of human TATA-binding protein with TATA-sequence DNA has been solved, complementing earlier TBP/DNA analyses from Saccharomyces cerevisiae and Arabidopsis thaliana. Special insight into TATA box specificity is provided by considering the TBP/DNA complex, not as a protein molecule with bound DNA, but as a DNA duplex with a particularly large minor groove ligand. This point of view provides explanations for: (1) why T.A base-pairs are required rather than C.G; (2) why an alternation of T and A bases is needed; (3) how TBP recognizes the upstream and downstream ends of the TATA box in order to bind properly; and (4) why the second half of the TATA box can be more variable than the first. PMID:8757291

Juo, Z S; Chiu, T K; Leiberman, P M; Baikalov, I; Berk, A J; Dickerson, R E

1996-08-16

396

Obstacle detection by recognizing binary expansion patterns  

NASA Technical Reports Server (NTRS)

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.

Baram, Yoram; Barniv, Yair

1993-01-01

397

Recognizing Diogenes syndrome: a case report  

PubMed Central

Background Diogenes syndrome is a behavioural disorder characterized by domestic squalor, extreme self-neglect, hoarding, and lack of shame regarding one’s living condition. Patients may present due to a range of reasons. Recognizing these will allow for earlier management of this high-mortality condition. Case presentation 61-year Caucasian female known with bipolar 1 disorder presented with manic symptoms. She was very unkempt and foul smelling. After being admitted involuntarily, she requested that someone go to her home to feed her pets. Her house was filled with garbage, rotting food, and animal feces. She had no insight into any personal hygiene or public health problems. Conclusions Patients with Diogenes syndrome may be difficult to identify. Knowledge of the characteristics of Diogenes syndrome can aid in earlier recognition of such individuals, in order to decrease morbidity and mortality, and to improve public health. PMID:24886174

2014-01-01

398

Why should physicians recognize compulsive gambling?  

PubMed

Compulsive gambling, which was recently recognized as a separate and primary illness, is a chronic disease that has as one of its facets poor impulse control. The illness is likely to be encountered by primary care physicians who look for it. A complete history, focusing on the destructive impact of gambling on the person's ability to function, and physical examination, including a search for coexisting cardiovascular disease and alcohol or substance abuse, are recommended for these patients. Diagnostic criteria have been described and shown in table form, as have therapeutic options. This condition is treatable, and the earlier it is discovered, the less damage will be done to the psychological, emotional, social, and financial well-being of the patient. PMID:3671195

Daghestani, A N

1987-10-01

399

Neural nets for radio Morse code recognizing  

NASA Astrophysics Data System (ADS)

This paper proposes a neural network recognition system for hand keying Radio Morse codes. The system has been trained and tested on real world data recorded from amateur radio Morse codes. The overall recognizing process can be partitioned into 3 major parts, the preprocessing, the feature extracting, and the character decoding. The whole operation is able to be performed in real-time on a PC/486 system. Self-Organizing Maps are used intensively in the recognition system to adaptively learn the variation of the Morse code signal. The average performance of the recognition system has been achieved about 96.4% with a rejection rate of 6.5%. It is hoped that many of the techniques would be applicable to a wide range of DSP and recognition tasks.

Fu, Hsin-Chia; Lin, Y. Y.; Pao, Hsiao-Tien

1993-09-01

400

Position, rotation, and intensity invariant recognizing method  

DOEpatents

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.

Ochoa, Ellen (Pleasanton, CA); Schils, George F. (San Ramon, CA); Sweeney, Donald W. (Alamo, CA)

1989-01-01

401

How can we recognize continuous quality improvement?  

PubMed Central

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

Rubenstein, Lisa; Khodyakov, Dmitry; Hempel, Susanne; Danz, Margie; Salem-Schatz, Susanne; Foy, Robbie; O'Neill, Sean; Dalal, Siddhartha; Shekelle, Paul

2014-01-01

402

WWF: Ecoregion Conservation Plan for the Alps  

NSDL National Science Digital Library

As part of an effort to curtail the loss of global biodiversity, WWF recognized the Alps as one of more than 200 significant ecoregions in the world. Building on this recognition, the WWF European Alpine Programme recently published the _Ecoregion Conservation Plan for the Alps_. In addition to a description of the Alps ecoregion, the 62-page pdf document includes specific sections on The Root Causes of Biodiversity Loss, Threats, Ecoregion Conservation, Policy Framework, and Priority Conservation Areas. The document also provides an overview of the WWF European Alpine Programme, and a description of the WWF Ecoregion Action Plan.

403

Conservation Island  

NSDL National Science Digital Library

In this lesson, learners will understand the concepts behind endangered and extinct animals and develop their own conservation plan to save three endangered species. Each group or pair of learners will receive an animal profile and sketch it from the description that is given. Then, they will consider the animal’s habitat, behavior, diet, and threats as well as the people’s need for cities, agricultural areas, and tribal lands and share this information with other groups. After learners become familiar with their animal (considering both animal and human needs), they must choose what sections of land to conserve and give a short presentation. This lesson plan includes wrap-up suggestions, educator resources, extension ideas, and is standards-based.

California Academy of Sciences

2008-01-01

404

Status and potential of locally-managed marine areas in the Pacific Island Region: meeting nature conservation and sustainable livelihood targets through wide-spread implementation of LMMAs  

Microsoft Academic Search

The South Pacific has experienced a remarkable proliferation of Marine Managed Areas in the last decade. These protected areas, implemented by over 500 communities spanning 15 independent countries and territories represent a unique global achievement. The approaches being developed at national levels are built on a unique feature of the region, customary tenure and resource access, and make use of,

Hugh Govan

2009-01-01

405

Linkage Mapping in Sheep and Deer Identifies a Conserved Pecora Ruminant Linkage Group Orthologous to Two Regions of HSA16 and a Portion of HSA7Q  

Microsoft Academic Search

Two orthologous linkage groups have been mapped in sheep and deer. Seven loci have been mapped in deer, and 12 in sheep. The sheep linkage group is assigned to ovine chromosome 24. The linkage groups consist of loci from the short arm of human chromosome 16, spanning the region containing the human Batten disease locus, and from human chromosome 7.

Judith E. Broom; Michael L. Tate; Ken G. Dodds

1996-01-01

406

The bounty of minor lakes: the role of small satellite water bodies in evolution and conservation of fishes in the Lake Victoria Region, East Africa  

Microsoft Academic Search

The Lake Victoria Region (LVR) encompasses the large lakes Victoria, Kyoga, Edward, George and Kivu, as well as scores of small satellite lakes within the parent catchments. Taken as a whole, the LVR originally harbored a unique fish fauna that included in excess of 600 endemic species of cichlid fishes. As a result of human influence, including a commercial fishery

Wilson W. Mwanja; Audrey S. Armoudlian; Silvester B. Wandera; Les Kaufman; Lizhao Wu; Gregory C. Booton; Paul A. Fuerst

2001-01-01

407

Conservative management of type II and III odontoid fractures in the elderly at a regional spine centre: A prospective and retrospective cohort study.  

PubMed

Background. The optimal management of odontoid fractures in the elderly population is unclear and management of this group of patients is complicated by multiple co-morbidities. This study aimed to determine the outcomes after conservative management strategies were applied in this patient group. Methods. We carried out retrospective and prospective analyses of all patients with axial cervical spine injuries, at a single centre. We included patients aged over 60 years with type II and III odontoid fractures. Information was gathered on demographics, ASA grading-associated injuries and complications. The outcome measures were rates and type of union, pain and neurological functions, specifically ambulation. Results. Fifty-seven adult patients with a median age of 78 years (range 60-92 years) were included. There were 42 type II and 15 type III odontoid fractures. Three patients required surgical fixation due to displaced fractures, which could not be reduced with manual traction. Twenty-four (41%) patients were managed with a rigid pinned halo orthosis to obtain adequate reduction and immobilisation. The remaining 30 (53%) were managed in a hard cervical collar. Patients managed with a halo were significantly younger and had more associated injuries than patients managed in a collar (age: t-test = 4.05, p < 0.01, associated injuries: Chi-square = 4.38, p < 0.05). At a mean follow-up of 25 weeks, 87% of type II and 100% of type III fractures had achieved bony union or stable, fibrous non-union. There were no statistical differences in fracture type, follow-up or neurological outcomes between the halo and collar groups. However, overall more patients managed in a collar developed stable fibrous non-union than bony fusion (Fisher's exact test, p < 0.05), although this was not significant when analysed by each fracture type individually. A regression model was constructed and identified fracture type as the only independent predictor of time to union, with type III fractures healing faster than type II. Conclusions. High rates of bony union and stable fibrous non-union with a good functional outcome can be achieved in the elderly population sustaining type II or III odontoid fractures, when managed non-surgically. Halo orthosis may not offer any clear advantage over hard collar in this group. Close follow-up is needed for late complications and there must be a willingness to perform surgery if conservative measures fail. PMID:25232807

Patel, Amit; Zakaria, Rasheed; Al-Mahfoudh, Rafid; Clark, Simon; Barrett, Chris; Sarsam, Zaid; Pillay, Robin; Pigott, Tim Drummond; Wilby, Martin J

2014-09-18

408

New Zealand Plant Conservation Network  

NSDL National Science Digital Library

The New Zealand Plant Conservation Network (NZPCN) provides information about native plants and their conservation, focusing primarily on nationally threatened plants and plant communities that require conservation management for their continued survival. The NZPCN web site features a database and search tool for locating information on nationally threatened plant species and lists of species that are regionally uncommon. Users may search for threatened plants, bryophytes, fungi, naturalized (introduced) plants, or animal pests by common name, taxonomic name, conservation status, or family. The information includes taxonomic nomenclature, common name, geographic distribution and habitat, a description, images, conservation status, cultural use or importance, and other data. Other materials at the site include information on New Zealand native plants and threats to native plant life, an archive and bibliography of publications, event announcements and news articles, and information on the organization's membership.

409

Selling energy conservation.  

PubMed

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

Hinrichsen, D

1995-01-01

410

Identification of highly conserved regions in L-segment of Crimean–Congo hemorrhagic fever virus and immunoinformatic prediction about potential novel vaccine  

PubMed Central

Crimean–Congo hemorrhagic fever (CCHF) is a tick-borne zoonotic viral disease with a disease fatality rate between 15% and 70%. Despite the wide range of distribution, the virus (CCHFV) is basically endemic in Africa, Asia, eastern Europe, and the Middle East. Acute febrile illness associated with petechiae, disseminated intravascular coagulation, and multiple-organ failure are the main symptoms of the disease. With all these fatal effects, CCHFV is considered a huge threat as no successful therapeutic approach is currently available for the treatment of this disease. In the present study, we have used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of CCHFV. Both the T-cell and B-cell epitopes were assessed, and the epitope “DCSSTPPDR” was found to be the most potential one, with 100% conservancy among all the strains of CCHFV. The epitope was also found to interact with both type I and II major histocompatibility complex molecules and is considered nonallergenic as well. In vivo study of our proposed peptide is advised for novel universal vaccine production, which might be an effective path to prevent CCHF disease. PMID:25609983

Oany, Arafat Rahman; Ahmad, Shah Adil Ishtiyaq; Hossain, Mohammad Uzzal; Jyoti, Tahmina Pervin

2015-01-01

411

Identification of highly conserved regions in L-segment of Crimean-Congo hemorrhagic fever virus and immunoinformatic prediction about potential novel vaccine.  

PubMed

Crimean-Congo hemorrhagic fever (CCHF) is a tick-borne zoonotic viral disease with a disease fatality rate between 15% and 70%. Despite the wide range of distribution, the virus (CCHFV) is basically endemic in Africa, Asia, eastern Europe, and the Middle East. Acute febrile illness associated with petechiae, disseminated intravascular coagulation, and multiple-organ failure are the main symptoms of the disease. With all these fatal effects, CCHFV is considered a huge threat as no successful therapeutic approach is currently available for the treatment of this disease. In the present study, we have used the immunoinformatics approach to design a potential epitope-based vaccine against the RNA-dependent RNA polymerase-L of CCHFV. Both the T-cell and B-cell epitopes were assessed, and the epitope "DCSSTPPDR" was found to be the most potential one, with 100% conservancy among all the strains of CCHFV. The epitope was also found to interact with both type I and II major histocompatibility complex molecules and is considered nonallergenic as well. In vivo study of our proposed peptide is advised for novel universal vaccine production, which might be an effective path to prevent CCHF disease. PMID:25609983

Oany, Arafat Rahman; Ahmad, Shah Adil Ishtiyaq; Hossain, Mohammad Uzzal; Jyoti, Tahmina Pervin

2015-01-01

412

A Conserved Family of Prolyl4-Hydroxylases That Modify HIF  

Microsoft Academic Search

Mammalian cells respond to changes in oxygen availability through a conserved pathway that is regulated by the hypoxia-inducible factor (HIF). The alpha subunit of HIF is targeted for degradation under normoxic conditions by a ubiquitin-ligase complex that recognizes a hydroxylated proline residue in HIF. We identified a conserved family of HIF prolyl hydoxylase (HPH) enzymes that appear to be responsible

Richard K. Bruick; Steven L. McKnight

2001-01-01

413

Allocating Conservation Resources under the Endangered Species Act  

Microsoft Academic Search

The necessity to develop a priority system to guide the allocation of resources to the conservation of endangered species is widely recognized. The economic theory of biodiversity has established a framework to do so, and has identified priority criteria that should be considered when making conservation decisions. This paper uses a random effects ordered probit model of endangered species recovery

Christian Langpap; Joe Kerkvliet

2007-01-01

414

Conflict between energy conservation and water pollution control standards  

Microsoft Academic Search

The potential conflict in national needs for both energy conservation and water pollution control is indicated. Meeting broader obligations in reconciling these apparent differences has failed. Major contributions to energy conservation efforts needed today could be made without giving up any important pollution control goals. Hopefully, state and Federal regulatory agencies soon will recognize their obligations in this respect and

Lamb

1980-01-01

415

Documenting Biogeographical Patterns of African Timber Species Using Herbarium Records: A Conservation Perspective Based on Native Trees from Angola  

PubMed Central

In many tropical regions the development of informed conservation strategies is hindered by a dearth of biodiversity information. Biological collections can help to overcome this problem, by providing baseline information to guide research and conservation efforts. This study focuses on the timber trees of Angola, combining herbarium (2670 records) and bibliographic data to identify the main timber species, document biogeographic patterns and identify conservation priorities. The study recognized 18 key species, most of which are threatened or near-threatened globally, or lack formal conservation assessments. Biogeographical analysis reveals three groups of species associated with the enclave of Cabinda and northwest Angola, which occur primarily in Guineo-Congolian rainforests, and evergreen forests and woodlands. The fourth group is widespread across the country, and is mostly associated with dry forests. There is little correspondence between the spatial pattern of species groups and the ecoregions adopted by WWF, suggesting that these may not provide an adequate basis for conservation planning for Angolan timber trees. Eight of the species evaluated should be given high conservation priority since they are of global conservation concern, they have very restricted distributions in Angola, their historical collection localities are largely outside protected areas and they may be under increasing logging pressure. High conservation priority was also attributed to another three species that have a large proportion of their global range concentrated in Angola and that occur in dry forests where deforestation rates are high. Our results suggest that timber tree species in Angola may be under increasing risk, thus calling for efforts to promote their conservation and sustainable exploitation. The study also highlights the importance of studying historic herbarium collections in poorly explored regions of the tropics, though new field surveys remain a priority to update historical information. PMID:25061858

Romeiras, Maria M.; Figueira, Rui; Duarte, Maria Cristina; Beja, Pedro; Darbyshire, Iain

2014-01-01

416

Conservation Planning for Ecosystem Services  

Microsoft Academic Search

Despite increasing attention to the human dimension of conservation projects, a rigorous, systematic methodology for planning for ecosystem services has not been developed. This is in part because flows of ecosystem services remain poorly characterized at local-to-regional scales, and their protection has not generally been made a priority. We used a spatially explicit conservation planning framework to explore the trade-offs

Kai M. A Chan; M. Rebecca Shaw; David R Cameron; Emma C Underwood; Gretchen C Daily

2006-01-01

417

A Single SNP in an Evolutionary Conserved Region within Intron 86 of the HERC2 Gene Determines Human Blue-Brown Eye Color  

Microsoft Academic Search

We have previously demonstrated that haplotypes of three single nucleotide polymorphisms (SNPs) within the first intron of the OCA2 gene are extremely strongly associated with variation in human eye color. In the present work, we describe additional fine association mappingof eyecolor SNPsin theintergenic region upstream of OCA2and withinthe neighboringHERC2 (hect domainand RLD2) gene. We screened an additional 92 SNPs in

Richard A. Sturm; David L. Duffy; Zhen Zhen Zhao; Fabio P. N. Leite; Mitchell S. Stark; Nicholas G. Martin; Grant W. Montgomery

2008-01-01

418

Position and sequence conservation in Amniota of polymorphic enhancer HS1.2 within the palindrome of IgH 3'Regulatory Region  

Microsoft Academic Search

Background  The Immunoglobulin heavy chain (IgH) 3' Regulatory Region (3'RR), located at the 3' of the constant alpha gene, plays a crucial\\u000a role in immunoglobulin production. In humans, there are 2 copies of the 3'RR, each composed of 4 main elements: 3 enhancers\\u000a and a 20 bp tandem repeat. The single mouse 3'RR differs from the two human ones for the

Pietro D’Addabbo; Moira Scascitelli; Vincenzo Giambra; Mariano Rocchi; Domenico Frezza

2011-01-01

419

The nitrogen-fixation island insertion site is conserved in diazotrophic Pseudomonas stutzeri and Pseudomonas sp. isolated from distal and close geographical regions.  

PubMed

The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution. PMID:25251496

Venieraki, Anastasia; Dimou, Maria; Vezyri, Eleni; Vamvakas, Alexandros; Katinaki, Pagona-Artemis; Chatzipavlidis, Iordanis; Tampakaki, Anastasia; Katinakis, Panagiotis

2014-01-01

420

The Nitrogen-Fixation Island Insertion Site Is Conserved in Diazotrophic Pseudomonas stutzeri and Pseudomonas sp. Isolated from Distal and Close Geographical Regions  

PubMed Central

The presence of nitrogen fixers within the genus Pseudomonas has been established and so far most isolated strains are phylogenetically affiliated to Pseudomonas stutzeri. A gene ortholog neighborhood analysis of the nitrogen fixation island (NFI) in four diazotrophic P. stutzeri strains and Pseudomonas azotifigens revealed that all are flanked by genes coding for cobalamin synthase (cobS) and glutathione peroxidise (gshP). The putative NFIs lack all the features characterizing a mobilizable genomic island. Nevertheless, bioinformatic analysis P. stutzeri DSM 4166 NFI demonstrated the presence of short inverted and/or direct repeats within both flanking regions. The other P. stutzeri strains carry only one set of repeats. The genetic diversity of eleven diazotrophic Pseudomonas isolates was also investigated. Multilocus sequence typing grouped nine isolates along with P. stutzeri and two isolates are grouped in a separate clade. A Rep-PCR fingerprinting analysis grouped the eleven isolates into four distinct genotypes. We also provided evidence that the putative NFI in our diazotrophic Pseudomonas isolates is flanked by cobS and gshP genes. Furthermore, we demonstrated that the putative NFI of Pseudomonas sp. Gr65 is flanked by inverted repeats identical to those found in P. stutzeri DSM 4166 and while the other P. stutzeri isolates harbor the repeats located in the intergenic region between cobS and glutaredoxin genes as in the case of P. stutzeri A1501. Taken together these data suggest that all putative NFIs of diazotrophic Pseudomonas isolates are anchored in an intergenic region between cobS and gshP genes and their flanking regions are designated by distinct repeats patterns. Moreover, the presence of almost identical NFIs in diazotrophic Pseudomonas strains isolated from distal geographical locations around the world suggested that this horizontal gene transfer event may have taken place early in the evolution. PMID:25251496

Venieraki, Anastasia; Dimou, Maria; Vezyri, Eleni; Vamvakas, Alexandros; Katinaki, Pagona-Artemis; Chatzipavlidis, Iordanis; Tampakaki, Anastasia; Katinakis, Panagiotis

2014-01-01

421

37 CFR 11.15 - Refusal to recognize a practitioner.  

Code of Federal Regulations, 2013 CFR

...2013-07-01 false Refusal to recognize a practitioner. 11.15 Section 11.15 Patents, Trademarks...Non-Patent Law § 11.15 Refusal to recognize a practitioner. Any practitioner authorized to appear before the Office...

2013-07-01

422

37 CFR 11.15 - Refusal to recognize a practitioner.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 false Refusal to recognize a practitioner. 11.15 Section 11.15 Patents, Trademarks...Non-Patent Law § 11.15 Refusal to recognize a practitioner. Any practitioner authorized to appear before the Office...

2010-07-01

423

37 CFR 11.15 - Refusal to recognize a practitioner.  

Code of Federal Regulations, 2012 CFR

...2012-07-01 false Refusal to recognize a practitioner. 11.15 Section 11.15 Patents, Trademarks...Non-Patent Law § 11.15 Refusal to recognize a practitioner. Any practitioner authorized to appear before the Office...

2012-07-01

424

37 CFR 11.15 - Refusal to recognize a practitioner.  

Code of Federal Regulations, 2014 CFR

...2014-07-01 false Refusal to recognize a practitioner. 11.15 Section 11.15 Patents, Trademarks...Non-Patent Law § 11.15 Refusal to recognize a practitioner. Any practitioner authorized to appear before the Office...

2014-07-01

425

37 CFR 11.15 - Refusal to recognize a practitioner.  

Code of Federal Regulations, 2011 CFR

...2011-07-01 false Refusal to recognize a practitioner. 11.15 Section 11.15 Patents, Trademarks...Non-Patent Law § 11.15 Refusal to recognize a practitioner. Any practitioner authorized to appear before the Office...

2011-07-01

426

76 FR 10500 - Nationally Recognized Testing Laboratories Fees  

Federal Register 2010, 2011, 2012, 2013, 2014

...Nationally Recognized Testing Laboratories Fees AGENCY: Occupational Safety and Health...the approach it uses for calculating the fees the Agency charges Nationally Recognized...and also is requiring prepayment of these fees. This adjustment increases the...

2011-02-25

427

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)

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