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1

Vaccine-elicited human T cells recognizing conserved protein regions inhibit HIV-1.  

PubMed

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

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

2014-02-01

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

Recognizing Objects in Range Data Using Regional Point Descriptors  

Microsoft Academic Search

Recognition of three dimensional (3D) objects in noisy and cluttered scenes is a challenging problem in 3D computer vision. One approach that has been successful in past research is the regional shape descriptor. In this paper, we introduce two new regional shape descrip- tors: 3D shape contexts and harmonic shape contexts. We evaluate the performance of these descriptors on the

Andrea Frome; Daniel Huber; Ravi Kolluri; Thomas Bülow; Jitendra Malik

2004-01-01

5

Human brain regions involved in recognizing environmental sounds.  

PubMed

To identify the brain regions preferentially involved in environmental sound recognition (comprising portions of a putative auditory 'what' pathway), we collected functional imaging data while listeners attended to a wide range of sounds, including those produced by tools, animals, liquids and dropped objects. These recognizable sounds, in contrast to unrecognizable, temporally reversed control sounds, evoked activity in a distributed network of brain regions previously associated with semantic processing, located predominantly in the left hemisphere, but also included strong bilateral activity in posterior portions of the middle temporal gyri (pMTG). Comparisons with earlier studies suggest that these bilateral pMTG foci partially overlap cortex implicated in high-level visual processing of complex biological motion and recognition of tools and other artifacts. We propose that the pMTG foci process multimodal (or supramodal) information about objects and object-associated motion, and that this may represent 'action' knowledge that can be recruited for purposes of recognition of familiar environmental sound-sources. These data also provide a functional and anatomical explanation for the symptoms of pure auditory agnosia for environmental sounds reported in human lesion studies. PMID:15166097

Lewis, James W; Wightman, Frederic L; Brefczynski, Julie A; Phinney, Raymond E; Binder, Jeffrey R; DeYoe, Edgar A

2004-09-01

6

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

7

Accomplishments of the Alaska Region's Habitat Conservation Division  

E-print Network

Fisheries Science Center; NOAA Fisheries Office of Habitat Conservation; NOAA General Counsel; and NOAAAccomplishments of the Alaska Region's Habitat Conservation Division in Fiscal Year 2006 This report provides highlights of Habitat Conservation Division (HCD) activities in support

8

76 FR 28954 - International Conservation and Management Measures Recognized by the United States  

Federal Register 2010, 2011, 2012, 2013

...conservation and management measures, as well as specify the permitting and vessel...Organization--NASCO); Convention on Future Multilateral Cooperation in the Northwest Atlantic...Tuna--CCSBT); Convention on Future Multilateral Cooperation in North-East...

2011-05-19

9

Regional Urban Planning for Energy Conservation: Alternative Approaches.  

ERIC Educational Resources Information Center

Discusses the role of urban and regional planners in redesigning land use patterns which reinforce energy conservation while preserving satisfying living conditions. A model for evaluating energy conservation planning alternatives for Perth, Australia is described. (AM)

Manohar, Shri

1982-01-01

10

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

11

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

12

Structural Constraints Imposed by the Conserved Fusion Peptide on the HIV-1 gp41 Epitope Recognized by the Broadly Neutralizing Antibody 2F5  

E-print Network

Structural Constraints Imposed by the Conserved Fusion Peptide on the HIV-1 gp41 Epitope RecognizedVised Manuscript ReceiVed: August 6, 2009 The HIV-1 gp41 epitope recognized by the broadly neutralizing 2F5 mimicking the linear 2F5 epitope (2F5ep) are however intrinsically disordered, while the structural

Pompeu Fabra, Universitat

13

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

14

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

15

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.

2006-04-04

16

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

17

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

18

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

19

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

20

Plectasin, First Animal Toxin-Like Fungal Defensin Blocking Potassium Channels through Recognizing Channel Pore Region  

PubMed Central

The potassium channels were recently found to be inhibited by animal toxin-like human ?-defensin 2 (hBD2), the first defensin blocker of potassium channels. Whether there are other defensin blockers from different organisms remains an open question. Here, we reported the potassium channel-blocking plectasin, the first defensin blocker from a fungus. Based on the similar cysteine-stabilized alpha-beta (CS??) structure between plectasin and scorpion toxins acting on potassium channels, we found that plectasin could dose-dependently block Kv1.3 channel currents through electrophysiological experiments. Besides Kv1.3 channel, plectasin could less inhibit Kv1.1, Kv1.2, IKCa, SKCa3, hERG and KCNQ channels at the concentration of 1 ??. Using mutagenesis and channel activation experiments, we found that outer pore region of Kv1.3 channel was the binding site of plectasin, which is similar to the interacting site of Kv1.3 channel recognized by animal toxin blockers. Together, these findings not only highlight the novel function of plectasin as a potassium channel inhibitor, but also imply that defensins from different organisms functionally evolve to be a novel kind of potassium channel inhibitors. PMID:25568977

Xiang, Fang; Xie, Zili; Feng, Jing; Yang, Weishan; Cao, Zhijian; Li, Wenxin; Chen, Zongyun; Wu, Yingliang

2015-01-01

21

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

22

Broadly Reactive Human CD8 T Cells that Recognize an Epitope Conserved between VZV, HSV and EBV  

PubMed Central

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

2014-01-01

23

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. #12;ii APPROVAL #12;iii ABSTRACT Instances of water scarcity are recurring with greater frequency in urban areas around the globe, yet per capita water consumption continues to increase. Faced

24

Informing the Development of a Regional Water Conservation Plan for the Roaring Fork Watershed.  

E-print Network

??Regional planning efforts have become increasingly prevalent in resource management initiatives, particularly in water conservation planning. This report informs the development of a water conservation… (more)

Steeland, Kara

2014-01-01

25

Non-arginine-aspartate (non-RD) kinases are associated with innate immune receptors that recognize conserved microbial signatures  

Technology Transfer Automated Retrieval System (TEKTRAN)

An important question in the field of plant-pathogen interactions is how the detection of pathogens is converted into an effective immune response. In recent years, substantial insight has been gained into the identities of both the plant receptors and the microbial molecules they recognize. Likew...

26

Regional nodal irradiation in the conservative treatment of breast cancer  

SciTech Connect

At this institution conservative treatment of breast cancer was begun in the 1960's. The following analysis represents our experience through 1984 with specific reference to the management of the regional lymph nodes. A total of 432 patients with clinical stage I and II breast cancer were treated between 1962 and 1984 with lumpectomy and radiation therapy. The breast was treated with tangential fields to a median dose of 4800 cGy and electron conedown to a total tumor bed dose of 6400 cGy. Axillary dissection was not routinely performed, particularly in the earlier years. More recently, axillary dissection has been used with increasing frequency if it was felt that the results of the dissection would influence systemic treatment. One hundred eighty-seven patients (43%) underwent axillary dissection and routinely received regional nodal irradiation to the internal mammary and supraclavicular lymph nodes. Two hundred forty-five patients (57%) did not undergo axillary dissection and routinely received regional nodal irradiation to the internal mammary, supraclavicular, and entire axillary regions to a total median dose of 4600 cGy. As of May 1989 with a median follow-up of 7.5 years, there have been a total of 12 nodal failures for an actuarial nodal control rate of 97% at 5 years and 96% at 10 years. The actuarial 5-year regional nodal control rate was the same for both the group of patients receiving regional RT alone without axillary dissection and the group of patients receiving axillary dissection and supraclavicular/internal mammary radiation. There has been minimal morbidity associated with this treatment policy. We conclude that regional nodal irradiation, with or without axillary dissection, results in a high rate of regional nodal control and minimal treatment morbidity in patients undergoing conservative treatment of early stage breast cancer.

Haffty, B.G.; Fischer, D.; Fischer, J.J. (Yale Univ. School of Medicine, New Haven, CT (USA))

1990-10-01

27

Induction of arthritis in BALB/c mice by cartilage link protein: involvement of distinct regions recognized by T and B lymphocytes.  

PubMed

Both type II collagen and the proteoglycan aggrecan are capable of inducing an erosive inflammatory polyarthritis in mice. In this study we provide the first demonstration that link protein (LP), purified from bovine cartilage, can produce a persistent, erosive, inflammatory polyarthritis when injected repeatedly intraperitoneally into BALB/c mice. We discovered a single T-cell epitope, located within residues 266 to 290 of bovine LP (NDGAQIAKVGQIFAAWKLLGYDRCD), which is recognized by bovine LP-specific T lymphocytes. We also identified three immunogenic regions in bovine LP that contain epitopes recognized by antibodies in hyperimmunized sera. One of these B-cell regions is found in the most species-variable domain of LP (residues 1 to 36), whereas the other epitopes are located in the most conserved regions (residues 186 to 230 and 286 to 310). The latter two regions contain an AGWLSDGSVQYP motif shared by the G1 globulin domain of aggrecan core protein, versican, neurocan, glial hyaluronan-binding protein, and the hyaluronan receptor CD44. Our data reveal that the induction of arthritis is associated with antibody reactivities to B-cell epitopes located at residues 1 to 19. Together, these observations show that another cartilage protein, LP, like type II collagen and the proteoglycan aggrecan, is capable of inducing an erosive inflammatory arthritis in mice and that the immunity to LP involves recognition of both T- and B-cell epitopes. This immunity may be of importance in the pathogenesis of inflammatory joint diseases, such as juvenile rheumatoid arthritis, in which cellular immunity to LP has been demonstrated. PMID:9777960

Zhang, Y; Guerassimov, A; Leroux, J Y; Cartman, A; Webber, C; Lalic, R; de Miguel, E; Rosenberg, L C; Poole, A R

1998-10-01

28

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

29

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

30

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.

31

Determination and application of immunodominant regions of SARS coronavirus spike and nucleocapsid proteins recognized by sera from different animal species.  

PubMed

Knowledge of immunodominant regions in major viral antigens is important for rational design of effective vaccines and diagnostic tests. Although there have been many reports of such work done for SARS-CoV, these were mainly focused on the immune responses of humans and mice. In this study, we aim to search for and compare immunodominant regions of the spike (S) and nucleocapsid (N) proteins which are recognized by sera from different animal species, including mouse, rat, rabbit, civet, pig and horse. Twelve overlapping recombinant protein fragments were produced in Escherichia coli, six each for the S and N proteins, which covered the entire coding region of the two proteins. Using a membrane-strip based Western blot approach, the reactivity of each antigen fragment against a panel of animal sera was determined. Immunodominant regions containing linear epitopes, which reacted with sera from all the species tested, were identified for both proteins. The S3 fragment (aa 402-622) and the N4 fragment (aa 220-336) were the most immunodominant among the six S and N fragments, respectively. Antibodies raised against the S3 fragment were able to block the binding of a panel of S-specific monoclonal antibodies (mAb) to SARS-CoV in ELISA, further demonstrating the immunodominance of this region. Based on these findings, one-step competition ELISAs were established which were able to detect SARS-CoV antibodies from human and at least seven different animal species. Considering that a large number of animal species are known to be susceptible to SARS-CoV, these assays will be a useful tool to trace the origin and transmission of SARS-CoV and to minimise the risk of animal-to-human transmission. PMID:18191140

Yu, Meng; Stevens, Vicky; Berry, Jody D; Crameri, Gary; McEachern, Jennifer; Tu, Changchun; Shi, Zhengli; Liang, Guodong; Weingartl, Hana; Cardosa, Jane; Eaton, Bryan T; Wang, Lin-Fa

2008-02-29

32

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

33

Regional Management Units for Marine Turtles: A Novel Framework for Prioritizing Conservation and Research  

E-print Network

Regional Management Units for Marine Turtles: A Novel Framework for Prioritizing Conservation for Conservation of Nature (IUCN)/SSC Marine Turtle Specialist Group ­ Burning Issues Working Group, Arlington, Virginia, United States of America, 2 Global Marine Division, Conservation International, Arlington

Florida, University of

34

Restricted immunoglobulin variable region gene usage by normal Ly-1 (CD5+) B cells that recognize phosphatidyl choline  

PubMed Central

5-15% of lymphocytes in the peritoneums of normal adult B10.H-2aH- 4bp/Wts (2a4b) mice are CD5+ (Ly-1) B cells that recognize phosphatidyl choline (PtC), a phospholipid component of all mammalian cells. We produced a set of IgM-secreting hybridomas from the peritoneal cells of normal, adult 2a4b mice. We found that this set of hybridomas shows a similarly high frequency of antibodies specific for PtC (21 of 86) that also react with bromelain-treated mouse erythrocytes. Restriction fragment analysis of Ig gene rearrangements and analysis of expressed Ig idiotypes reveal that these cells use a restricted set of variable region genes to generate the PtC-specific antibodies. The Ig genes used by the PtC-specific hybridomas appear to be the same as those found in the PtC-specific Ly-1 B cell lymphomas, CH27 and CH34. PMID:2499651

1989-01-01

35

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...

36

MAPPING SPATIAL ATTRIBUTES FOR CONSERVATION AND TOURISM PLANNING, OTWAYS REGION VICTORIA  

E-print Network

MAPPING SPATIAL ATTRIBUTES FOR CONSERVATION AND TOURISM PLANNING, OTWAYS REGION VICTORIA SURVEY-in-Publication Brown, Greg. Mapping spatial attributes for conservation and tourism planning, Otways region, Victoria : a survey of residents and visitors. Bibliography. ISBN 1 920704 76 0. 1. Ecotourism - Victoria - Otway

Brown, Gregory G.

37

Cysteine-poor region-specific EpCAM monoclonal antibody recognizing native tumor cells with high sensitivity.  

PubMed

EpCAM is a ?40?kDa transmembrane glycoprotein. EpCAM overexpression is a popular trait of almost all carcinomas and is considered as a targeted cancer immunotherapy as well as a practical marker for circulating tumor cells (CTC). Its extracellular part (EpEx) consists of an N-terminal EGF-like (EGF) domain, a TY-like (TY) domain, and an uncharacterized cysteine-poor (CP) region. Most commercially available murine monoclonal antibodies (MAbs) to EpCAM, such as HEA 125 and VU-1D9, bind to the small EGF domain. In a previous study, we introduced iCeap (intact CTC enumeration and analysis procedure), keeping cellular integrity during the whole process. Unlike the CellSearch(®) CTC Test, iCeap enables downstream molecular analysis from detected CTC. Use of two EpCAM MAbs, one for immunomagnetic enrichment of rare CTC from blood samples and the other for labeling, is a concept of iCeap while an ideal MAb pair has not been found. In order to obtain a better MAb that recognizes a part of EpEx as different from EGF domain, we established a mouse hybridoma clone producing a new EpCAM MAb, KIJY2. Fluorophore-conjugated KIJY2 and HEA 125-FITC can concomitantly stain the tumor cell line LNCaP within indistinguishable cellular compartments (i.e., the cell surface). Epitope mapping reveals that KIJY2 binds to the CP region. The epitope for KIJY2 is sensitive to paraformaldehyde fixation, but native cells including MCF-7 (EpCAM high-expressing cell line) and PC-3 (EpCAM low and heterogeneously expressing cell line) are detected by KIJY2. In particular, KIJY2 detects all PC-3 cells regardless of their EpCAM expression levels. Therefore, KIJY2 and an EGF domain-directed MAb are a promising pair to form the EpCAM sandwich in iCeap. We demonstrate that KIJY2 incorporated into iCeap yielded favorable results in spike-in experiments of MCF-7 and PC-3. PMID:23607341

Takao, Masashi; Nagai, Yutaka; Torii, Tokiji

2013-04-01

38

Conservation of Babesia bovis Small Heat Shock Protein (Hsp20) among Strains and Definition of T Helper Cell Epitopes Recognized by Cattle with Diverse Major Histocompatibility Complex Class II Haplotypes  

PubMed Central

Babesia bovis small heat shock protein (Hsp20) is recognized by CD4+ T lymphocytes from cattle that have recovered from infection and are immune to challenge. This candidate vaccine antigen is related to a protective antigen of Toxoplasma gondii, Hsp30/bag1, and both are members of the ?-crystallin family of proteins that can serve as molecular chaperones. In the present study, immunofluorescence microscopy determined that Hsp20 is expressed intracellularly in all merozoites. Importantly, Hsp20 is also expressed by tick larval stages, including sporozoites, so that natural tick-transmitted infection could boost a vaccine-induced response. The predicted amino acid sequence of Hsp20 from merozoites is completely conserved among different B. bovis strains. To define the location of CD4+ T-cell epitopes for inclusion in a multiepitope peptide or minigene vaccine construct, truncated recombinant Hsp20 proteins and overlapping peptides were tested for their ability to stimulate T cells from immune cattle. Both amino-terminal (amino acids [aa] 1 to 105) and carboxy-terminal (aa 48 to 177) regions were immunogenic for the majority of cattle in the study, stimulating strong proliferation and IFN-? production. T-cell lines from all individuals with distinct DRB3 haplotypes responded to aa 11 to 62 of Hsp20, which contained one or more immunodominant epitopes for each animal. One epitope, DEQTGLPIKS (aa 17 to 26), was identified by T-cell clones. The presence of strain-conserved T helper cell epitopes in aa 11 to 62 of the ubiquitously expressed Hsp20 that are presented by major histocompatibility complex class II molecules represented broadly in the Holstein breed supports the inclusion of this region in vaccine constructs to be tested in cattle. PMID:14742557

Norimine, Junzo; Mosqueda, Juan; Palmer, Guy H.; Lewin, Harris A.; Brown, Wendy C.

2004-01-01

39

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...

40

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.

Robertson, William C.

2002-01-01

41

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

42

BIOPROSPECTOR: DISCOVERING CONSERVED DNA MOTIFS IN UPSTREAM REGULATORY REGIONS  

E-print Network

610, Harvard University Cambridge MA 02138 (jliu@stat.stanford.edu) The development of genome these modifications greatly improve the performance of the program. Although testing and development are still step is to examine the upstream region of genes in the same expression pattern group and look

Liu, Xiaole Shirley

43

Sequence conservation at human and mouse orthologous common fragile regions,  

E-print Network

orthologous to the fragile epicenter of FRA3B, and determined the Fhit deletion break points in a mouse kidney). Deletions and structural rearrangements in FRA3B have been observed in a large fraction of tumor types. The tumor sup- presser gene FHIT encompasses the FRA3B fragile region and is altered by deletion

Miller, Webb

44

Cloned cytotoxic T lymphocytes that recognize an I-A region product in the context of a class I antigen.  

PubMed

Cloned CTLs QM3 and QM7 isolated from a bulk CTL line B10.QBR anti-B10.MBR recognized a combination of the H-2Kb molecule and an I-Ak subregion gene product. Such a combinatorial specificity was revealed by complementation of the target antigen in F1 animals between two negative parental strains carrying H-2Kb and I-Ak, respectively. We confirmed the involvement of the H-2Kb molecule by blocking killing with anti-Kb mAb and failure of certain mutant H-2Kb genes to complement with I-Ak to generate the determinant in F1 animals. Although the nature of the I-Ak subregion gene product is not definitive, there was a correlation between the expression of Ia antigens on the cell surface and susceptibility of the cells to lysis by these CTLs, suggesting that it is the classical I-Ak class II antigen. PMID:3485175

Shinohara, N; Bluestone, J A; Sachs, D H

1986-04-01

45

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

the protection of these ecosystems on which we all depend on both small and large scales. Moreover, sea turtlesStrategy 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

Prestwich, Ken

46

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

PubMed Central

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

Ando, Amy W.; Mallory, Mindy L.

2012-01-01

47

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.

48

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

49

Achieving conservation when opportunity costs are high: optimizing reserve design in Alberta's oil sands region.  

PubMed

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

50

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

PubMed Central

The human beta-globin locus activation region (LAR) comprises four erythroid-specific DNase I hypersensitive sites (I-IV) thought to be largely responsible for activating the beta-globin domain and facilitating high-level erythroid-specific globin gene expression. We identified the goat beta-globin LAR, determined 10.2 kilobases of its sequence, and demonstrated its function in transgenic mice. The human and goat LARs share 6.5 kilobases of homologous sequences that are as highly conserved as the epsilon-globin gene promoters. Furthermore, the overall spatial organization of the two LARs has been conserved. These results suggest that the functionally relevant regions of the LAR are large and that in addition to their primary structure, the spatial relationship of the conserved elements is important for LAR function. Images PMID:2236034

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

1990-01-01

51

Conservation area networks for the Indian region: Systematic methods and future prospects  

Microsoft Academic Search

Abstract A framework for systematic conservation planning for biodiversity is presented with an emphasis onthe,Indian context. The use of this framework,is then illustrated by the,analysis of two,data 25 sets from the Indian region consisting of environmental and physical parameters that serve as surrogates for biodiversity. The first data set included the entire region ,while the second was limited to the

Sahotra Sarkar; Michael Mayfield; Susan Cameron; Trevon Fuller; Justin Garson

2008-01-01

52

A Protocol for Wildlife Conservation Planning in an Afforestable Montane Grassland Region  

Microsoft Academic Search

The grassland biome is the biome most transformed by human activity in South Africa. At least thirteen percent of the biome is suitable for pine afforestation. There is a need for conservation evaluations before large-scale commercial afforestation to determine which areas are required to maintain biological diversity in the afforestable region and which areas can be planted. This paper gives

A. J. Armstrong; H. J. van Hensbergen

1997-01-01

53

Land use change in a Mediterranean metropolitan region and its periphery: assessment of conservation policies through  

E-print Network

Land use change in a Mediterranean metropolitan region and its periphery: assessment biodiversity which is linked in part to traditional land use practices and which is currently threatened by global change. The effectiveness of one-decade conservation policies against land use changes

Bravo de la Parra, Rafael

54

Habitat Conservation Division Protection of Deep Sea Corals in the Greater Atlantic Region  

E-print Network

Unlike the tropical corals that we are most familiar with that grow and form reefs in shallow, warm deepsea corals from physical damage from fishing gear. Previously existing provisions of the Act were Habitat Conservation Division Protection of Deep Sea Corals in the Greater Atlantic Region

55

Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands  

E-print Network

, §Computer Science and Artificial Intelligence Laboratory, and Department of Biology, Massachusetts InstituteSystematic discovery of regulatory motifs in conserved regions of the human genome, including of Technology and Harvard Medical School, Cambridge, MA 02142; Division of Health Sciences and Technology

Kellis, Manolis

56

Conservation of crop diversity for sustainable landscape development in the mountains of the Indian Himalayan region  

Microsoft Academic Search

Purpose – The purpose of this paper is to emphasize the conservation and management of crop diversity in traditional agro-ecosystems as a crucial component for sustainable landscape development in the mountains of the Indian Himalayan region. The results indicate that mountain farming has the potential to produce good output from a low input system where farmers still use local resources

Sunil Nautiyal; Harald Kaechele

2007-01-01

57

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

58

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

59

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

60

Rapid profiling of the antigen regions recognized by serum antibodies using massively parallel sequencing of antigen-specific libraries.  

PubMed

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

61

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

62

IDENTIFICATION OF HLA-A2 RESTRICTED T-CELL EPITOPES WITHIN THE CONSERVED REGION OF THE IMMUNOGLOBULIN G HEAVY-  

E-print Network

IDENTIFICATION OF HLA-A2 RESTRICTED T-CELL EPITOPES WITHIN THE CONSERVED REGION : 10.1111/j.1600-0609.2008.01076.x #12;IGG HEAVY-CHAIN T-CELL EPITOPE 1. ABSTRACT Objective: The aim of this study is the identification of HLA-A2 restricted T-cell epitopes in the conserved region

Paris-Sud XI, Université de

63

Extensive conservation of alpha and beta chains of the human T-cell antigen receptor recognizing HLA-A2 and influenza A matrix peptide.  

PubMed Central

The major histocompatibility complex class I molecule HLA-A2.1 presents the influenza A virus matrix peptide 57-68 to cytotoxic T lymphocytes in all individuals with this common HLA type and is among the most thoroughly studied immune responses in humans. We have studied the T-cell receptor (TCR) heterogeneity of T cells specific for HLA-A2 and influenza A matrix peptide using the polymerase chain reaction. The usage of V alpha and V beta sequences seen on these T cells is remarkably conserved as are certain junctional sequences associated with alpha and beta chains. Furthermore, two unrelated HLA-A2 individuals have a similar pattern of TCR usage, implying that this is a predominant response in HLA-A2 populations. Analysis in one individual showed that the conserved TCR V alpha and V beta genes are minor members of the peripheral blood TCR repertoire. The sequences provide important information on the TCR necessary for the final structural analysis of this ternary complex. PMID:1833769

Moss, P A; Moots, R J; Rosenberg, W M; Rowland-Jones, S J; Bodmer, H C; McMichael, A J; Bell, J I

1991-01-01

64

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

ERIC Educational Resources Information Center

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

Carr, Allen Terry

1996-01-01

65

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

66

Functional Analyses of a Conserved Region in Glucosyltransferases of Streptococcus mutans  

Microsoft Academic Search

Streptococcus mutans glucosyltransferases (GTFs; GtfB, -C, and -D) synthesize water-soluble and -insoluble glucan polymers from sucrose. We have identified previously a conserved region of 19 amino acids (aa) (Gtf-P1; aa 409 to 427 of GtfB and aa 435 to 453 of GtfC) which is functionally important for both enzymatic activity and bacterial adherence. Monoclonal antibodies directed against Gtf-P1 selectively inhibited

JEAN-SAN CHIA; CZAU-SIUNG YANG; JEN-YANG CHEN

1998-01-01

67

Transcriptional control by adenovirus E1A conserved region 3 via p300\\/CBP  

Microsoft Academic Search

The human adenovirus type 5 (HAdV-5) E1A 13S oncoprotein is a potent regulator of gene expression and is used extensively as a model for transcriptional activation. It possesses two inde- pendent transcriptional activation domains located in the N-terminus\\/conserved region (CR) 1 and CR3. The protein acetyltransferase p300 was previously identified by its association with the N-terminus\\/ CR1 portion of E1A

Peter Pelka; Jailal N. G. Ablack; Joseph Torchia; Andrew S. Turnell; Roger J. A. Grand; Joe S. Mymryk

2009-01-01

68

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.

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

2014-01-01

69

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

70

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

71

Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential.  

PubMed Central

A DNA affinity column containing a synthetic double-stranded nuclear matrix attachment region (MAR) was used to purify a 100-kDa protein from human erythroleukemia K562 cells. This protein was identified as nucleolin, the key nucleolar protein of dividing cells, which is thought to control rRNA gene transcription and ribosome assembly. Nucleolin is known to bind RNA and single-stranded DNA. We report here that nucleolin is also a MAR-binding protein. It binds double-stranded MARs from different species with high affinity. Nucleolin effectively distinguishes between a double-stranded wild-type synthetic MAR sequence with a high base-unpairing potential and its mutated version that has lost the unpairing capability but is still A+T rich. Thus, nucleolin is not merely an A+T-rich sequence-binding protein but specifically binds the base-unpairing region of MARs. This binding specificity is similar to that of the previously cloned tissue-specific MAR-binding protein SATB1. Unlike SATB1, which binds only double-stranded MARs, nucleolin binds the single-stranded T-rich strand of the synthetic MAR probe approximately 45-fold more efficiently than its complementary A-rich strand, which has an affinity comparable to that of the double-stranded form of the MAR. In contrast to the high selectivity of binding to double-stranded MARs, nucleolin shows only a small but distinct sequence preference for the T-rich strand of the wild-type synthetic MAR over the T-rich strand of its mutated version. The affinity to the T-rich synthetic MAR is severalfold higher than to its corresponding RNA and human telomere DNA. Quantitative cellular fractionation and extraction experiments indicate that nucleolin is present both as a soluble protein and tightly bound to the matrix, similar to other known MAR-binding proteins. PMID:7799955

Dickinson, L A; Kohwi-Shigematsu, T

1995-01-01

72

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

73

Conserved regions of the timeless (tim) clock gene in Drosophila analyzed through phylogenetic and functional studies.  

PubMed

Circadian (approximately 24-hr) rhythms in Drosophila melanogaster depend upon cyclic expression of the period (per) and timeless (tim) genes, which encode interacting components of the endogenous clock. The per gene has been isolated from other insects and, more recently, a per ortholog was found in mammals where its expression oscillates in a circadian fashion. We report here the complete sequence of a tim gene from another species, Drosophila virilis. TIM is better conserved than the PER protein is between these two species (76 vs. 54% overall amino acid identity), and putative functional domains, such as the PER interaction domains and the nuclear localization signal, are highly conserved. The acidic domain and the cytoplasmic localization domain, however, are within the least conserved regions. In addition, the initiating methionine in the D. virilis gene lies downstream of the proposed translation start for the original D. melanogaster tim cDNA and corresponds to the one used by D. simulans and D. yakuba. Among the most conserved parts of TIM is a region of unknown function near the N terminus. We show here that deletion of a 32 amino acid segment within this region affects rescue of rhythms in arrhythmic tim01 flies. Flies carrying a full-length tim transgene displayed rhythms with approximately 24-hr periods, indicating that a fully functional clock can be restored in tim01 flies through expression of a tim transgene. Deletion of the segment mentioned above resulted in very long activity rhythms with periods ranging from 30.5 to 48 hr. PMID:9504927

Ousley, A; Zafarullah, K; Chen, Y; Emerson, M; Hickman, L; Sehgal, A

1998-02-01

74

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

PubMed Central

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

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

2013-01-01

75

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

76

Identification of a region in G protein ? subunits conserved across species but hypervariable among subunit isoforms  

PubMed Central

The heterotrimeric GTP binding proteins, G proteins, consist of three distinct subunits: ?, ?, and ?. There are 12 known mammalian ? subunit genes whose products are the smallest and most variable of the G protein subunits. Sequencing of the bovine brain ?10 protein by electrospray mass spectrometry revealed that it differs from the human protein by an Ala to Val substitution near the N-terminus. Comparison of ? isoform subunit sequences indicated that they vary substantially more at the N-terminus than at other parts of the protein. Thus, species variation of this region might reflect the lack of conservation of a functionally unimportant part of the protein. Analysis of 38 ? subunit sequences from four different species shows that the N-terminus of a given ? subunit isoform is as conserved between different species as any other part of the protein, including highly conserved regions. These data suggest that the N-terminus of ? is a functionally important part of the protein exhibiting substantial isoform-specific variation. PMID:11714923

Cook, Lana A.; Schey, Kevin L.; Cleator, John H.; Wilcox, Michael D.; Dingus, Jane; Hildebrandt, John D.

2001-01-01

77

Conserved regions of ribonucleoprotein ribonuclease MRP are involved in interactions with its substrate  

PubMed Central

Ribonuclease (RNase) MRP is a ubiquitous and essential site-specific eukaryotic endoribonuclease involved in the metabolism of a wide range of RNA molecules. RNase MRP is a ribonucleoprotein with a large catalytic RNA moiety that is closely related to the RNA component of RNase P, and multiple proteins, most of which are shared with RNase P. Here, we report the results of an ultraviolet-cross-linking analysis of interactions between a photoreactive RNase MRP substrate and the Saccharomyces cerevisiae RNase MRP holoenzyme. The results show that the substrate interacts with phylogenetically conserved RNA elements universally found in all enzymes of the RNase P/MRP family, as well as with a phylogenetically conserved RNA region that is unique to RNase MRP, and demonstrate that four RNase MRP protein components, all shared with RNase P, interact with the substrate. Implications for the structural organization of RNase MRP and the roles of its components are discussed. PMID:23700311

Esakova, Olga; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S.

2013-01-01

78

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

79

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

80

including thousands of CTCF insulator sites Systematic discovery of regulatory motifs in conserved regions of the human genome,  

E-print Network

Sciences and Technology, §Computer Science and Artificial Intelligence Laboratory, and Departmentincluding thousands of CTCF insulator sites Systematic discovery of regulatory motifs in conserved.pnas.org/misc/reprints.shtml To order reprints, see: Notes: #12;Systematic discovery of regulatory motifs in conserved regions

Xie, Xiaohui Sunney

81

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.

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

2014-01-01

82

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

PubMed

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

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

2013-11-01

83

A Conserved Amphipathic Ligand Binding Region Influences K-Path Dependent Activity of Cytochrome c Oxidase  

PubMed Central

A conserved, crystallographically-defined bile acid binding site was originally identified in the membrane domain of mammalian and bacterial cytochrome c oxidase (CcO). Current studies show other amphipathic molecules including detergents, fatty acids, steroids, and porphyrins bind to this site and affect the already 50% inhibited activity of the E101A mutant of Rhodobacter sphaeroides CcO, as well as altering the activity of wildtype and bovine enzymes. Dodecyl maltoside, Triton X100, C12E8, lysophophatidylcholine and CHOBIMALT detergents further inhibit RsCcO E101A, with lesser inhibition observed in wildtype. The detergent inhibition is overcome in the presence of ?M concentrations of steroids and porphyrin analogs including deoxycholate, cholesteryl hemisuccinate, bilirubin, and protoporphyrin IX. In addition to alleviating detergent inhibition, amphipathic carboxylates including arachidonic, docosahexanoic, and phytanic acids stimulate the activity of E101A to wildtype levels by providing the missing carboxyl group. Computational modeling of dodecyl maltoside, bilirubin, and protoporphyrin IX into the conserved steroid site shows energetically favorable binding modes for these ligands and suggests that a groove at the interface of subunit I and II, including the entrance to the K-path and helix VIII of subunit I, mediates the observed competitive ligand interactions involving two overlapping sites. Spectral analysis indicates that ligand binding to this region affects CcO activity by altering the K path dependent electron transfer equilibrium between heme a and heme a3. The high affinity and specificity of a number of compounds for this region, and its conservation and impact on CcO activity, support its physiological significance. PMID:23351100

Hiser, Carrie; Buhrow, Leann; Liu, Jian; Kuhn, Leslie; Ferguson-Miller, Shelagh

2013-01-01

84

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

85

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

86

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

87

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

USGS Publications Warehouse

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

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

2006-01-01

88

Evaluating the impact of water conservation on fate of outdoor water use: a study in an arid region.  

PubMed

In this research, the impact of several water conservation policies and return flow credits on the fate of water used outdoors in an arid region is evaluated using system dynamics modeling approach. Return flow credits is a strategy where flow credits are obtained for treated wastewater returned to a water body, allowing for the withdrawal of additional water equal to the amount returned as treated wastewater. In the return credit strategy, treated wastewater becomes a resource. This strategy creates a conundrum in which conservation may lead to an apparent decrease in water supply because less wastewater is generated and returned to water body. The water system of the arid Las Vegas Valley in Nevada, USA is used as basis for the dynamic model. The model explores various conservation scenarios to attain the daily per capita demand target of 752 l by 2035: (i) status quo situation where conservation is not implemented, (ii) conserving water only on the outdoor side, (iii) conserving water 67% outdoor and 33% indoor, (iv) conserving equal water both in the indoor and outdoor use (v) conserving water only on the indoor side. The model is validated on data from 1993 to 2008 and future simulations are carried out up to 2035. The results show that a substantial portion of the water used outdoor either evapo-transpires (ET) or infiltrates to shallow groundwater (SGW). Sensitivity analysis indicated that seepage to groundwater is more susceptible to ET compared to any other variable. The all outdoor conservation scenario resulted in the highest return flow credits and the least ET and SGW. A major contribution of this paper is in addressing the water management issues that arise when wastewater is considered as a resource and developing appropriate conservation policies in this backdrop. The results obtained can be a guide in developing outdoor water conservation policies in arid regions. PMID:21511392

Qaiser, Kamal; Ahmad, Sajjad; Johnson, Walter; Batista, Jacimaria

2011-08-01

89

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

90

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

91

Intron positions are conserved in the 5' end region of myosin heavy-chain genes.  

PubMed

We have determined the 5' end sequence of the rat embryonic skeletal muscle myosin heavy-chain (MHC) gene comprising the first three amino-terminal coding exons. Comparison with the corresponding regions of the rat ventricular alpha and the nematode Caenorhabditis elegans unc-54 MHC genes (Mahdavi, V., Chambers, A.P., and Nadal-Ginard, B. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 2626-2630; Karn, J., Brenner, S., and Barnett, L. (1983) Proc. Natl. Acad. Sci. U.S.A. 80, 4253-4257) shows that the degree of amino acid sequence conservation increases from the first to the third exon. Intron positions between these exons are maintained in all three genes studied, whereas size and sequence of corresponding introns are highly divergent. In contrast to the rat MHC genes where the coding region is highly split throughout its entire length, only the 5' end region is frequently interrupted by introns in the nematode gene indicating the potential importance of these introns in gene structure and expression. The occurrence of "preferential" intron positions in the MHC genes suggests the existence of a highly split ancestral MHC gene from which different evolutionary lineages removed and/or added specific sets of introns. PMID:2981212

Strehler, E E; Mahdavi, V; Periasamy, M; Nadal-Ginard, B

1985-01-10

92

Identification of Biodiversity Conservation Priorities using Predictive Modeling: An Application for the Equatorial Pacific Region of South America  

Microsoft Academic Search

We used predictive modeling of species distributions to identify conservation priority areas in the equatorial Pacific region\\u000a of western Ecuador and northwestern Peru. Museum and herbarium data and predictive models of species distributions are increasingly\\u000a being used to assess the conservation status of individual species. In this study, we assembled occurrence data for 28 species\\u000a of vascular plants, birds, and

Manuel Peralvo; Rodrigo Sierra; Kenneth R. Young; Carmen Ulloa-Ulloa

2007-01-01

93

Identification of a human-specific epitope in a conserved region of the La/SS-B autoantigen.  

PubMed Central

Human anti-La/SS-B autoantibodies are known to react with highly conserved epitopes suggested to be functional or active sites on the La/SS-B polypeptide. This study was designed to determine whether the autoantibodies also react with poorly conserved regions of La/SS-B as predicted by an antigen-driven autoimmune response. Binding of human autoantibodies to purified human, mouse, and bovine recombinant fragments representing immunodominant regions of the La/SS-B polypeptide was compared using Western blotting and ELISA. A cross-reactive epitope was located in the highly conserved NH2-terminal region of La/SS-B. Significantly, human-specific epitopes were identified in both the conserved RNA-recognition motif and a poorly conserved COOH-terminal fragment, providing direct evidence for an autoantigen-driven response. The lack of autoantibody cross-reactivity with a conserved domain of mouse and bovine La/SS-B implies that a small number of residues in human autoepitopes may be critical for autoimmunogenicity. Images PMID:7688758

Weng, Y M; McNeilage, J; Topfer, F; McCluskey, J; Gordon, T

1993-01-01

94

Conserving Madagascar's Freshwater Biodiversity  

NSDL National Science Digital Library

This peer-reviewed article from BioScience is about conserving freshwater diversity in Madagascar. The island nation of Madagascar, an international conservation priority, is now also recognized as a global hotspot for freshwater biodiversity. Three emerging characteristics of Madagascar's threatened freshwater biota deserve increased attention from the scientific and conservation communities. First, species richness is not low, as was once assumed for both the freshwater fishes and the invertebrates. Second, many species are restricted to a specific region or even to single river basins. Often these species are also limited to streams or rivers draining primary forest habitat. Finally, many of the island's freshwater fishes are basal taxa, having diverged earlier than any other extant members of their clade. As such, these taxa assume disproportional phylogenetic importance. In the face of ongoing environmental threats, links among microendemism, forest stream specialization, and basal phylogenetic position highlight the importance and vulnerability of these species and provide a powerful incentive for immediate conservation action.

JONATHAN P. BENSTEAD, PATRICK H. DE RHAM, JEAN-LUC GATTOLLIAT, FRANÃ?OIS-MARIE GIBON, PAUL V. LOISELLE, MICHEL SARTORI, JOHN S. SPARKS, and MELANIE L. J. STIASSNY (; )

2003-11-01

95

Identification of Conserved Regions and Residues within Hedgehog Acyltransferase Critical for Palmitoylation of Sonic Hedgehog  

PubMed Central

Background Sonic hedgehog (Shh) is a palmitoylated protein that plays key roles in mammalian development and human cancers. Palmitoylation of Shh is required for effective long and short range Shh-mediated signaling. Attachment of palmitate to Shh is catalyzed by Hedgehog acyltransferase (Hhat), a member of the membrane bound O-acyl transferase (MBOAT) family of multipass membrane proteins. The extremely hydrophobic composition of MBOAT proteins has limited their biochemical characterization. Except for mutagenesis of two conserved residues, there has been no structure-function analysis of Hhat, and the regions of the protein required for Shh palmitoylation are unknown. Methodology/Principal Findings Here we undertake a systematic approach to identify residues within Hhat that are required for protein stability and/or enzymatic activity. We also identify a second, novel MBOAT homology region (residues 196–234) that is required for Hhat activity. In total, ten deletion mutants and eleven point mutants were generated and analyzed. Truncations at the N- and C-termini of Hhat yielded inactive proteins with reduced stability. Four Hhat mutants with deletions within predicted loop regions and five point mutants retained stability but lost palmitoylation activity. We purified two point mutants, W378A and H379A, with defective Hhat activity. Kinetic analyses revealed alterations in apparent Km and Vmax for Shh and/or palmitoyl CoA, changes that likely explain the catalytic defects observed for these mutants. Conclusions/Significance This study has pinpointed specific regions and multiple residues that regulate Hhat stability and catalysis. Our findings should be applicable to other MBOAT proteins that mediate lipid modification of Wnt proteins and ghrelin, and should serve as a model for understanding how secreted morphogens are modified by palmitoyl acyltransferases. PMID:20585641

Buglino, John A.; Resh, Marilyn D.

2010-01-01

96

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

PubMed

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. PMID:2975753

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

1988-09-01

97

Bovine papillomavirus-like particles presenting conserved epitopes from membrane-proximal external region of HIV-1 gp41 induced mucosal and systemic antibodies.  

PubMed

Two conserved epitopes, located in the membrane-proximal external region (MPER) of the human immunodeficiency virus type 1 (HIV-1) gp41, are recognized by two HIV-1 broadly neutralizing antibodies 2F5 and 4E10, and are promising targets for vaccine design in efforts to elicit anti-HIV-1 broadly neutralizing antibodies. Since most HIV-1 infections initiate at mucosal surfaces, induction of mucosal neutralizing antibodies is necessary and of utmost importance to counteract HIV-1 infection. Here, we utilized a mucosal vaccine vector, bovine papillomavirus (BPV) virus-like particles (VLPs), as a platform to present HIV-1 neutralizing epitopes by inserting the extended 2F5 or 4E10 epitope or the MPER domain into D-E loop of BPV L1 respectively. The chimeric VLPs presenting MPER domain resembled the HIV-1 natural epitopes better than the chimeric VLPs presenting single epitopes. Oral immunization of mice with the chimeric VLPs displaying the 2F5 epitope or MPER domain elicited epitope-specific serum IgGs and mucosal secretory IgAs. The induced antibodies specifically recognized the native conformation of MPER in the context of HIV-1 envelope protein. The antibodies induced by chimeric VLPs presenting MPER domain are able to partially neutralize HIV-1 viruses from clade B and clade C. PMID:24055348

Zhai, Yougang; Zhong, Zhenyu; Zariffard, Mohammadreza; Spear, Gregory T; Qiao, Liang

2013-11-01

98

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

PubMed

A survey of mammals and birds was carried out in a semi-deciduous forest fragment of 150 ha located in a zone of intensive agriculture in Ribeirão Preto, State of São Paulo, south-eastern Brazil. Line transect sampling was used to census mammals and birds during six days, totalling 27.8 km of trails and 27.8 hours of observation. Twenty mammal species were confirmed in the area (except bats and small mammals), including rare or endangered species, such as the mountain lion (Puma concolor), the maned wolf (Chrysocyon brachyurus), and the ocelot (Leopardus pardalis). The brown capuchin monkey (Cebus apella) and the black-tufted-ear marmoset (Callithrix penicillata) were found frequently, suggesting high population density in the fragment. Regarding the avifauna, 49 bird species were recorded, most of them typical of open areas or forest edges. Some confirmed species, however, are becoming increasingly rare in the region, as for example the muscovy duck (Cairina moschata) and the toco toucan (Ramphastos toco). The results demonstrate that forest fragment of this size are refuges for native fauna in a region dominated almost exclusively by sugar-cane plantations. Besides faunal aspects, the conservation of these fragments is of great importance for the establishment of studies related to species preservation in the long term, including reintroduction and translocation projects, as well as studies related to genetic health of isolated populations. PMID:10959107

Chiarello

2000-05-01

99

From the Levant to Gibraltar: a regional perspective for marine conservation in the Mediterranean Sea.  

PubMed

Marine protected areas (MPAs) are critical to the well-being of threatened ecosystems and thus can be highly beneficial to humans, especially to those residing nearby. We explore the qualities of 117 MPAs in the Mediterranean basin and develop a taxonomy of their characteristics. We relate the spatial distribution of the MPAs to the various characteristics of the taxonomy (size, distance from shore, protection levels, management regimes, etc.) and to areas of high human impact and influence levels. To do this we use information on biogeographic regions and information from two different human influence models; one model developed for the marine environment and one covering the littoral terrestrial environment. Our analysis provides insights to planners and managers working in a regional capacity and trying to build MPA networks. Generally, current MPAs have not been established in high impact areas despite their being close to shores containing intense human activity. Decision-makers wishing to design and establish new MPAs may seek out areas of high cumulative human impacts (near the marine-terrestrial interface) or avoid them depending on marine conservation objectives, including the desire to vary types of MPAs within a network. Limitations of our analysis and methodology indicate areas for further research. PMID:22851348

Portman, Michelle E; Nathan, Daniel; Levin, Noam

2012-11-01

100

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

101

Conserved gene arrangement in the origin region of the Streptomyces coelicolor chromosome.  

PubMed Central

A 23-kb fragment of the Streptomyces coelicolor chromosome spanning the dnaA region has been isolated as a cosmid clone. Nucleotide sequence analysis of a 5-kb portion shows that the genes for the RNase P protein (rnpA), ribosomal protein L34 (rpmH), the replication initiator protein (dnaA), and the beta subunit of DNA polymerase III (dnaN) are present in the highly conserved gene arrangement found in all eubacterial genomes studied so far. The dnaA-dnaN intergenic region is approximately 1 kb and contains a cluster of at least 12 DnaA boxes with a consensus sequence of TTGTCCACA matching the consensus DnaA box in the phylogenetically related Micrococcus luteus. Two DnaA boxes precede the dnaA sequence. We propose that the chromosomal origin (oriC) of S. coelicolor lies between dnaA and dnaN. In related work, J. Zakrzewska-Czerwinska and H. Schrempf (J. Bacteriol. 174:2688-2693, 1992) have identified the homologous sequence from the closely-related Streptomyces lividans as capable of self-replication. PMID:1577691

Calcutt, M J; Schmidt, F J

1992-01-01

102

Terrestrial Carbon Dynamics in Prairie Remnants and Conservation Reserve Program Lands of the Palouse Region  

NASA Astrophysics Data System (ADS)

Conversion of marginal agricultural lands to perennial grassland vegetation has been proposed as a way to enhance terrestrial carbon sequestration. The Conservation Reserve Program (CRP) has facilitated this transition and promoted carbon sequestration in highly erodible agricultural lands of the Palouse Region of northern Idaho and eastern Washington. Currently little is known about the potential of these lands to act as a carbon sinks in this region. We studied terrestrial carbon dynamics in CRP set asides planted with exotic grasses and in native prairie remnants of the Palouse Region. To study plant decomposition, the species Festuca idahoensis and Symphoricarpos albus were used as representatives of the native prairie community and Bromus inermis was used for CRP sites. Above- and belowground net primary productivity (from 170.9 to 216.0 g m-2 yr-1) and litter fall (from 15.6 to 31.0 g m-2 yr-1) were similar between grassland types. However, root biomass, soil macroaggregates and soil carbon were higher in prairie remnants. Decomposition rates of leaf litter were not different among plant species, however root decomposition was slower in S. albus (k = 0.28 yr-1) than in F. idahoensis (k = 0.56 yr-1) or B. inermis (k = 0.64 yr-1). These results demonstrate that aboveground processes and carbon inputs in CRP sites have reached similar levels to native prairies. However, belowground carbon pools (i.e. root biomass and soil carbon) are still higher in prairie remnants. Belowground decomposition rates were related to root chemical composition as S. albus roots had the highest lignin to nitrogen ratio. The results of this study suggest that efforts to promote carbon sequestration in CRP grasslands of the Palouse should be focused on belowground pools and processes. Management practices that could increase the amount of carbon sequestered in these CRP sites include increasing the amount of root biomass production through fertilization and increasing the density of plants with recalcitrant litter inputs.

Sánchez-de León, Y.; Johnson-Maynard, J.

2007-12-01

103

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

104

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

105

ITS Region-An Efficient Genetic Tool to Identify Non-hybrid Butternut for Butternut (Juglans cinerea L.) Conservation  

E-print Network

of butternut, Japanese walnut, and black walnut were compared. Conserved regions flanking polymorphism were-8: butternut standard Japanese walnut standard, black walnut standard. M=100bp molecular DNA size marker Tsp509 Butternut (Juglans cinerea L.), also called white walnut, is an ecologically and economically valuable tree

106

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

107

Hundreds of conserved non-coding genomic regions are independently lost in mammals  

PubMed Central

Conserved non-protein-coding DNA elements (CNEs) often encode cis-regulatory elements and are rarely lost during evolution. However, CNE losses that do occur can be associated with phenotypic changes, exemplified by pelvic spine loss in sticklebacks. Using a computational strategy to detect complete loss of CNEs in mammalian genomes while strictly controlling for artifacts, we find >600 CNEs that are independently lost in at least two mammalian lineages, including a spinal cord enhancer near GDF11. We observed several genomic regions where multiple independent CNE loss events happened; the most extreme is the DIAPH2 locus. We show that CNE losses often involve deletions and that CNE loss frequencies are non-uniform. Similar to less pleiotropic enhancers, we find that independently lost CNEs are shorter, slightly less constrained and evolutionarily younger than CNEs without detected losses. This suggests that independently lost CNEs are less pleiotropic and that pleiotropic constraints contribute to non-uniform CNE loss frequencies. We also detected 35 CNEs that are independently lost in the human lineage and in other mammals. Our study uncovers an interesting aspect of the evolution of functional DNA in mammalian genomes. Experiments are necessary to test if these independently lost CNEs are associated with parallel phenotype changes in mammals. PMID:23042682

Hiller, Michael; Schaar, Bruce T.; Bejerano, Gill

2012-01-01

108

Hundreds of conserved non-coding genomic regions are independently lost in mammals.  

PubMed

Conserved non-protein-coding DNA elements (CNEs) often encode cis-regulatory elements and are rarely lost during evolution. However, CNE losses that do occur can be associated with phenotypic changes, exemplified by pelvic spine loss in sticklebacks. Using a computational strategy to detect complete loss of CNEs in mammalian genomes while strictly controlling for artifacts, we find >600 CNEs that are independently lost in at least two mammalian lineages, including a spinal cord enhancer near GDF11. We observed several genomic regions where multiple independent CNE loss events happened; the most extreme is the DIAPH2 locus. We show that CNE losses often involve deletions and that CNE loss frequencies are non-uniform. Similar to less pleiotropic enhancers, we find that independently lost CNEs are shorter, slightly less constrained and evolutionarily younger than CNEs without detected losses. This suggests that independently lost CNEs are less pleiotropic and that pleiotropic constraints contribute to non-uniform CNE loss frequencies. We also detected 35 CNEs that are independently lost in the human lineage and in other mammals. Our study uncovers an interesting aspect of the evolution of functional DNA in mammalian genomes. Experiments are necessary to test if these independently lost CNEs are associated with parallel phenotype changes in mammals. PMID:23042682

Hiller, Michael; Schaar, Bruce T; Bejerano, Gill

2012-12-01

109

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

PubMed

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

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

2014-01-01

110

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

111

Distribution and Conservation of Genetic Diversity Among UK Calcareous Grassland Regions: A Case Study Using Insects  

Microsoft Academic Search

Conservation strategies for whole communities at the landscape scale have rarely been able to take into account genetic diversity because of the number of species involved. However, if species can be grouped together by geographic distribution of genetic diversity and patterns of relatedness, then landscape and genetic conservation might be more effectively combined to cope with problems of fragmentation. We

Bo-Chi G. Lai; Andrew S. Pullin

2005-01-01

112

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

Microsoft Academic Search

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

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

2008-01-01

113

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

114

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

115

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

PubMed

Seabuckthorn is regarded as a main eco-economical tree species, and plays an increasing important role in eco-environmental construction in Northwest, Northeast and North China. Our study on artificial seabuckthorn forest in loess hilly region showed that the average rainfall interception rate of 7-10 ages seabuckthorn canopy was 8.5%, and the litter layer of 5-10 ages seabuckthorn forest could intercept 0.89 mm rainfall. Seabuckthorn forest could improve soil infiltration and anti-strike ability through improving soil physical and chemical properties, and the numbers of its hair roots and the depth of its litter layer were the main indices of soil anti-strike ability. The effects of seabuckthorn forest on soil and water conservation increased with its increasing age. In 2-3 ages stage, the effects were weak, and the runoff and sediment were mainly affected by the characters of rainfall. In 4-5 ages stage when the forest became maturing, the annual runoff depth and annual erosion modulus were 1.8-3.2 mm and 24.64 t x km(-2), respectively. In 6-12 ages stage when the forest matured, the runoff and sediment on seabuckthorn woodland changed slowly, the annual runoff depth and annual erosion modulus being 0.3 -3.4 mm and 0-6.75 t x km(-2), respectively, and the characters of rainfall had much less effect on them. In the stage from young (2-5 ages) to mature forest, the sediment charge in runoff changed sharply, ranged from 77. 31 kg x m(-3) to 9.12 kg x m(-3), but in 6-12 ages stage, the sediment content in runoff changed very slowly, and the range was 0-5.09 kg x m(-3). PMID:16011150

Chen, Yunming; Liu, Guobin; Xu, Bingcheng

2005-04-01

116

Protein engineering of selected residues from conserved sequence regions of a novel Anoxybacillus ?-amylase.  

PubMed

The ?-amylases from Anoxybacillus species (ASKA and ADTA), Bacillus aquimaris (BaqA) and Geobacillus thermoleovorans (GTA, Pizzo and GtamyII) were proposed as a novel group of the ?-amylase family GH13. An ASKA yielding a high percentage of maltose upon its reaction on starch was chosen as a model to study the residues responsible for the biochemical properties. Four residues from conserved sequence regions (CSRs) were thus selected, and the mutants F113V (CSR-I), Y187F and L189I (CSR-II) and A161D (CSR-V) were characterised. Few changes in the optimum reaction temperature and pH were observed for all mutants. Whereas the Y187F (t1/2 43?h) and L189I (t1/2 36?h) mutants had a lower thermostability at 65°C than the native ASKA (t1/2 48?h), the mutants F113V and A161D exhibited an improved t1/2 of 51?h and 53?h, respectively. Among the mutants, only the A161D had a specific activity, k(cat) and k(cat)/K(m) higher (1.23-, 1.17- and 2.88-times, respectively) than the values determined for the ASKA. The replacement of the Ala-161 in the CSR-V with an aspartic acid also caused a significant reduction in the ratio of maltose formed. This finding suggests the Ala-161 may contribute to the high maltose production of the ASKA. PMID:25069018

Ranjani, Velayudhan; Jane?ek, Stefan; Chai, Kian Piaw; Shahir, Shafinaz; Abdul Rahman, Raja Noor Zaliha Raja; Chan, Kok-Gan; Goh, Kian Mau

2014-01-01

117

Conservation Conservation ResourcesConservation Resources  

E-print Network

, conservation development, wind cost & availability, climate change science and policycost & availability, climate change science and policy #12;slide 5 Northwest Power and Conservation Council ES-10 Base PlanAcquisitions(aMW) BPA and Utility Programs Alliance Programs Since 1980 the Region'sSince 1980 the Region's Utilities

118

A vertebrate-conserved cis -regulatory module for targeted expression in the main hypothalamic regulatory region for the stress response.  

PubMed

BackgroundThe homeodomain transcription factor orthopedia (Otp) is an evolutionarily conserved regulator of neuronal fates. In vertebrates, Otp is necessary for the proper development of different regions of the brain and is required in the diencephalon to specify several hypothalamic cell types, including the cells that control the stress response. To understand how this widely expressed transcription factor accomplishes hypothalamus-specific functions, we performed a comprehensive screening of otp cis-regulatory regions in zebrafish.ResultsHere, we report the identification of an evolutionarily conserved vertebrate enhancer module with activity in a restricted area of the forebrain, which includes the region of the hypothalamus that controls the stress response. This region includes neurosecretory cells producing Corticotropin-releasing hormone (Crh), Oxytocin (Oxt) and Arginine vasopressin (Avp), which are key components of the stress axis. Lastly, expression of the bacterial nitroreductase gene under this specific enhancer allowed pharmacological attenuation of the stress response in zebrafish larvae.ConclusionVertebrates share many cellular and molecular components of the stress response and our work identified a striking conservation at the cis-regulatory level of a key hypothalamic developmental gene. In addition, this enhancer provides a useful tool to manipulate and visualize stress-regulatory hypothalamic cells in vivo with the long-term goal of understanding the ontogeny of the stress axis in vertebrates. PMID:25427861

Gutierrez-Triana, Jose; Herget, Ulrich; Lichtner, Patrick; Castillo-Ramírez, Luis A; Ryu, Soojin

2014-11-27

119

Conservation genomics of Atlantic salmon: variation in gene expression between and within regions of the Bay of Fundy.  

PubMed

Due to difficulties in identifying important within-species biodiversity for effective species management and conservation, the use of multiple complementary sources of information is required to identify and assess the designation of conservation units based on the degree of variation among populations within a species. In this study, we combined estimates of microsatellite and transcriptomic variation to assess the population structure and potential for adaptive variation of threatened Atlantic salmon, Salmo salar, among rivers in the Bay of Fundy. In general, population structure identified by genetic differentiation was consistent with the patterns of variation in gene expression, although there was not a strong correlation between neutral genetic variation and variation in gene expression. Both data sets provided clear indication of strong regional differentiation between rivers located within the inner Bay of Fundy relative to rivers located within the outer Bay of Fundy or the Southern Upland region, and there was also support for more refined population structure. Both data sets indicated that Atlantic salmon populations from the inner and outer Bay of Fundy reflect unique genetic lineages, with some evidence of population differentiation between regions of the inner Bay of Fundy, and between individual rivers within a region. Consistency of the microarray data across 2 years helped to validate the use of this technique as a useful tool in assessment of variation among wild populations for species conservation. PMID:20529070

Vandersteen Tymchuk, Wendy; O'Reilly, Patrick; Bittman, Jesse; Macdonald, Danielle; Schulte, Patricia

2010-05-01

120

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...

121

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

Microsoft Academic Search

In nature reserves and habitat conservation areas, monitoring is required to determine if reserves are meeting their goals\\u000a for preserving species, ecological communities, and ecosystems. Increasingly, reserves are established to protect multiple\\u000a species and communities, each with their own conservation goals and objectives. As resources are always inadequate to monitor\\u000a all components, criteria must be applied to prioritize both species

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

2008-01-01

122

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.

1993-01-01

123

Non-conservative Mutations are Well Tolerated in the Globular Region of Yeast Histone H4  

Microsoft Academic Search

Yeast histone H4 has been mutagenized at several positions which participate in the globular core of the nucleosome. The native protein contains residues at those positions which are invariant or highly conserved over all known H4 sequences, whether from yeast,Tetrahymenaor higher eukaryotes. Nonetheless the protein is tolerant of non-conservative mutations. At the level of cell function the mutant proteins cause

Seema Agarwal; Michael J. Behe

1996-01-01

124

Coat protein gene sequence analysis of potato virus X and potato virus Y: conserved regions to design gene silencing cassette.  

PubMed

Potato virus X(PVX) and Potato virus Y(PVY) are two of the three most prevalent viruses that cause significant yield declines in potato. Twenty-seven PVX and thirty-seven PVY accessions were analyzed for nucleotide sequence variation of the coat protein gene. The average and variance of genetic distance for PVX were estimated at 0.118 and 0.004 and 0.118 and 0.005 for PVY using the neighbour joining method. Results of phylogenetic trees and their certification via stepwise discriminant analysis led us to classify of PVX sequences in four groups and PVY sequences in three groups. One purpose of this project was to determine suitable conserved regions to make of gene silencing constructs. Length of identified conserved regions were enough to silence of the virus coat protein genes on infected plants, many of which were located consequently with short gap spacers. In this term, some of groups were divided into subgroups to obtain conserved regions under minimum length of25 nt, enough length to design specific diagnostic-primers. PMID:19102033

Darbani, Behrooz; Stewart, C Neal; Razban, H Ahmad; Noeparvar, Shahin

2007-10-01

125

Incomplete paternal inheritance of chloroplast DNA recognized in Chamaecyparis obtusa using an intraspecific polymorphism of the trnD-trnY intergenic spacer region  

Microsoft Academic Search

Using a fluorescence-based PCR-SSCP (single-strand conformation polymorphism), we verified imperfectibility in the paternal\\u000a inheritance of chloroplast DNA (cpDNA) in Chamaecyparis\\u000a obtusa (Cupressaceae) controlled crosses. An intraspecific sequence polymorphism of the intergenic spacer region between the trnD and trnY genes was utilized as a molecular marker. Of 361 progenies, in which the cpDNA haplotypes of their female and male parents\\u000a were

S. Shiraishi; H. Maeda; T. Toda; K. Seido; Y. Sasaki

2001-01-01

126

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

ERIC Educational Resources Information Center

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

Shaluk, Cathy

2007-01-01

127

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

E-print Network

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

Illinois at Chicago, University of

128

Local and regional-scale societal dynamics in grizzly bear conservation  

Microsoft Academic Search

Conserving grizzly bear populations is a significant challenge for wildlife managers throughout North America. Much fruitful research has been conducted on the biology of grizzlies, but the human dimensions of bear management remain poorly understood. This imbalance has created conflicts between management agencies and local inhabitants that can jeopardize ecosystem management and planning programs in which grizzlies often feature as

Douglas Andrew Clark

2007-01-01

129

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

130

Identification of a region in G protein gamma subunits conserved across species but hypervariable among subunit isoforms.  

PubMed

The heterotrimeric GTP binding proteins, G proteins, consist of three distinct subunits: alpha, beta, and gamma. There are 12 known mammalian gamma subunit genes whose products are the smallest and most variable of the G protein subunits. Sequencing of the bovine brain gamma(10) protein by electrospray mass spectrometry revealed that it differs from the human protein by an Ala to Val substitution near the N-terminus. Comparison of gamma isoform subunit sequences indicated that they vary substantially more at the N-terminus than at other parts of the protein. Thus, species variation of this region might reflect the lack of conservation of a functionally unimportant part of the protein. Analysis of 38 gamma subunit sequences from four different species shows that the N-terminus of a given gamma subunit isoform is as conserved between different species as any other part of the protein, including highly conserved regions. These data suggest that the N-terminus of gamma is a functionally important part of the protein exhibiting substantial isoform-specific variation. PMID:11714923

Cook, L A; Schey, K L; Cleator, J H; Wilcox, M D; Dingus, J; Hildebrandt, J D

2001-12-01

131

Vaccination with Conserved Regions of Erythrocyte-Binding Antigens Induces Neutralizing Antibodies against Multiple Strains of Plasmodium falciparum  

PubMed Central

Background A highly effective vaccine against Plasmodium falciparum malaria should induce potent, strain transcending immunity that broadly protects against the diverse population of parasites circulating globally. We aimed to identify vaccine candidates that fulfill the criteria. Methods We have measured growth inhibitory activity of antibodies raised to a range of antigens to identify those that can efficiently block merozoite invasion for geographically diverse strains of P. falciparum. Results This has shown that the conserved Region III-V, of the P. falciparum erythrocyte-binding antigen (EBA)-175 was able to induce antibodies that potently inhibit merozoite invasion across diverse parasite strains, including those reliant on invasion pathways independent of EBA-175 function. Additionally, the conserved RIII-V domain of EBA-140 also induced antibodies with strong in vitro parasite growth inhibitory activity. Conclusion We identify an alternative, highly conserved region (RIV-V) of EBA-175, present in all EBA proteins, that is the target of potent, strain transcending neutralizing antibodies, that represents a strong candidate for development as a component in a malaria vaccine. PMID:24039774

Healer, Julie; Thompson, Jennifer K.; Riglar, David T.; Wilson, Danny W.; Chiu, Yu-H.C.; Miura, Kazutoyo; Chen, Lin; Hodder, Anthony N.; Long, Carole A.; Hansen, Diana S.; Baum, Jake; Cowman, Alan F.

2013-01-01

132

Recognizing Chemical Hazards Module  

NSDL National Science Digital Library

The Center for the Advancement of Process Technology presents this free sample module on recognizing chemical hazards. It focuses on chemical hazards specific to process industries, and their impact on safety, health and the environment. The material also introduces the purpose and components of an MSDS.

2013-01-09

133

[Recognizing correctly of SCI].  

PubMed

The actual effect will be investigated by realizing the origin, background, founding purpose and the function of SCI. Thereby, the source of SCI and its irrationality, harmfulness are analyzed. And it will remind the scientific circle to recognize correctly and clearly of SCI. PMID:20654208

Huang, Yi-bin

2010-05-01

134

Learning to recognize plankton  

Microsoft Academic Search

We present a system to recognize underwater plankton images from the Shadow Image Particle Profiling Evaluation Recorder. As some images do not have clear contours, we developed several features that do not heavily depend on the contour information. A soft margin support vector machine (SVM) was used as the classifier. We developed a new way to assign probability after multi-class

Tong Luo; Kurt Kramer; Dmitry Goldgof; L. O. Hall; S. Samson; A. Remsen; T. Hopkins

2003-01-01

135

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

PubMed

SUMMARY 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

136

Regions recognized on the light chain of botulinum neurotoxin type A by T lymphocytes of SJL and BALB/c mice primed with inactivated toxin.  

PubMed

Lymph node cells (LNC) from SJL (H-2(s)) and BALB/c (H-2(d)) mice primed once with inactivated botulinum neurotoxin type A (BoNT/A) were examined for their T-cell responses to each of 32 synthetic overlapping peptides (19 residues each, L1-L32) that encompass the entire L chain (residues 1-448) of BoNT/A. LNC of SJL gave strong responses to 6 regions on, L2 (residues 15-23), L10/11/12 (127-173), L19 (253-271) and L21 (281-299), and moderate to weak responses to L9 (113-131), L14/15 (183-215) and L27 (365-383). In BALB/c, LNC gave a substantial T-cell response only against peptide L12 (residues 155-173), and responded very weakly to 9 other peptides. The results were compared with the recognition profiles determined previously in these two strains after multiple BoNT/A injections. Overall responses to the L-chain peptides of T cells in later profiles were found to be somewhat weakened in SJL and stayed essentially at a similar level in BALB/c, although responses to BoNT/A increased. In SJL, response to L10 (127-145) remained the highest in the later profile. Strong responses against L12 (155-173) observed in both strains at early stage were reduced to an insignificant level. Cross-reactivity to tetanus neurotoxin by BoNT/A-specific T cells was observed in SJL but not in BALB/c. Design of an effective synthetic peptide vaccine will require incorporation of both T cell- and Ab-recognition elements of the BoNT molecule. Significance and possible implications of these results on BoNT/A-specific T-cell responses of BoNT-treated patients are discussed. PMID:25151501

Oshima, Minako; Aoki, K Roger; Atassi, M Zouhair

2014-12-01

137

Spatial and temporal analysis of the distribution of forest specialists in an urban-fragmented landscape (Madrid, Spain) Implications for local and regional bird conservation  

Microsoft Academic Search

Management strategies for the regional conservation of forest birds sometimes do not consider explicitly their applicability to areas with different degrees of urbanization. I studied the spatial and temporal distribution of forest passerines in wooded parks in the city of Madrid during two consecutive breeding seasons to identify factors relevant to local conservation, and compared these results to previous studies

Esteban Fernández-Juricic

2004-01-01

138

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

SciTech Connect

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

Harrer, B J; Lezberg, A J

1985-03-01

139

Assessing wheat (Triticum aestivum) genotypes for "Yr" resistance genes using conserved regions and simple-sequence motifs.  

PubMed

Analysis of DNA sequence variation among genotypes is useful for differentiation of wheat accessions, selection strategies and genetic development of crop plants. We screened molecular markers for yellow rust resistance genes (Yr7, Yr9, Yr15, Yr18, Yr26, and YrH52), which are in the gene-rich regions of wheat chromosomes 1B, 2B, and 7D, to investigate DNA sequence differences and repeat motifs and numbers between wheat cultivars resistant (Izgi2001, Sonmez2001, PI178383) and susceptible (Aytin98, ES14, Harmankaya99) to yellow rust. The F(2) individuals derived from the crosses were evaluated for yellow rust resistance at both the seedling and adult stages to identify DNA markers genetically linked to yellow rust resistance. The most repeated motif was found to be GA and the least repeated motif TAGA among the cultivars. When we examined DNA sequence differences (insertion, deletion and single nucleotide changes), the molecular markers Xgwm526 (Yr7) and Xgwm273 (YrH52) were found to have the most conserved regions and Yr15 (Xgwm413) the least conserved regions among the cultivars. This DNA sequence information can be used for selection of suitable parents, creating mapping populations and developing molecular markers associated with yellow rust resistance in plant breeding programs. PMID:22180070

Cabuk, E; Aydin, Y; Uncuoglu, A A

2011-01-01

140

Conservative mutations in the immunosuppressive region of the bovine leukemia virus transmembrane protein affect fusion but not infectivity in vivo.  

PubMed

Many retroviruses, including bovine leukemia virus (BLV), contain a highly conserved region located about 40 amino acids downstream from the fusion peptide within the sequence of the external domain of the transmembrane (TM) protein. This region is notably thought to be involved in the presentation of the NH2-terminal peptide to allow cell fusion. By using hydrophobic cluster analysis and by analogy with the influenza A hemagglutinin structures, the core of the TM structure including this particular region was predicted to consist, in the BLV and other retroviral envelope proteins, of an alpha-helix followed by a loop region, both docked against a subsequent alpha-helix that forms a triple-stranded coiled coil. The loop region could undergo, as in hemagglutinin, a major refolding into an alpha-helix integrating the coiled coil structure and putting the fusion peptide to one tip of the molecule. Based on this model, we have identified amino acids that may be essential to the BLV TM structure, and a series of mutations were introduced in the BLV env gene of an infectious molecular clone. A first series of mutations was designed to disturb the coiled coil structure (substitutions with proline residues), whereas others would maintain the general TM structure. When expressed by Semliki Forest virus recombinants, all the mutated envelope proteins were stable and efficiently synthesized in baby hamster kidney cells. Both proline-substituted and conservative mutants were strongly affected in their capacity to fuse to CC81 indicator cells. In addition, it appeared that the integrity of the TM coiled coil structure is essential for envelope protein multimerization, as analyzed by metrizamide gradient centrifugation. Finally, to gain insight into the role of this coiled coil in the infectious potential of BLV in vivo, the mutated TM genes were introduced in an infectious and pathogenic molecular clone and injected into sheep. It appeared that only the conservative mutations (A60V and A64S) allowed maintenance of viral infectivity in vivo. Since these mutations destroyed the ability to induce syncytia, we conclude that efficient fusion capacity of the recombinant envelopes is not a prerequisite for the infectious potential of BLV in vivo. Viral propagation of these mutants was strongly affected in some of the infected sheep. However, the proviral loads within half of the infected animals (2 out of 2 for A60V and 1 out of 4 for A64S) were close to the wild-type levels. In these sheep, it thus appears that the A60V and A64S mutants propagate efficiently despite being unable to induce syncytia in cell culture. PMID:9582317

Gatot, J S; Callebaut, I; Mornon, J P; Portetelle, D; Burny, A; Kerkhofs, P; Kettmann, R; Willems, L

1998-05-22

141

On recognizing ignorance  

NASA Technical Reports Server (NTRS)

How an expert system reasons about its own ability to deal with a particular problem is studied. Ideally, an expert system ought to rapidly recognize that a particular problem is beyond its abilities and defer to another, perhaps human, expert. This capability is extremely important in domains where expert systems may control life critical processes such as air traffic control, medicine, strategic defense, and manned space exploration. The methods used by knowledge engineers to infuse an expert system with knowledge of its own limitations is surveyed. A computability theory is employed to analyze the general problem of meta-knowledge and to give insight into the efficacy of specific solutions.

Greene, Richard J.

1988-01-01

142

Implementation Study of Energy Conservation Recommendations in the Upper Midwest Region  

E-print Network

The South Dakota State University (SDSU) Industrial Energy Optimization Program (IEOP) and Energy Analysis and Diagnostic Center (EADC) program perform energy audits for industrial companies in the Upper Midwest region of the United States. Each...

Heisinger, K. P.; Bassett, K.; Twedt, M. P.

143

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

144

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

145

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

NASA Astrophysics Data System (ADS)

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

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

2011-12-01

146

Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies  

PubMed Central

Background With over 20 parapatric races differing in their warningly colored wing patterns, the butterfly Heliconius erato provides a fascinating example of an adaptive radiation. Together with matching races of its co-mimic Heliconius melpomene, H. erato also represents a textbook case of Müllerian mimicry, a phenomenon where common warning signals are shared amongst noxious organisms. It is of great interest to identify the specific genes that control the mimetic wing patterns of H. erato and H. melpomene. To this end we have undertaken comparative mapping and targeted genomic sequencing in both species. This paper reports on a comparative analysis of genomic sequences linked to color pattern mimicry genes in Heliconius. Results Scoring AFLP polymorphisms in H. erato broods allowed us to survey loci at approximately 362 kb intervals across the genome. With this strategy we were able to identify markers tightly linked to two color pattern genes: D and Cr, which were then used to screen H. erato BAC libraries in order to identify clones for sequencing. Gene density across 600 kb of BAC sequences appeared relatively low, although the number of predicted open reading frames was typical for an insect. We focused analyses on the D- and Cr-linked H. erato BAC sequences and on the Yb-linked H. melpomene BAC sequence. A comparative analysis between homologous regions of H. erato (Cr-linked BAC) and H. melpomene (Yb-linked BAC) revealed high levels of sequence conservation and microsynteny between the two species. We found that repeated elements constitute 26% and 20% of BAC sequences from H. erato and H. melpomene respectively. The majority of these repetitive sequences appear to be novel, as they showed no significant similarity to any other available insect sequences. We also observed signs of fine scale conservation of gene order between Heliconius and the moth Bombyx mori, suggesting that lepidopteran genome architecture may be conserved over very long evolutionary time scales. Conclusion Here we have demonstrated the tractability of progressing from a genetic linkage map to genomic sequence data in Heliconius butterflies. We have also shown that fine-scale gene order is highly conserved between distantly related Heliconius species, and also between Heliconius and B. mori. Together, these findings suggest that genome structure in macrolepidoptera might be very conserved, and show that mapping and positional cloning efforts in different lepidopteran species can be reciprocally informative. PMID:18647405

Papa, Riccardo; Morrison, Clayton M; Walters, James R; Counterman, Brian A; Chen, Rui; Halder, Georg; Ferguson, Laura; Chamberlain, Nicola; ffrench-Constant, Richard; Kapan, Durrell D; Jiggins, Chris D; Reed, Robert D; McMillan, William O

2008-01-01

147

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...

148

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

SciTech Connect

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

Deng, Z.M.; Siciliano, M.J. [Univ. of Texas M.D. Anderson Cancer Center, Houston, TX (United States); Davisson, M.T. [Jackson Lab., Bar Harbor, ME (United States)] [and others

1994-09-01

149

Evolutionarily conserved amino acids in TCR V regions and MHC control their interaction  

PubMed Central

Alpha/beta T cell receptors (TCRs) react with major histocompatibility complex proteins (MHC) plus peptides, a poorly understood phenomenon, probably because thymocytes bearing TCRs that manifest MHC-reactivity too well are lost by negative selection. Only TCRs with attenuated ability to react with MHC appear on mature T cells. Also, the interaction sites between TCRs and MHC may be inherently flexible and hence difficult to spot. Contacts between TCRs and MHC in the solved structures of their complexes were reevaluated with these points in mind. The results show that frequently used amino acids in TCR CDR1 and CDR2 regions are often used to bind MHC, in areas around small amino acids on the surfaces of MHC ? helices that form a cup, allowing somewhat flexible binding of the TCRs. The TCR amino acids involved are specific to families of V regions and partially different rules govern recognition of MHC1 versus MHCII. PMID:18304006

Marrack, Philippa; Scott-Browne, James P.; Dai, Shaodong; Gapin, Laurent; Kappler, John W.

2011-01-01

150

Bryozoan biodiversity in the New Zealand region and implications for marine conservation  

Microsoft Academic Search

Marine biodiversity and its distribution in the New Zealand region were determined using historical data for an appropriate indicator taxon, the Bryozoa. Bryozoans were identified as belonging to three communities, termed Intertidal\\/Shelf\\/Slope (ISS) and Deep-Sea 1 and 2 (DS1 and DS2). Biodiversity was assessed using measures based on relatedness of species, average taxonomic distinctness and variation in taxonomic distinctness. High

A. A. Rowden; R. M. Warwick; D. P. Gordon

2004-01-01

151

Conserved leucine residue in the head region of morbillivirus fusion protein regulates the large conformational change during fusion activity.  

PubMed

Paramyxovirus cell entry is controlled by the concerted action of two viral envelope glycoproteins, the fusion (F) and the receptor-binding (H) proteins, which together with a cell surface receptor mediate plasma membrane fusion activity. The paramyxovirus F protein belongs to class I viral fusion proteins which typically contain two heptad repeat regions (HR). Particular to paramyxovirus F proteins is a long intervening sequence (IS) located between both HR domains. To investigate the role of the IS domain in regulating fusogenicity, we mutated in the canine distemper virus (CDV) F protein IS domain a highly conserved leucine residue (L372) previously reported to cause a hyperfusogenic phenotype. Beside one F mutant, which elicited significant defects in processing, transport competence, and fusogenicity, all remaining mutants were characterized by enhanced fusion activity despite normal or slightly impaired processing and cell surface targeting. Using anti-CDV-F monoclonal antibodies, modified conformational F states were detected in F mutants compared to the parental protein. Despite these structural differences, coimmunoprecipitation assays did not reveal any drastic modulation in F/H avidity of interaction. However, we found that F mutants had significantly enhanced fusogenicity at low temperature only, suggesting that they folded into conformations requiring less energy to activate fusion. Together, these data provide strong biochemical and functional evidence that the conserved leucine 372 at the base of the HRA coiled-coil of F(wt) controls the stabilization of the prefusogenic state, restraining the conformational switch and thereby preventing extensive cell-cell fusion activity. PMID:19705836

Plattet, Philippe; Langedijk, Johannes P M; Zipperle, Ljerka; Vandevelde, Marc; Orvell, Claes; Zurbriggen, Andreas

2009-09-29

152

The highly conserved region of the co-repressor Sin3A functionally interacts with the co-repressor Alien  

PubMed Central

The Sin3 proteins are evolutionarily conserved co-repressors (CoR) that function as mediators of gene repression for a variety of transcriptional silencers. The paired amphipathic helices of Sin3A were identified and studied as protein–protein interacting domains. Previously we have shown the interaction of Sin3A with the CoR Alien in vivo and in vitro. Here, we show that Alien and Sin3A reside together in vivo with the vitamin D3 receptor on the human 24-hydroxylase (CYP24) promoter containing vitamin D3 response elements by chromatin immunoprecipitation. We delineated and characterized the interaction domains of Sin3A with Alien. Interestingly, the highly conserved region (HCR) of Sin3A, which has not yet been functionally characterized, interacts with Alien. The HCR encompasses only 134 amino acids, shares more than 80% identity with Sin3B and binds to the N-terminus of Alien, which harbours a transferable silencing function. Functionally, co-expression of Sin3A enhances Alien-mediated gene repression and overexpression of the HCR alone leads to the inhibition of Alien-mediated repression and to the induction of the endogenous CYP24 promoter. Our results therefore indicate a novel functional role of the Sin3 HCR and give novel insights into Alien-mediated gene repression. PMID:15173382

Moehren, Udo; Dressel, Uwe; Reeb, Christina A.; Väisänen, Sami; Dunlop, Thomas W.; Carlberg, Carsten; Baniahmad, Aria

2004-01-01

153

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

154

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

155

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

156

Innovative technology conserves resources and generates savings: a case study from the Sunnybrook Regional Processing Centre.  

PubMed

The regional processing centre at Sunnybrook Health Sciences Centre recently faced the substantial challenge of increasing cleaning capacity to meet the current workload and anticipated future demand without increasing its operating budget. The solution, upgrading its cleaning and decontamination system to a highly automated system, met both objectives. An analysis of the impact of the change found that the new system provided additional benefits, including improved productivity and cleaning quality; decreased costs; reduced water, electricity and chemical use; improved worker safety and morale; and decreased overtime. Investing in innovative technology improved key departmental outcomes while meeting institutional environmental and cost savings objectives. PMID:20057236

Karim, Abdool Z

2009-01-01

157

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

158

One exon of the human LSF gene includes conserved regions involved in novel DNA-binding and dimerization motifs.  

PubMed Central

The transcription factor LSF, identified as a HeLa protein that binds the simian virus 40 late promoter, recognizes direct repeats with a center-to-center spacing of 10 bp. The characterization of two human cDNAs, representing alternatively spliced mRNAs, provides insight into the unusual DNA-binding and oligomerization properties of LSF. The sequence of the full-length LSF is identical to that of the transcription factors alpha CP2 and LBP-1c and has similarity to the Drosophila transcription factor Elf-1/NTF-1. Using an epitope-counting method, we show that LSF binds DNA as a homodimer. LSF-ID, which is identical to LBP-1d, contains an in-frame internal deletion of 51 amino acids resulting from alternative mRNA splicing. Unlike LSF, LSF-ID did not bind LSF DNA-binding sites. Furthermore, LSF-ID did not affect the binding of LSF to DNA, suggesting that the two proteins do not interact. Of three short regions with a high degree of homology between LSF and Elf-1/NTF-1, LSF-ID lacks two, which are predicted to form beta-strands. Double amino acid substitutions in each of these regions eliminated specific DNA-binding activity, similarly to the LSF-ID deletion. The dimerization potential of these mutants was measured both by the ability to inhibit the binding of LSF to DNA and by direct protein-protein interaction studies. Mutations in one homology region, but not the other, functionally eliminated dimerization. Images PMID:8035790

Shirra, M K; Zhu, Q; Huang, H C; Pallas, D; Hansen, U

1994-01-01

159

Merging Disparate Data Sources Into a Paleoanthropological Geodatabase for Research, Education, and Conservation in the Greater Hadar Region (Afar, Ethiopia)  

NASA Astrophysics Data System (ADS)

Understanding the geographic, temporal, and environmental contexts of human evolution requires the ability to compare wide-ranging datasets collected from multiple research disciplines. Paleoanthropological field- research projects are notoriously independent administratively even in regions of high transdisciplinary importance. As a result, valuable opportunities for the integration of new and archival datasets spanning diverse archaeological assemblages, paleontological localities, and stratigraphic sequences are often neglected, which limits the range of research questions that can be addressed. Using geoinformatic tools we integrate spatial, temporal, and semantically disparate paleoanthropological and geological datasets from the Hadar sedimentary basin of the Afar Rift, Ethiopia. Applying newly integrated data to investigations of fossil- rich sediments will provide the geospatial framework critical for addressing fundamental questions concerning hominins and their paleoenvironmental context. We present a preliminary cyberinfrastructure for data management that will allow scientists, students, and interested citizens to interact with, integrate, and visualize data from the Afar region. Examples of our initial integration efforts include generating a regional high-resolution satellite imagery base layer for georeferencing, standardizing and compiling multiple project datasets and digitizing paper maps. We also demonstrate how the robust datasets generated from our work are being incorporated into a new, digital module for Arizona State University's Hadar Paleoanthropology Field School - modernizing field data collection methods, on-the-fly data visualization and query, and subsequent analysis and interpretation. Armed with a fully fused database tethered to high-resolution satellite imagery, we can more accurately reconstruct spatial and temporal paleoenvironmental conditions and efficiently address key scientific questions, such as those regarding the relative importance of internal and external ecological, climatological, and tectonic forcings on evolutionary change in the fossil record. In close association with colleagues working in neighboring project areas, this work advances multidisciplinary and collaborative research, training, and long-range antiquities conservation in the Hadar region.

Campisano, C. J.; Dimaggio, E. N.; Arrowsmith, J. R.; Kimbel, W. H.; Reed, K. E.; Robinson, S. E.; Schoville, B. J.

2008-12-01

160

Reindeer papillomavirus transforming properties correlate with a highly conserved E5 region.  

PubMed Central

A papillomavirus was isolated from the epithelial layer of a cutaneous fibropapilloma on a Swedish reindeer (Rangifer tarandus). Reindeer papillomavirus (RPV) is morphologically indistinguishable from other papillomaviruses, but the restriction enzyme cleavage pattern of its genome is different. No sequence homology was detected between RPV DNA and the DNAs of bovine papillomavirus type 1 (BPV-1) and avian papillomavirus when hybridization was performed under stringent conditions. However, the RPV genome hybridized to the genome of the European elk papillomavirus and the deer papillomavirus under stringent conditions. A physical map of the RPV genome was constructed, and selected regions of the genome, covering the open translational reading frame (ORF) E5 and part of the E1 and L1 ORFs, were studied by nucleotide sequence analysis. The results made it possible to align the RPV genome with the genome of BPV-1. The E5 ORF of RPV has the potential to encode a 44-amino-acid, exceptionally hydrophobic polypeptide which is very similar to the E5 polypeptides of BPV-1 and deer and European elk papillomaviruses. RPV is oncogenic for hamsters and transforms C127 mouse cells in vitro. Several virus-specific mRNAs were detected in RPV-transformed C127 cells. Images PMID:2822949

Moreno-Lopez, J; Ahola, H; Eriksson, A; Bergman, P; Pettersson, U

1987-01-01

161

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

162

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

163

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

164

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

165

Immunization with the RTS,S/AS malaria vaccine induces IFN-?(+)CD4 T cells that recognize only discrete regions of the circumsporozoite protein and these specificities are maintained following booster immunizations and challenge.  

PubMed

In a Phase 2a trial of the RTS,S/AS vaccine, we described significant association between protection against infection and vaccine-induced CD4 T cells. To determine whether processing of the circumsporozoite protein as a component of the RTS,S particulate antigen yields the same HLA-DR-restricted epitopes as those recognized by CD4 T cells from donors immunized by exposure to attenuated or infectious sporozoites we mapped the specificities of the RTS,S primed CD4 T cells by measuring IFN-? cultured Elispot responses to pairs of overlapping 15 a.a. peptides that span the protein's C-terminus. Peptide pairs representing the previously described TH2R, T* and CS.T3 epitopes, were immunoprevalent and immunodominant. There was no response to the peptides corresponding to the human thrombospondin homology region. Responses to the CD4 T cell epitopes were restricted by multiple HLA-DR haplotypes. Of note, HLA-DR4 and HLA-DR11 restricted epitopes in the T* region and in the location on the CS protein defined by peptide pair 4, respectively. We conclude that processing of the CS protein derived from the RTS,S antigen leads to the generation of HLA-DR-restricted epitopes that are similar to those identified previously using CD4 T cells from subjects immunized with and protected by attenuated sporozoites or exposed to infectious sporozoites. This may in part account for the protective efficacy of the RTS,S/AS vaccine. PMID:21983360

Schwenk, Robert; Lumsden, Joanne M; Rein, Lisa E; Juompan, Laure; Kester, Kent E; Heppner, D Gray; Krzych, Urszula

2011-11-01

166

Identification of RNA-binding proteins in RAW 264.7 cells that recognize a lipopolysaccharide-responsive element in the 3-untranslated region of the murine cyclooxygenase-2 mRNA.  

PubMed

RAW 264.7 cells rapidly induce cyclooxygenase-2 (COX-2) in response to lipopolysaccharide treatment. Part of the increased COX-2 expression occurred through post-transcriptional mechanisms mediated through specific regions of the 3'-untranslated region (UTR) of the message. The proximal region of the 3'-UTR of COX-2 contains a highly conserved AU-rich element that was able to confer lipopolysaccharide regulation of a chimeric reporter-gene. Electrophoretic mobility shift assays demonstrated that the RNA-binding proteins TIAR, AUF1, HuR, and TIA-1 all form an RNA-protein complex with the first 60 nucleotides of the 3'-UTR of COX-2. Biotinylated RNA probes were used to isolate additional proteins that bind the 3'-UTR of COX-2. We identified several RNA-binding proteins including TIAR, AUF1, CBF-A, RBM3, heterogeneous nuclear ribonucleoprotein (hnRNP) A3, and hnRNP A2/B1. We identified four alternatively spliced isoforms of AUF1 which migrated at multiple isoelectric points. Likewise, we identified alternatively spliced isoforms of CBF-A, hnRNP A3, and hnRNP A2/B1. Western analysis of two-dimensional gels identified multiple isoforms of TIA-1, TIAR, and AUF1 at pI values that spanned nearly 3 pH units. Thus, through a combination of alternative splicing and post-translational modification cells are able to increase greatly the repertoire of protein species expressed at a given time or in response to extracellular stimuli. PMID:14662769

Cok, Steven J; Acton, Stephen J; Sexton, Alison E; Morrison, Aubrey R

2004-02-27

167

Evolutionarily conserved and divergent regulatory sequences in the fish rod opsin promoter  

Microsoft Academic Search

Fish have multiple types and subtypes of opsin genes that are expressed in a highly regulated manner in retinal photoreceptor cells. In the rod opsin proximal promoter region (RPPR) of zebrafish (Danio rerio), the BAT 1 regulatory region contains highly conserved OTX (GATTA) and OTX-like (TATTA) sequences that can be recognized by the mammalian cone–rod homeobox (CRX) protein. However, binding

Shoji Kawamura; Kumiko Takeshita; Taro Tsujimura; Satoshi Kasagi; Yoshifumi Matsumoto

2005-01-01

168

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

169

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

170

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

171

The potential for electricity generation from on-shore wind energy under the constraints of nature conservation: a case study for two regions in Germany  

Microsoft Academic Search

In spite of the well-acknowledged environmental benefits of electricity generation from wind energy, there is increasing concern about impacts from wind turbines on local ecosystems and on the natural scenery. A GIS-based approach is developed to analyse the effect of different nature conservation criteria on the wind energy potential in quantitative terms. Results for two case study regions in Germany,

W. Krewitt; J. Nitsch

2003-01-01

172

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

SciTech Connect

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

Quinn, A.; Cunningham, M.W. [Univ. of Oklahoma Health Sciences Center, Oklahoma City, OK (United States); Adderson, E.E. [Univ. of Utah, Salt Lake City, UT (United States)] [and others

1995-04-15

173

[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

174

[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

175

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

176

A conserved and essential basic region mediates tRNA binding to the Elp1 subunit of the Saccharomyces cerevisiae Elongator complex.  

PubMed

Elongator is a conserved, multi-protein complex discovered in Saccharomyces cerevisiae, loss of which confers a range of pleiotropic phenotypes. Elongator in higher eukaryotes is required for normal growth and development and a mutation in the largest subunit of human Elongator (Elp1) causes familial dysautonomia, a severe recessive neuropathy. Elongator promotes addition of mcm(5) and ncm(5) modifications to uridine in the tRNA anticodon 'wobble' position in both yeast and higher eukaryotes. Since these modifications are required for the tRNAs to function efficiently, a translation defect caused by hypomodified tRNAs may therefore underlie the variety of phenotypes associated with Elongator dysfunction. The Elp1 carboxy-terminal domain contains a highly conserved arginine/lysine-rich region that resembles a nuclear localization sequence (NLS). Using alanine substitution mutagenesis, we show that this region is essential for Elongator's function in tRNA wobble uridine modification. However, rather than acting to determine the nucleo-cytoplasmic distribution of Elongator, we find that the basic region plays a critical role in a novel interaction between tRNA and the Elp1 carboxy-terminal domain. Thus the conserved basic region in Elp1 may be essential for tRNA wobble uridine modification by acting as tRNA binding motif. PMID:24750273

Di Santo, Rachael; Bandau, Susanne; Stark, Michael J R

2014-06-01

177

A conserved and essential basic region mediates tRNA binding to the Elp1 subunit of the Saccharomyces cerevisiae Elongator complex  

PubMed Central

Elongator is a conserved, multi-protein complex discovered in Saccharomyces cerevisiae, loss of which confers a range of pleiotropic phenotypes. Elongator in higher eukaryotes is required for normal growth and development and a mutation in the largest subunit of human Elongator (Elp1) causes familial dysautonomia, a severe recessive neuropathy. Elongator promotes addition of mcm5 and ncm5 modifications to uridine in the tRNA anticodon ‘wobble’ position in both yeast and higher eukaryotes. Since these modifications are required for the tRNAs to function efficiently, a translation defect caused by hypomodified tRNAs may therefore underlie the variety of phenotypes associated with Elongator dysfunction. The Elp1 carboxy-terminal domain contains a highly conserved arginine/lysine-rich region that resembles a nuclear localization sequence (NLS). Using alanine substitution mutagenesis, we show that this region is essential for Elongator's function in tRNA wobble uridine modification. However, rather than acting to determine the nucleo-cytoplasmic distribution of Elongator, we find that the basic region plays a critical role in a novel interaction between tRNA and the Elp1 carboxy-terminal domain. Thus the conserved basic region in Elp1 may be essential for tRNA wobble uridine modification by acting as tRNA binding motif. PMID:24750273

Di Santo, Rachael; Bandau, Susanne; Stark, Michael J R

2014-01-01

178

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

179

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

180

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

181

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

182

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

183

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

184

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

USGS Publications Warehouse

Implementation of the U.S. Department of Agriculture (USDA) Conservation Reserve Program (CRP) and Wetlands Reserve Program (WRP) has resulted in the restoration of approximately 2,200,000 ha (5,436,200 acres) of wetland and grassland habitats in the Prairie Pothole Region. These restored habitats are known to provide various ecosystem services; however, little work has been conducted to quantify and verify benefits on program lands (lands enrolled in the CRP and WRP) in agriculturally dominated landscapes of the Prairie Pothole Region. To address this need, the U.S. Geological Survey (USGS), in collaboration with the USDA Farm Service Agency and Natural Resources Conservation Service, initiated a study to develop and apply approaches to quantify changes in ecosystem services resulting from wetland restoration activities funded by the USDA. To accomplish this goal, the USGS conducted a comprehensive, stratified survey of 204 catchments (wetland and surrounding uplands contributing runoff to the wetland) in 1997 and 270 catchments in 2004 to gather data necessary for estimating various ecosystem services. In 1997 and 2004, the surveys included catchments with seasonal and semipermanent wetlands that were restored as part of USDA conservation programs, as well as nonprogram catchments in native prairie. Additionally, in 2004 data collection was expanded to include temporary wetlands for all treatments and nonprogram cropped catchments for all wetland classes: temporary, seasonal, and semipermanent. A key element in the sample design is that catchments span an alteration gradient ranging from highly altered, such as cropland, to minimally altered, such as native prairie. Therefore, we evaluated restoration programs by comparing changes in program (restored) catchments to nonprogram (cropland and native prairie) catchments. Information collected during both surveys included easily measured soil, vegetation, and morphological variables that were used to estimate the following ecosystem services: plant community quality and richness, carbon sequestration, floodwater storage, sediment and nutrient reduction, and potential wildlife habitat suitability. In this report, we evaluate the extent that these ecosystem services changed in restored wetlands relative to cropland and native prairie baselines. In most cases, our results indicate restoration activities funded by the USDA have positively influenced ecosystem services in comparison to a cropped wetland baseline; however, most benefits were only considered at a site-specific scale, and better quantification of off-site benefits associated with conservation programs will require detailed spatial data on all land areas enrolled in conservation programs.

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

2008-01-01

185

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

186

Our Vision: To be recognized  

E-print Network

mentoring of students · Adjust workloads of graduate faculty to support increased expectations for research, and global communities through publications, readings, consultations, performances, teacher · Recruit and foster outstanding teacher-scholars who excel at research · Recognize, facilitate, and reward

Barrash, Warren

187

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

188

Developing Spatially Explicit Habitat Models for Grassland Bird Conservation Planning in the Prairie Pothole Region of North Dakota1  

Microsoft Academic Search

Conservation planning for birds is increasingly focused on landscapes. However, little spatially explicit infor- mation is available to guide landscape-level conserva- tion planning for many species of birds. We used geo- referenced 1995 Breeding Bird Survey (BBS) data in conjunction with land-cover information to develop a spatially explicit habitat model predicting the occurrence of Northern Harrier (Circus cyaneus) in the

Neal D. Niemuth; Michael E. Estey; Charles R. Loesch

189

Conservation Focus and Executive  

E-print Network

Northwest Power and Conservation Council Focus and Executive Summary Background Power Committee Walla Walla May 12, 2009 #12;Northwest Power and Conservation Council Conditions Facing the Region and Conservation Council Resource Alternatives · Increased cost-effective efficiency potential ­ Technological

190

Conserved domains of subtype C nef from South African HIV type 1-infected individuals include cytotoxic T lymphocyte epitope-rich regions.  

PubMed

We have characterized 43 nef sequences from subtype C HIV-1-infected South Africans and compared deduced amino acid sequences with other subtypes to identify areas of conservation. Our Nef amino acid sequences were aligned with a consensus subtype B, HXB2 reference strain and a consensus subtype C sequence. All were found to be highly homologous to subtype B in the central region of Nef, but more variable at the N and C termini of the molecule. Alignment of a consensus amino acid sequence generated from South African subtype C Nef with subtypes A, B, and D underscores cross-clade conservation in the central domain of the molecule. This domain is also rich in previously described cytotoxic T lymphocyte (CTL) epitopes that are restricted by commonly found HLA molecules in the South African population. PMID:11779357

Mashishi, T; Loubser, S; Hide, W; Hunt, G; Morris, L; Ramjee, G; Abdool-Karim, S; Williamson, C; Gray, C M

2001-11-20

191

Binding of c-Raf1 kinase to a conserved acidic sequence within the carboxyl-terminal region of the HIV-1 Nef protein.  

PubMed

Nef is a membrane-associated cytoplasmic phosphoprotein that is well conserved among the different human (HIV-1 and HIV-2) and simian immunodeficiency viruses and has important roles in down-regulating the CD4 receptor and modulating T-cell signaling pathways. The ability to modulate T-cell signaling pathways suggests that Nef may physically interact with T-cell signaling proteins. In order to identify Nef binding proteins and map their site(s) of interaction, we targeted a highly conserved acidic sequence at the carboxyl-terminal region of Nef sharing striking similarity with an acidic sequence at the c-Raf1-binding site within the Ras effector region. Here, we used deletion and site-specific mutagenesis to generate mutant Nef proteins fused to bacterial glutathione S-transferase in in vitro precipitation assays and immunoblot analysis to map the specific interaction between the HIV-1LAI Nef and c-Raf1 to a conserved acidic sequence motif containing the core sequence Asp-Asp-X-X-X-Glu (position 174-179). Significantly, we demonstrate that substitution of the nonpolar glycine residue for either or both of the conserved negatively charged aspartic acid residues at positions 174 and 175 in the full-length recombinant Nef protein background completely abrogated binding of c-Raf1 in vitro. In addition, lysates from a permanent CEM T-cell line constitutively expressing the native HIV-1 Nef protein was used to coimmunoprecipitate a stable Nef-c-Raf1 complex, suggesting that molecular interactions between Nef and c-Raf1, an important downstream transducer of cell signaling through the c-Raf1-MAP kinase pathway, occur in vivo. This interaction may account for the Nef-induced perturbations of T-cell signaling and activation pathways in vitro and in vivo. PMID:9624170

Hodge, D R; Dunn, K J; Pei, G K; Chakrabarty, M K; Heidecker, G; Lautenberger, J A; Samuel, K P

1998-06-19

192

Functional Analysis of Conserved Non-Coding Regions Around the Short Stature hox Gene (shox) in Whole Zebrafish Embryos  

PubMed Central

Background Mutations in the SHOX gene are responsible for Leri-Weill Dyschondrosteosis, a disorder characterised by mesomelic limb shortening. Recent investigations into regulatory elements surrounding SHOX have shown that deletions of conserved non-coding elements (CNEs) downstream of the SHOX gene produce a phenotype indistinguishable from Leri-Weill Dyschondrosteosis. As this gene is not found in rodents, we used zebrafish as a model to characterise the expression pattern of the shox gene across the whole embryo and characterise the enhancer domains of different CNEs associated with this gene. Methodology/Principal Findings Expression of the shox gene in zebrafish was identified using in situ hybridization, with embryos showing expression in the blood, putative heart, hatching gland, brain pharyngeal arch, olfactory epithelium, and fin bud apical ectodermal ridge. By identifying sequences showing 65% identity over at least 40 nucleotides between Fugu, human, dog and opossum we uncovered 35 CNEs around the shox gene. These CNEs were compared with CNEs previously discovered by Sabherwal et al., resulting in the identification of smaller more deeply conserved sub-sequence. Sabherwal et al.'s CNEs were assayed for regulatory function in whole zebrafish embryos resulting in the identification of additional tissues under the regulatory control of these CNEs. Conclusion/Significance Our results using whole zebrafish embryos have provided a more comprehensive picture of the expression pattern of the shox gene, and a better understanding of its regulation via deeply conserved noncoding elements. In particular, we identify additional tissues under the regulatory control of previously identified SHOX CNEs. We also demonstrate the importance of these CNEs in evolution by identifying duplicated shox CNEs and more deeply conserved sub-sequences within already identified CNEs. PMID:21731768

Kenyon, Emma J.; McEwen, Gayle K.; Callaway, Heather; Elgar, Greg

2011-01-01

193

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

194

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

195

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

196

Developmental Regulation of Ganglioside Antigens Recognized by the JONES Antibody  

Microsoft Academic Search

The JONES monoclonal antibody has been immunocyto- chemically associated with regions of the developing rat brain where cell and axon migrations are occurring (Mender- Otero et al., 1988, 1988). In the present study the antigens recognized by the JONES antibody were analyzed in a va- riety of brain regions and at developmental ages selected to correspond to the preceding immunocytochemical

Burkhard Schlosshauer; Andrew S. Blum; Rosalia Mendez-Otero; Colin J. Barnstable; Martha Constantine-Paton

1988-01-01

197

The impact of the number of excised axillary nodes and of the percentage of involved nodes on regional nodal failure in patients treated by breast-conserving surgery with or without regional irradiation  

SciTech Connect

Purpose: After breast-conserving surgery, recommendations for regional nodal radiotherapy are usually based on the number of positive nodes. This number is dependent on the number of nodes removed during the axillary dissection. This study examines whether the percentage of positive nodes may help to select patients for regional radiotherapy. Methods and Materials: A retrospective study was conducted on 1,372 T1-T2 node-positive breast cancer patients treated at L'Hotel-Dieu de Quebec Hospital between 1972 and 1997. Results: Among the patients who did not receive regional radiotherapy, the percentage of involved nodes was significantly associated with axillary failure. Ten-year axillary control rates were 97% and 91% when the percentage of involved nodes was <50% and {>=}50%, respectively (p = 0.007). In addition, regional radiotherapy is always significantly associated with a decrease in overall regional failure (axillary and/or supraclavicular), regardless of the percentage of involved nodes. However, regional radiotherapy reduced the axillary failure rate (2% vs. 9%, p = 0.007) only when more than a specific percentage of nodes was involved ({>=}40% if N1-3 and {>=}50% if N>3 nodes). Conclusions: The percentage of involved nodes should be taken into consideration in selecting patients for regional radiotherapy. Irradiation of the axilla should be reserved for patients with a specific ratio: >40% involved nodes if N1-3 and {>=}50% involved nodes if N>3 nodes.

Fortin, Andre [Department of Radiation Oncology, L'Hotel-Dieu de Quebec, Quebec City, Quebec (Canada)]. E-mail: afortin@videotron.ca; Dagnault, Anne [Department of Radiation Oncology, L'Hotel-Dieu de Quebec, Quebec City, Quebec (Canada); Blondeau, Lucie [Department of Radiation Oncology, L'Hotel-Dieu de Quebec, Quebec City, Quebec (Canada); Thi Trinh Thuc Vu [Department of Radiation Oncology, L'Hotel-Dieu de Quebec, Quebec City, Quebec (Canada); Larochelle, Marie [Department of Radiation Oncology, L'Hotel-Dieu de Quebec, Quebec City, Quebec (Canada)

2006-05-01

198

Assignment of the hypoxia-inducible factor 1alpha gene to a region of conserved synteny on mouse chromosome 12 and human chromosome 14q.  

PubMed

Hypoxia-inducible factor 1 (HIF-1) is a basic helix-loop-helix transcription factor that mediates homeostatic responses to hypoxia. HIF-1 is a heterodimer consisting of HIF-1alpha, which is encoded by the HIF1A gene, complexed with HIF-1beta, which is encoded by the ARNT gene. In this paper we report the assignment of Hif1a and HIF1A to mouse chromosome 12 and human chromosome 14, respectively. HIF1A was assigned to human chromosome 14q21-q24 by analysis of somatic cell hybrids and by fluorescence in situ hybridization. Hif1a was localized by interspecific backcross analysis within a region of mouse chromosome 12 encompassing >30 cM that demonstrates conservation of synteny with a region of human chromosome 14 extending from PAX9 at 14q12-q13 to IGHC at 14q32.33. PMID:8786149

Semenza, G L; Rue, E A; Iyer, N V; Pang, M G; Kearns, W G

1996-06-15

199

Highly conserved motifs in non-coding regions of Sirevirus retrotransposons: the key for their pattern of distribution within and across plants?  

PubMed Central

Background Retrotransposons are key players in the evolution of eukaryotic genomes. Moreover, it is now known that some retrotransposon classes, like the abundant and plant-specific Sireviruses, have intriguingly distinctive host preferences. Yet, it is largely unknown if this bias is supported by different genome structures. Results We performed sensitive comparative analysis of the genomes of a large set of Ty1/copia retrotransposons. We discovered that Sireviruses are unique among Pseudoviridae in that they constitute an ancient genus characterized by vastly divergent members, which however contain highly conserved motifs in key non-coding regions: multiple polypurine tract (PPT) copies cluster upstream of the 3' long terminal repeat (3'LTR), of which the terminal PPT tethers to a distinctive attachment site and is flanked by a precisely positioned inverted repeat. Their LTRs possess a novel type of repeated motif (RM) defined by its exceptionally high copy number, symmetry and core CGG-CCG signature. These RM boxes form CpG islands and lie a short distance upstream of a conserved promoter region thus hinting towards regulatory functions. Intriguingly, in the envelope-containing Sireviruses additional boxes cluster at the 5' vicinity of the envelope. The 5'LTR/internal domain junction and a polyC-rich integrase signal are also highly conserved domains of the Sirevirus genome. Conclusions Our comparative analysis of retrotransposon genomes using advanced in silico methods highlighted the unique genome organization of Sireviruses. Their structure may dictate a life cycle with different regulation and transmission strategy compared to other Pseudoviridae, which may contribute towards their pattern of distribution within and across plants. PMID:20132532

2010-01-01

200

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

PubMed Central

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

Seufi, AlaaEddeen M

2008-01-01

201

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

202

Recognizing new medical knowledge computationally.  

PubMed Central

Can new medical knowledge be recognized computationally? We know knowledge is changing, and our knowledge-based systems will need to accommodate that change in knowledge on a regular basis if they are to stay successful. Computational recognition of these changes seems desirable. It is unlikely that low level objects in the computational universe, bits and characters, will change much over time, higher level objects of language, where meaning begins to emerge, may show change. An analysis of ten arbitrarily selected paragraphs from the Medical Knowledge Self-Assessment Program of the American College of Physicians was used as a test bed for nominal phrase recognition. While there were words not known to Meta-1.2, only 8 of the 32 concepts new to the primary author were pointed to by new words. Use of a barrier word method was successful in identifying 23 of the 32 new concepts. Use of co-occurrence (in sentences) of putative nominal phrases may reduce the amount of human effort involved in recognizing the emergence of new relationships. PMID:8130505

Nelson, S. J.; Cole, W. G.; Tuttle, M. S.; Olson, N. E.; Sherertz, D. D.

1993-01-01

203

Force-dependent isomerization kinetics of a highly conserved proline switch modulates the mechanosensing region of filamin  

PubMed Central

Proline switches, controlled by cis–trans isomerization, have emerged as a particularly effective regulatory mechanism in a wide range of biological processes. In this study, we use single-molecule mechanical measurements to develop a full kinetic and energetic description of a highly conserved proline switch in the force-sensing domain 20 of human filamin and how prolyl isomerization modulates the force-sensing mechanism. Proline isomerization toggles domain 20 between two conformations. A stable cis conformation with slow unfolding, favoring the autoinhibited closed conformation of filamin’s force-sensing domain pair 20–21, and a less stable, uninhibited conformation promoted by the trans form. The data provide detailed insight into the folding mechanisms that underpin the functionality of this binary switch and elucidate its remarkable efficiency in modulating force-sensing, thus combining two previously unconnected regulatory mechanisms, proline switches and mechanosensing. PMID:24706888

Rognoni, Lorenz; Möst, Tobias; Žoldák, Gabriel; Rief, Matthias

2014-01-01

204

A perennial ryegrass CBF gene cluster is located in a region predicted by conserved synteny between Poaceae species.  

PubMed

CBF/DREB1 proteins are the most important regulators of the cold temperature signaling pathway in many plants. CBF genes are candidates for low-temperature tolerance QTL in wheat and barley. Ten novel putative CBF cDNAs of perennial ryegrass (Lolium perenne L.) have been isolated from cold-treated leaf tissue. Their primary structures contain some conserved motifs, characteristic of the gene class. Phylogenetic analysis revealed that LpCBF genes were attributable to the HvCBF3-, and HvCBF4-subgroups following the previously proposed classification of barley CBF genes. RT-PCR analysis revealed that the expression of LpCBF genes was rapidly induced in response to low temperature and that the expression pattern under the low-temperature conditions for a long period was different between the various LpCBF genes. Five of the ten LpCBF genes were assigned to the genetic linkage map using the p150/112 reference mapping population. LpCBFIb, LpCBFII, LpCBFIIIb and LpCBFIIIc were mapped on LG5 forming a cluster within 2.2 cM, while LpCBFVb was located on LG1. Based on comparative genetic studies, conserved synteny for CBF gene family was observed between the Triticeae cereals and perennial ryegrass. Information on the perennial ryegrass CBF genes at both the molecular and genetic level obtained in this study would be useful for the further study on the role of CBF genes and low-temperature tolerance in grasses. PMID:17075706

Tamura, K; Yamada, T

2007-01-01

205

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.

206

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

207

CUSP: an algorithm to distinguish structurally conserved and unconserved regions in protein domain alignments and its application in the study of large length variations  

PubMed Central

Background Distantly related proteins adopt and retain similar structural scaffolds despite length variations that could be as much as two-fold in some protein superfamilies. In this paper, we describe an analysis of indel regions that accommodate length variations amongst related proteins. We have developed an algorithm CUSP, to examine multi-membered PASS2 superfamily alignments to identify indel regions in an automated manner. Further, we have used the method to characterize the length, structural type and biochemical features of indels in related protein domains. Results CUSP, examines protein domain structural alignments to distinguish regions of conserved structure common to related proteins from structurally unconserved regions that vary in length and type of structure. On a non-redundant dataset of 353 domain superfamily alignments from PASS2, we find that 'length- deviant' protein superfamilies show > 30% length variation from their average domain length. 60% of additional lengths that occur in indels are short-length structures (< 5 residues) while 6% of indels are > 15 residues in length. Structural types in indels also show class-specific trends. Conclusion The extent of length variation varies across different superfamilies and indels show class-specific trends for preferred lengths and structural types. Such indels of different lengths even within a single protein domain superfamily could have structural and functional consequences that drive their selection, underlying their importance in similarity detection and computational modelling. The availability of systematic algorithms, like CUSP, should enable decision making in a domain superfamily-specific manner. PMID:18513436

Sandhya, Sankaran; Pankaj, Barah; Govind, Madabosse Kande; Offmann, Bernard; Srinivasan, Narayanaswamy; Sowdhamini, Ramanathan

2008-01-01

208

Mapping of ATP binding regions in poly(A) polymerases by photoaffinity labeling and by mutational analysis identifies a domain conserved in many nucleotidyltransferases.  

PubMed Central

We have identified regions in poly(A) polymerases that interact with ATP. Conditions were established for efficient cross-linking of recombinant bovine and yeast poly(A) polymerases to 8-azido-ATP. Mn2+ strongly stimulated this reaction due to a 50-fold lower Ki for 8-azido-ATP in the presence of Mn2+. Mutations of the highly conserved Asp residues 113, 115, and 167, critical for metal binding in the catalytic domain of bovine poly(A) polymerase, led to a strong reduction of cross-linking efficiency, and Mn2+ no longer stimulated the reaction. Sites of 8-azido-ATP cross-linking were mapped in different poly(A) polymerases by CNBr-cleavage and analysis of tryptic peptides by mass spectroscopy. The main cross-link in Schizosaccharomyces pombe poly(A) polymerase could be assigned to the peptide DLELSDNNLLK (amino acids 167-177). Database searches with sequences surrounding the cross-link site detected significant homologies to other nucleotidyltransferase families, suggesting a conservation of the nucleotide-binding fold among these families of enzymes. Mutations in the region of the "helical turn motif" (a domain binding the triphosphate moiety of the nucleotide) and in the suspected nucleotide-binding helix of bovine poly(A) polymerase impaired ATP binding and catalysis. The results indicate that ATP is bound in part by the helical turn motif and in part by a region that may be a structural analog to the fingers domain found in many polymerases. PMID:10595540

Martin, G.; Jenö, P.; Keller, W.

1999-01-01

209

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...

210

Merging Disparate Data Sources Into a Paleoanthropological Geodatabase for Research, Education, and Conservation in the Greater Hadar Region (Afar, Ethiopia)  

Microsoft Academic Search

Understanding the geographic, temporal, and environmental contexts of human evolution requires the ability to compare wide-ranging datasets collected from multiple research disciplines. Paleoanthropological field- research projects are notoriously independent administratively even in regions of high transdisciplinary importance. As a result, valuable opportunities for the integration of new and archival datasets spanning diverse archaeological assemblages, paleontological localities, and stratigraphic sequences are

C. J. Campisano; E. N. Dimaggio; J. R. Arrowsmith; W. H. Kimbel; K. E. Reed; S. E. Robinson; B. J. Schoville

2008-01-01

211

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

212

Advances in universal influenza virus vaccine design and antibody mediated therapies based on conserved regions of the hemagglutinin.  

PubMed

The threat of novel influenza viruses emerging into the human population from animal reservoirs, as well as the short duration of protection conferred by licensed vaccines against human seasonal strains has spurred research efforts to improve upon current vaccines and develop novel therapeutics against influenza viruses. In recent years these efforts have resulted in the identification of novel, highly conserved epitopes for neutralizing antibodies on the influenza virus hemagglutinin protein, which are present in both the stalk and globular head domains of the molecule. The existence of such epitopes may allow for generation of novel therapeutic antibodies, in addition to serving as attractive targets of novel vaccine design. The aims of developing improved vaccines include eliciting broader protection from drifted strains, inducing long-lived immunity against seasonal strains, and allowing for the rational design of vaccines that can be stockpiled for use as pre-pandemic vaccines. In addition, an increased focus on influenza virus vaccine research has prompted an improved understanding of how the immune system responds to influenza virus infection. PMID:25007847

Krammer, Florian; Palese, Peter; Steel, John

2015-01-01

213

A very conservative region of ApoB-100 in the putative binding region to the LDL receptor in the Toulouse population.  

PubMed

The nucleotide sequence of the putative binding site of ApoB-100 was studied in Hypercholesterolemic IIa patients and controls from the Toulouse area. Only one patient possesses the 3,500 mutation, which is responsible for defective familial hypercholesterolemia. The other individuals (including 39 patients and 14 controls) display the same nucleotide sequence although four nucleotide substitutions have been described in this region. This homogeneity of the Toulouse population in the putative binding site of ApoB-100 is discussed. PMID:1483706

Avoustin, P; Mostachi, H; Perret, B; Cambou, J P; Cambien, F; de Préval, C

1992-12-01

214

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

215

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

216

Conserved proline-rich region of Ebola virus matrix protein VP40 is essential for plasma membrane targeting and virus-like particle release.  

PubMed

The matrix protein VP40 is essential for Ebola virus (EBOV) and Marburg virus assembly and budding at the plasma membrane. In this study we have investigated the effect of single amino acid substitutions in a conserved proline-rich region of the EBOV VP40 located in the carboxy-terminal part of the protein. We demonstrate that substitutions within this region result in an alteration of intracellular VP40 localization and also cause a reduction or a complete block of virus-like particle budding, a benchmark of VP40 function. Furthermore, some mutated VP40s revealed an enhanced binding with cellular Sec24C, a part of the coat protein complex II (COPII) vesicular transport system. Analysis of the 3-dimensional structure of VP40 revealed the spatial proximity of the proline-rich region and an earlier identified site of interaction with Sec24C, thus allowing us to hypothesize that the altered intracellular localization of the VP40 mutants is a consequence of defects in their interaction with COPII-mediated vesicular transport. PMID:21987765

Reynard, Olivier; Nemirov, Kirill; Page, Audrey; Mateo, Mathieu; Raoul, Hervé; Weissenhorn, Winfried; Volchkov, Viktor E

2011-11-01

217

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

218

Recognizing characters of ancient manuscripts  

NASA Astrophysics Data System (ADS)

Considering printed Latin text, the main issues of Optical Character Recognition (OCR) systems are solved. However, for degraded handwritten document images, basic preprocessing steps such as binarization, gain poor results with state-of-the-art methods. In this paper ancient Slavonic manuscripts from the 11th century are investigated. In order to minimize the consequences of false character segmentation, a binarization-free approach based on local descriptors is proposed. Additionally local information allows the recognition of partially visible or washed out characters. The proposed algorithm consists of two steps: character classification and character localization. Initially Scale Invariant Feature Transform (SIFT) features are extracted which are subsequently classified using Support Vector Machines (SVM). Afterwards, the interest points are clustered according to their spatial information. Thereby, characters are localized and finally recognized based on a weighted voting scheme of pre-classified local descriptors. Preliminary results show that the proposed system can handle highly degraded manuscript images with background clutter (e.g. stains, tears) and faded out characters.

Diem, Markus; Sablatnig, Robert

2010-02-01

219

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

220

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

221

The Thai Phase III HIV Type 1 Vaccine Trial (RV144) Regimen Induces Antibodies That Target Conserved Regions Within the V2 Loop of gp120  

PubMed Central

Abstract The Thai Phase III clinical trial (RV144) showed modest efficacy in preventing HIV-1 acquisition. Plasma collected from HIV-1-uninfected trial participants completing all injections with ALVAC-HIV (vCP1521) prime and AIDSVAX B/E boost were tested for antibody responses against HIV-1 gp120 envelope (Env). Peptide microarray analysis from six HIV-1 subtypes and group M consensus showed that vaccination induced antibody responses to the second variable (V2) loop of gp120 of multiple subtypes. We further evaluated V2 responses by ELISA and surface plasmon resonance using cyclic (Cyc) and linear V2 loop peptides. Thirty-one of 32 vaccine recipients tested (97%) had antibody responses against Cyc V2 at 2 weeks postimmunization with a reciprocal geometric mean titer (GMT) of 1100 (range: 200–3200). The frequency of detecting plasma V2 antibodies declined to 19% at 28 weeks post-last injection (GMT: 110, range: 100–200). Antibody responses targeted the mid-region of the V2 loop that contains conserved epitopes and has the amino acid sequence KQKVHALFYKLDIVPI (HXB2 Numbering sequence 169–184). Valine at position 172 was critical for antibody binding. The frequency of V3 responses at 2 weeks postimmunization was modest (18/32, 56%) with a GMT of 185 (range: 100–800). In contrast, naturally infected HIV-1 individuals had a lower frequency of antibody responses to V2 (10/20, 50%; p=0.003) and a higher frequency of responses to V3 (19/20, 95%), with GMTs of 400 (range: 100–3200) and 3570 (range: 200–12,800), respectively. RV144 vaccination induced antibodies that targeted a region of the V2 loop that contains conserved epitopes. Early HIV-1 transmission events involve V2 loop interactions, raising the possibility that anti-V2 antibodies in RV144 may have contributed to viral inhibition. PMID:23035746

Billings, Erik; Rao, Mangala; Williams, Constance; Zolla-Pazner, Susan; Bailer, Robert T.; Koup, Richard A.; Madnote, Sirinan; Arworn, Duangnapa; Shen, Xiaoying; Tomaras, Georgia D.; Currier, Jeffrey R.; Jiang, Mike; Magaret, Craig; Andrews, Charla; Gottardo, Raphael; Gilbert, Peter; Cardozo, Timothy J.; Rerks-Ngarm, Supachai; Nitayaphan, Sorachai; Pitisuttithum, Punnee; Kaewkungwal, Jaranit; Paris, Robert; Greene, Kelli; Gao, Hongmei; Gurunathan, Sanjay; Tartaglia, Jim; Sinangil, Faruk; Korber, Bette T.; Montefiori, David C.; Mascola, John R.; Robb, Merlin L.; Haynes, Barton F.; Ngauy, Viseth; Michael, Nelson L.; Kim, Jerome H.; de Souza, Mark S.

2012-01-01

222

Bat assemblages in conservation areas of a metropolitan region in Southeastern Brazil, including an important karst habitat.  

PubMed

Species richness and abundance of bats were studied in four nature reserves, including a karst area which has many potential rocky shelters for bats, such as caves and rock crevices. The reserves were located in the greater Belo Horizonte metropolitan area, one of the most populated regions of Brazil, within the Atlantic Forest, and Cerrado (Brazilian savanna) ecological domains. Bats were sampled using mist-nets and, in the karst area, also by active searches in shelters. A total of 1,599 bats were captured representing 30 species belonging to four families. There was little similarity among the four chiropteran faunas. The greatest species richness was found in the karst area with 22 species recorded whereas richness estimates in the other areas indicated the need for further studies. Two hundred and sixty-five individuals of 14 species were captured from 56 shelters. Most of the shelters were frequently used for diurnal roosts, and all the bats found belonged to the Phyllostomidae, with the exception of Myotis nigricans (Vespertilionidae), Nyctinomops laticaudatus (Molossidae) and Peropteryx macrotis (Emballonuridae). The sanguinivorous Desmodus rotundus was the most common species in the shelters. The results of this study demonstrate the importance of maintaining multiple protected areas to ensure a representative fauna of bats in a region characterized by a vegetation transition zone and with intense economic activity and high environmental impact. This study also demonstrates the importance of rock shelters for maintaining local bat richness and the importance of active searches for bats in their diurnal roosts for a more thorough sampling of the bat fauna at a given locality. PMID:23917558

Talamoni, S A; Coelho, D A; Dias-Silva, L H; Amaral, A S

2013-05-01

223

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

224

Attending, Foveating and Recognizing Objects in Real World Scenes  

E-print Network

Attending, Foveating and Recognizing Objects in Real World Scenes M°arten Bj¨orkman and Jan will show with practical experiments, robust recognition is easier if the object is foveated and subtendsD size guides the foveal cameras towards the most salient regions. With the object foveated

Björkman, Mårten

225

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

226

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

PubMed

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

2013-01-15

227

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

228

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

229

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

230

Recognizing speech of goats, wolves, sheep and ... non-natives  

Microsoft Academic Search

This paper reviews the current understanding of acoustic–phonetic issues and the problems arising when trying to recognize speech from non-native speakers. Conceptually, regional accents are well modeled by systematic shifts in pronunciation. Therefore, simultaneous recognition of multiple regional variants may be performed by using multiple acoustic models in parallel, or by adding pronunciation variants in the dictionary. Recognition of non-native

Dirk Van Compernolle

2001-01-01

231

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

232

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

E-print Network

-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 the protection, conservation and recovery of sea turtle populations and of the habitats on which they depend

233

Global biodiversity conservation priorities.  

PubMed

The location of and threats to biodiversity are distributed unevenly, so prioritization is essential to minimize biodiversity loss. To address this need, biodiversity conservation organizations have proposed nine templates of global priorities over the past decade. Here, we review the concepts, methods, results, impacts, and challenges of these prioritizations of conservation practice within the theoretical irreplaceability/vulnerability framework of systematic conservation planning. Most of the templates prioritize highly irreplaceable regions; some are reactive (prioritizing high vulnerability), and others are proactive (prioritizing low vulnerability). We hope this synthesis improves understanding of these prioritization approaches and that it results in more efficient allocation of geographically flexible conservation funding. PMID:16825561

Brooks, T M; Mittermeier, R A; da Fonseca, G A B; Gerlach, J; Hoffmann, M; Lamoreux, J F; Mittermeier, C G; Pilgrim, J D; Rodrigues, A S L

2006-07-01

234

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

235

77 FR 15352 - Endangered and Threatened Wildlife and Plants; Expanding Incentives for Voluntary Conservation...  

Federal Register 2010, 2011, 2012, 2013

...Expanding Incentives for Voluntary Conservation Actions Under the Endangered Species...landowners and others to take voluntary conservation actions to benefit species that may...that the benefits of such voluntary conservation actions will be recognized as...

2012-03-15

236

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

237

Optimal Conservation of Migratory Species  

Microsoft Academic Search

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

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

2007-01-01

238

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, additional assistance is also available. Local county conservation districts and the USDA's Natural Resources

Kaye, Jason P.

239

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

PubMed Central

To explore the role of individual residues in the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39), 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 cosynthesized 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. Images PMID:2116005

Fitchen, J H; Knight, S; Andersson, I; Branden, C I; McIntosh, L

1990-01-01

240

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

241

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

242

SUNNYBROOK PRIZE RECOGNIZING EXCELLENCE IN UNDERGRADUATE RESEARCH  

E-print Network

SUNNYBROOK PRIZE RECOGNIZING EXCELLENCE IN UNDERGRADUATE RESEARCH $10,000 PRIZE AWARDED TO THE WINNER 2 0 1 4 The competition recognizes excellence in undergraduate research and 3rd and 4th year undergraduate students are invited to submit their applications. Eligibility ·Should be in your 3rd or 4th year

Barthelat, Francois

243

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

244

Evidence on how a conserved glycine in the hinge region of HapR regulates its DNA binding ability: lessons from a natural variant.  

PubMed

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 HapR(V2)) 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 HapR(V2) to interact with various cognate promoters. Reinstatement of glycine at position 39 restores DNA binding ability of HapR(V2) (HapR(V2G)), thereby rescuing the protease-negative phenotype of this strain. The elution profile of HapR(V2) and HapR(V2G) 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

2011-04-29

245

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

246

DELAITRE, LAPTEV, SIVIC: RECOGNIZING HUMAN ACTIONS IN STILL IMAGES. 1 Recognizing human actions in still images  

E-print Network

DELAITRE, LAPTEV, SIVIC: RECOGNIZING HUMAN ACTIONS IN STILL IMAGES. 1 Recognizing human actions.delaitre@ens-lyon.org Ivan Laptev2 ivan.laptev@inria.fr Josef Sivic2 josef.sivic@ens.fr 1 �cole Normale Supérieure de Lyon 2 or electronic forms. #12;2 DELAITRE, LAPTEV, SIVIC: RECOGNIZING HUMAN ACTIONS IN STILL IMAGES. Interacting

247

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

248

Covariant Conservation Laws in General Relativity  

Microsoft Academic Search

A set of covariant conservation laws is constructed in the general theory of relativity. Their relationship to the generators of infinitesimal coordinate transformations is indicated. In a given coordinate system certain of these quantities may be naturally identified as energy and momentum. We can continue to recognize these conserved quantities in all coordinate systems due to the covariant character of

Arthur Komar

1959-01-01

249

Forest Conservation Portal  

NSDL National Science Digital Library

The Forest Conservation Portal is maintained by Forests.org, a non-governmental organization dedicated to "ending deforestation, preserving old-growth forests, conserving all forests, maintaining climatic systems and commencing the age of ecological restoration." At the Portal, users will find a large series of news articles and resources on forests, forest regions, forest ecology, forest destruction and protection, and related information. Intended for activists and activism, this site contains current news with international coverage.

250

Metal-organic frameworks: Recognizing the unrecognizable  

NASA Astrophysics Data System (ADS)

Separating carbon monoxide from chemically similar nitrogen gas is particularly challenging. Now, a flexible porous coordination polymer has been developed that recognizes carbon monoxide over nitrogen, with structural changes in the material leading to its accelerated adsorption.

Walton, Krista S.

2014-04-01

251

A Selective Advantage for Conservative Viruses  

E-print Network

In this letter we study the full semi-conservative treatment of a model for the co-evolution of a virus and an adaptive immune system. Regions of viability are calculated for both conservatively and semi-conservatively replicating viruses interacting with a realistic semi-conservatively 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 semi-conservative counterpart. This may help explain the existence of a rich range of viruses with conservatively replicating genomes, a trait which is found nowhere else in nature.

Yisroel Brumer; Eugene I. Shakhnovich

2004-01-16

252

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

253

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

254

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

255

Conservation of glp-1 regulation and function in nematodes.  

PubMed Central

The Caenorhabditis elegans (Ce) glp-1 gene encodes a Notch-like receptor. We have cloned glp-1 from C. briggsae (Cb) and C. remanei (Cr), two Caenorhabditis species that have diverged from C. elegans by roughly 20-40 million years. By sequence analysis, we find that the Cb-GLP-1 and Cr-GLP-1 proteins have retained the same motif architecture as Ce-GLP-1, including number of domains. In addition, two regions (CC-linker and regions flanking the ANK repeats) are as highly conserved as regions previously recognized as essential for signaling (e.g., ANK repeats). Phylogenetic analysis of glp-1 sequences suggests a C. briggsae/C. remanei clade with C. elegans as a sister taxon. Using RNAi to test biological functions, we find that Ce-glp-1, Cb-glp-1, and Cr-glp-1 are all required for proliferation of germline stem cells and for specifying blastomere fates in the embryo. In addition, certain biological roles of Cb-glp-1, e.g., in the vulva, have diverged from those of Ce-glp-1 and Cr-glp-1, suggesting a change in either regulation or function of the Cb-glp-1 gene during evolution. Finally, the regulation of glp-1 mRNA, previously analyzed for Ce-glp-1, is conserved in Cb-glp-1, and we identify conserved 3' UTR sequences that may serve as regulatory elements. PMID:11156985

Rudel, D; Kimble, J

2001-01-01

256

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

257

Breaking the Silence Recognizing, Responding, and  

E-print Network

Breaking the Silence Recognizing, Responding, and Treating Childhood Sexual Abuse NYAMFT Annual complex trauma. Traumatic experiences elicit responses that often get in the way of helping us grow, the Collaborative Stage Model of Trauma Treatment, which details for clinicians and for their clients a clear road

Raina, Ramesh

258

TDNN labeling for a HMM recognizer  

Microsoft Academic Search

A system which combines the good short-time classification properties of the time delay neural network (TDNN) with the good integration and overall recognition capabilities of hidden Markov models (HMMs) is proposed for a speaker-independent speech recognizer. The standard vector quantization is replaced by a TDNN labeler giving phonelike labels. In order to avoid hand segmentation for the training of the

Weiye Ma; Dirk Van Compernolle

1990-01-01

259

How State Laws Recognize Advanced Nursing Practice.  

ERIC Educational Resources Information Center

Reviews modifications in state health practice statutes to recognize the expanded scope of nursing practice in view of the disparity between medical functions actually performed by nurses and those considered within the legal definition. Various state approaches indicate a trend to give legal validity to acts performed by nurses. (MF)

Trandel-Korenchuk, Darlene M.; Trandel-Korenchuk, Keith M.

1978-01-01

260

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

261

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

262

50 CFR 665.208 - Protected species conservation.  

...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

263

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

264

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

265

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.

266

Use of crop residue and manure to conserve water and enhance nutrient availability and pearl millet yields in an arid tropical region  

Microsoft Academic Search

Crop residues and manures are often used in temperate regions to control soil erosion and maintain soil organic matter. Because crop residues and manures oxidize more rapidly in warmer climates, benefits from use of these materials may not be as evident for tropical as for temperate region agriculture, especially in drier regions where residues are limited. In 1991 and 1992,

R. K. Aggarwal; Praveen-Kumar; J. F. Power

1997-01-01

267

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

268

PRECISION CONSERVATION  

Technology Transfer Automated Retrieval System (TEKTRAN)

Precision conservation utilizes a set of technologies and procedures that link mapped variables with analytical capabilities to appropriate management actions. It requires the integration of spatial technologies of global positioning systems, remote sensing and geographic information systems with t...

269

7 CFR 1465.36 - Environmental services credits for conservation improvements.  

Code of Federal Regulations, 2010 CFR

...2010-01-01 false Environmental services credits for conservation...AND OTHER OPERATIONS AGRICULTURAL MANAGEMENT ASSISTANCE ...Administration § 1465.36 Environmental services credits for conservation... NRCS recognizes that environmental benefits will be...

2010-01-01

270

Analysis of Potato virus Y Coat Protein Epitopes Recognized by Three Commercial Monoclonal Antibodies  

PubMed Central

Background Potato virus Y (PVY, genus Potyvirus) causes substantial economic losses in solanaceous plants. Routine screening for PVY is an essential part of seed potato certification, and serological assays are often used. The commercial, commonly used monoclonal antibodies, MAb1128, MAb1129, and MAb1130, recognize the viral coat protein (CP) of PVY and distinguish PVYN strains from PVYO and PVYC strains, or detect all PVY strains, respectively. However, the minimal epitopes recognized by these antibodies have not been identified. Methodology/Principal Findings SPOT peptide array was used to map the epitopes in CP recognized by MAb1128, MAb1129, and MAb1130. Then alanine replacement as well as N- and C-terminal deletion analysis of the identified peptide epitopes was done to determine critical amino acids for antibody recognition and the respective minimal epitopes. The epitopes of all antibodies were located within the 30 N-terminal-most residues. The minimal epitope of MAb1128 was 25NLNKEK30. Replacement of 25N or 27N with alanine weakened the recognition by MAb1128, and replacement of 26L, 29E, or 30K nearly precluded recognition. The minimal epitope for MAb1129 was 16RPEQGSIQSNP26 and the most critical residues for recognition were 22I and 23Q. The epitope of MAb1130 was defined by residues 5IDAGGS10. Mutation of residue 6D abrogated and mutation of 9G strongly reduced recognition of the peptide by MAb1130. Amino acid sequence alignment demonstrated that these epitopes are relatively conserved among PVY strains. Finally, recombinant CPs were produced to demonstrate that mutations in the variable positions of the epitope regions can affect detection with the MAbs. Conclusions/Significance The epitope data acquired can be compared with data on PVY CP-encoding sequences produced by laboratories worldwide and utilized to monitor how widely the new variants of PVY can be detected with current seed potato certification schemes or during the inspection of imported seed potatoes as conducted with these MAbs. PMID:25542005

Lankinen, Hilkka; Valkonen, Jari P. T.

2014-01-01

271

A speech recognizer with selectable model parameters  

Microsoft Academic Search

This paper presents the design and simulation results of a hidden Markov model (HMM) based isolated word recognizer IC. The new design can handle any combination of states and mixtures (up to 16 states and 8 mixtures). The speech IC has been verified with 353 test speech data. The recognition accuracy is 93.8% (48-bit) with no truncation and 88.9% with

Wei Han; Cheong-fat Chan; Chiu-sing Choy; Kong-pang Pun

2005-01-01

272

Eelgrass ( Zostera marina L.) in the Chesapeake Bay Region of Mid-Atlantic Coast of the USA: Challenges in Conservation and Restoration  

Microsoft Academic Search

Decreases in seagrass abundance reported from numerous locations around the world suggest that seagrass are facing a global\\u000a crisis. Declining water quality has been identified as the leading cause for most losses. Increased public awareness is leading\\u000a to expanded efforts for conservation and restoration. Here, we report on abundance patterns and environmental issues facing\\u000a eelgrass (Zostera marina), the dominant seagrass

Robert J. Orth; Scott R. Marion; Kenneth A. Moore; David J. Wilcox

2010-01-01

273

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

274

Predicting the conservation status of data-deficient species.  

PubMed

There is little appreciation of the level of extinction risk faced by one-sixth of the over 65,000 species assessed by the International Union for Conservation of Nature. Determining the status of these data-deficient (DD) species is essential to developing an accurate picture of global biodiversity and identifying potentially threatened DD species. To address this knowledge gap, we used predictive models incorporating species' life history, geography, and threat information to predict the conservation status of DD terrestrial mammals. We constructed the models with 7 machine learning (ML) tools trained on species of known status. The resultant models showed very high species classification accuracy (up to 92%) and ability to correctly identify centers of threatened species richness. Applying the best model to DD species, we predicted 313 of 493 DD species (64%) to be at risk of extinction, which increases the estimated proportion of threatened terrestrial mammals from 22% to 27%. Regions predicted to contain large numbers of threatened DD species are already conservation priorities, but species in these areas show considerably higher levels of risk than previously recognized. We conclude that unless directly targeted for monitoring, species classified as DD are likely to go extinct without notice. Taking into account information on DD species may therefore help alleviate data gaps in biodiversity indicators and conserve poorly known biodiversity. Predección del Estado de Conservación de Especies con Deficiencia de Datos. PMID:25124400

Bland, Lucie M; Collen, Ben; Orme, C David L; Bielby, Jon

2015-02-01

275

Recognizing Materials using Perceptually Inspired Features.  

PubMed

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

2013-07-01

276

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

277

Generation of robust CD8+ T-cell responses against subdominant epitopes in conserved regions of HIV-1 by repertoire mining with mimotopes.  

PubMed

HLA-A 0201-restricted virus-specific CD8(+) CTL do not appear to control HIV effectively in vivo. To enhance the immunogenicity of a highly conserved subdominant epitope, TV9 (TLNAWVKVV, p24 Gag(19-27)), mimotopes were designed by screening a large combinatorial nonapeptide library with TV9-specific CTL primed in vitro from healthy donors. A mimic peptide with a low binding affinity to HLA-A 0201, TV9p6 (KINAWIKVV), was studied further. Parallel cultures of in vitro-primed CTL showed that TV9p6 consistently activated cross-reactive and equally functional CTL as measured by cytotoxicity, cytokine production and suppression of HIV replication in vitro. Comparison of TCRB gene usage between CTL primed from the same donors with TV9 or TV9p6 revealed a degree of clonal overlap in some cases and an example of a conserved TCRB sequence encoded distinctly at the nucleotide level between individuals (a "public" TCR); however, in the main, distinct clonotypes were recruited by each peptide antigen. These findings indicate that mimotopes can mobilize functional cross-reactive clonotypes that are less readily recruited from the naïve T-cell pool by the corresponding WT epitope. Mimotope-induced repertoire diversification could potentially override subdominance under certain circumstances and enhance vaccine-induced responses to conserved but poorly immunogenic determinants within the HIV proteome. PMID:20432235

Schaubert, Keri L; Price, David A; Salkowitz, Janelle R; Sewell, Andrew K; Sidney, John; Asher, Tedi E; Blondelle, Sylvie E; Adams, Sharon; Marincola, Francesco M; Joseph, Aviva; Sette, Alessandro; Douek, Daniel C; Ayyavoo, Velpandi; Storkus, Walter; Leung, Ming-Ying; Ng, Hwee L; Yang, Otto O; Goldstein, Harris; Wilson, Darcy B; Kan-Mitchell, June

2010-07-01

278

Socioeconomic contexts of primate conservation: population, poverty, global economic demands, and sustainable land use.  

PubMed

Recent assessments by the International Union for Conservation of Nature (IUCN) indicate the existence of about 612 recognized primate species and subspecies (IUCN RedList, 2012), but close to 50% of these taxa are at risk of extinction as a result of human action. In this article, I call attention to underlying regional and global socioeconomic contexts of primate conservation. Using information from FAO and UN databases and other sources, I examine, for the Neotropics, sub-Saharan Africa, and Southeast Asia, trends in forest loss and human demographics and social condition, discuss the impact of global market pressures upon primate habitats, and examine land-use patterns that may favor primate conservation. Between 1990 and 2010, an estimated 149 million ha of forest were lost in the three regions and additional losses are expected in the future. Global human population will increase from 7 billion in 2012 to 9 billion in 2050. Currently, 2 billion people live in the three primate range regions under high levels of poverty. Large-scale deforestation is related to global market demands, especially from developed and developing nations, for food (e.g., cattle), domestic animal feed (e.g., soybeans), biofuel-based crops (e.g., oil palm), and industrial round wood. The growth of protected areas in the three regions has been steady for several decades, but it is not enough to ensure long-term conservation of many primate taxa. Other conservations tools involving sustainable land use and biodiversity conservation corridors are required at the landscape level. The above assessment can easily be applied at the local level by primatologists, giving more precision to conservation initiatives. PMID:23047543

Estrada, Alejandro

2013-01-01

279

The supply of land for conservation uses: evidence from the conservation reserve program  

Microsoft Academic Search

From 1987 to 1990, the Conservation Reserve Program (CRP) operated similarly to a competitive market for conservation lands. Using CRP data on counties from this period, we estimate supply functions for conservation lands for nine US regions. The results allow regions to be grouped according to low (Mountain, North Plains), moderate (Cornbelt, Lake States, South Plains), and high (Appalachian, Delta

Andrew J Plantinga; Ralph Alig; Hsiang-tai Cheng

2001-01-01

280

A Recognized Leader in Marine & Atmospheric  

E-print Network

for Ecosystem Science and Policy · National Resource Center of Aplysia · R.J. Dunlap Marine Conservation Program Health · Tropical Marine Ecosystem · Weather, Climate and Society · Weather Forecasting Ph and everything in between. · Fisheries and Marine Ecosystems · Coral Reef Studies · Observational Oceanography

Miami, University of

281

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

282

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

283

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

284

Conservation of closed loops.  

PubMed

The closed loop hypothesis of Berezovsky and Trifonov implicates the closure of loops of length 25-35 through hydrophobic interactions at the 'locks' as a key event in protein folding. The hypothesis is supported by published analyses of nine major superfolds. Here, we have generated multiple sequence alignments for the nine superfolds with PDB codes lthb, 1ilb, 256b, 2rhe, 1aps, 2stv, 4fxn (2fox), lubq and 7tim and have analysed the degree of conservation at the loop ends. Seventy percent of these loop ends are found to be well conserved and the peak in the distribution of distances between these well conserved regions lies at around 25 residues; both observations are consistent with the Berezovsky and Trifonov's hypothesis. PMID:17459747

Yew, Boon K; Chintapalli, Sree V; Upton, Graham G C; Reynolds, Christopher A

2007-10-01

285

The Cost of Conserved Carbon: Weighing the Monetary, Social, and Climactic Implications of Regional-, National-, and Global-Scale Carbon Abatement Strategies  

NASA Astrophysics Data System (ADS)

Previous schema for analyzing carbon mitigation methods often have lacked realistic costs, comprehensive accounting of trade-offs, and methodological transparency. We offer a dynamic model for evaluating diverse carbon mitigation scenarios based on economics, policy traction, and interplay with climate, society and ecosystems. The model will test the impacts of policy changes across more than two dozen strategies for conserving or avoiding carbon emissions. Users will be able to access the model at rael-c3.berkeley.edu and change underlying assumptions as desired.

Kantner, J. W.; Hoffman, I.; Johnston, J. L.; Kammen, D. M.; Levin, J. E.; Komiyama, R.; Motschenbacher, A.; Gimon, E.

2008-05-01

286

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

287

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

288

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

289

MITOCHONDRIAL PHYLOGEOGRAPHY AND CONSERVATION GENETICS OF WOLVERINE  

E-print Network

the Holarctic Region by the International Union for Conservation of Nature and Natural Resources, is designated, and Sweden (International Union for the Conservation of Nature and Natural Resources 2002). In North America and Asia (International Union for Conservation of Nature and Natural Resources 2002). The International

290

Hepatitis C Virus-Encoded Enzymatic Activities and Conserved RNA Elements in the 3? Nontranslated Region Are Essential for Virus Replication In Vivo  

PubMed Central

Hepatitis C virus (HCV) infection is a widespread major human health concern. Significant obstacles in the study of this virus include the absence of a reliable tissue culture system and a small-animal model. Recently, we constructed full-length HCV cDNA clones and successfully initiated HCV infection in two chimpanzees by intrahepatic injection of in vitro-transcribed RNA (A. A. Kolykhalov et al., Science 277:570–574, 1997). In order to validate potential targets for development of anti-HCV therapeutics, we constructed six mutant derivatives of this prototype infectious clone. Four clones contained point mutations ablating the activity of the NS2-3 protease, the NS3-4A serine protease, the NS3 NTPase/helicase, and the NS5B polymerase. Two additional clones contained deletions encompassing all or part of the highly conserved 98-base sequence at the 3? terminus of the HCV genome RNA. The RNA transcript from each of the six clones was injected intrahepatically into a chimpanzee. No signs of HCV infection were detected in the 8 months following the injection. Inoculation of the same animal with nonmutant RNA transcripts resulted in productive HCV infection, as evidenced by viremia, elevated serum alanine aminotransferase, and HCV-specific seroconversion. These data suggest that these four HCV-encoded enzymatic activities and the conserved 3? terminal RNA element are essential for productive replication in vivo. PMID:10644379

Kolykhalov, Alexander A.; Mihalik, Kathy; Feinstone, Stephen M.; Rice, Charles M.

2000-01-01

291

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

292

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

293

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

294

Economic value of terrestrial and marine biodiversity in the Cape Floristic Region: implications for defining effective and socially optimal conservation strategies  

Microsoft Academic Search

The rich biodiversity of the Cape Floristic Region makes a substantial contribution to the regional (particularly the Western Cape) and national economy. Harvesting of marine resources, such as linefish, rock lobster, abalone and bait species, is worth over R1300 million year?1, or R1.12 million km?1year?1. Harvests of fynbos products such as wildflowers and thatching reed, and forest products, timber and

Jane K Turpie; Barry J Heydenrych; Stephen J Lamberth

2003-01-01

295

[Conservation Units.  

ERIC Educational Resources Information Center

Each of the six instructional units deals with one aspect of conservation: forests, water, rangeland, minerals (petroleum), and soil. The area of the elementary school curriculum with which each correlates is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the…

Texas Education Agency, Austin.

296

[Conservation Units.  

ERIC Educational Resources Information Center

Instructional units deal with each aspect of conservation: forests, wildlife, rangelands, water, minerals, and soil. The area of the secondary school curriculum with which each is correlated is indicated. Lists of general and specific objectives are followed by suggested teaching procedures, including ideas for introducing the topic, questions to…

Texas Education Agency, Austin.

297

Conservatively Speaking.  

ERIC Educational Resources Information Center

An estimated 4,000 members of the politically active fundamentalist Christian Coalition organization met in September 1995. The two-day convention featured speeches from prominent conservative politicians. Ralph Reed, executive director, touched upon the Coalition's growing emphasis on local politics, especially school boards. (MLF)

Vail, Kathleen

1995-01-01

298

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

299

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.

Project, Molecular L.

300

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

301

The East Marine Bioregional Plan Bioregional Profile A Description of the Ecosystems, Conservation Values and Uses of the East Marine RegionMinisterial Foreword  

E-print Network

Australia is responsible for around 60 000 kilometres of coastline and around 15 million square kilometres of ocean, an area almost twice the size of our continental land mass. As an island continent we have one of the biggest Exclusive Economic Zones of any country. The Australian people are known around the world for our connections with the ocean. Australia’s marine systems encompass the tropical seas of the north to the Antarctic ice-shelves of the south. The extraordinary natural diversity and biological richness of our oceans means that Australians are significant global stewards of marine biodiversity. Our national record in marine conservation is a mixed one. We have certainly led the world in the protection of coral reef systems and in our protection of iconic marine

unknown authors

302

EPA recognizes industry leaders for beneficial use  

SciTech Connect

The EPA's Coal Combustion Products Partnership C{sup 2}P{sup 2})recognized industry leaders in beneficial use during the second annual C{sup 2}P{sup 2} awards ceremony held 23 October 2006 in Atlanta, Georgia. The C{sup 2}P{sup 2} program is led by the EPA with the ACAA, DOE, FHWA, USDA - Agricultural Research Services (ARS), and Utilities Solid Waste Activities Group (USWAG). The award for overall achievement went to Great River Energy of Underwood, ND who partnered with more than 10 public and private organizations to develop an extensive market for fly ash from Coal Creek Station, the world's largest lignite-fired plant. Other awards were given for environmental achievement, innovation, partnership, research and communications and outreach. 9 photos.

Goss, D. [American Coal Ash Association (United States)

2007-07-01

303

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

304

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

305

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

306

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

307

Learning to Recognize Volcanoes on Venus  

E-print Network

Dramatic improvements in sensor and image acquisition technology have created a 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 learns to recognize volcanoes in a large data set of Venusian imagery. A machine learning approach is used because it is much easier for geologists to identify examples of volcanoes in the imagery than it is to specify domain knowledge as a set of pixellevel constraints. This approach can also provide portability to other domains without the need for explicit reprogramming; the user simply supplies the system with a new set of training examples. We show how the development of such a system requires a completely different set of skills than are required for applying machine learning to "toy world" domains. This paper discusses important aspects of the application process not commonly encountered in the "toy world," including obtaining labeled training d...

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

1998-01-01

308

Recognizing familial myeloid leukemia in adults  

PubMed Central

Germline testing for familial cases of myeloid leukemia in adults is becoming more common with the recognition of multiple genetic syndromes predisposing people to bone marrow disease. Currently, Clinical Laboratory Improvement Amendments approved testing exists for several myeloid leukemia predisposition syndromes: familial platelet disorder with propensity to acute myeloid leukemia (FPD/AML), caused by mutations in RUNX1; familial AML with mutated CEBPA; familial myelodysplastic syndrome and acute leukemia with mutated GATA2; and the inherited bone marrow failure syndromes, including dyskeratosis congenita, a disease of abnormal telomere maintenance. With the recognition of additional families with a genetic component to their leukemia, new predisposition alleles will likely be identified. We highlight how to recognize and manage these cases as well as outline the characteristics of the major known syndromes. We look forward to future research increasing our understanding of the scope of inherited myeloid leukemia syndromes. PMID:23926458

Nickels, Eric M.; Soodalter, Jesse; Churpek, Jane E.

2013-01-01

309

Polymorphisms of MICA recognized by human alloantibodies.  

PubMed

MICA antigens are polymorphic glycoproteins expressed on the surface of human endothelial cells and other cells. Antibodies against MICA have been found in transplant recipients and were found to be associated with decreased survival of kidney allografts. In the present work, we investigated the polymorphisms that are recognized by antibodies against MICA. Soluble MICA recombinant proteins representing 11 common alleles, two hybrid alleles, and two single amino acid mutated alleles were produced. Patterns of reactivity were determined with MICA bound to Luminex beads. In some studies, sera containing antibodies against MICA were absorbed by cell lines transfected with MICA*001, MICA*002, MICA*008, and MICA*009 or with untransfected cells, followed by testing of antibody reactivity against MICA proteins bound to beads. The monoclonal antibodies and sera used in this study were found to recognize up to 14 distinct MICA epitopes as demonstrated by their differential absorption/reactivity patterns. Among these, nine epitopes correlated with a single unique amino acid: one shared two signature amino acids, one shared three signature amino acids in close proximity, and three epitopes involved multiple amino acids in a nonlinear sequence. Two groups of public epitopes (MICA-G1 and MICA-G2) were characterized. MICA shared epitopes were determined by reactivity loss in single MICA antigen bead assays by absorption with MICA transfectants. Since these epitopes may be targets for antibody binding and possibly antibody-mediated allograft rejection, epitope identification may help understand the development of MICA antibodies and to identify suitable donors for sensitized transplant recipients. PMID:19066881

Zou, Yizhou; Qin, Zhiqiang; Silveus, Allison; Fan, Yisun; Stastny, Peter

2009-02-01

310

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

311

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 animalâs habitat, behavior, diet, and threats as well as the peopleâs 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.

Sciences, California A.

2008-01-01

312

Impact assessment of changes in land use\\/conservation practices on soil erosion in the Penedès–Anoia vineyard region (NE Spain)  

Microsoft Academic Search

Soil erosion by water is one of the most important land degradation processes in the Mediterranean basin. In comparison with other typical crops in this region, vineyards are the agricultural land use that cause the highest soil losses. The changes in land use types and management that have involved the intensification of agriculture from the 1950s have contributed to the

José A Mart??nez-Casasnovas; Inés Sánchez-Bosch

2000-01-01

313

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.

314

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

315

Conservation reaches new heights.  

PubMed

The conservation program with the management assistance of the Woodlands Mountain Institute in 2 contiguous parks, the Mount Everest National Park in Nepal and the Qomolangma Nature Reserve in China, in 2 countries is described. The focus is on conservation of the complex ecosystem with sustainable development by showing local people how to benefit from the park without environmental damage. Cultural diversity is as important as biological diversity. The area has been designated by UNESCO as a World Heritage Site with the "last pure ecological seed" of the Himalayas. The regional geography and culture are presented. Population growth has impacted natural resources through overgrazing, cultivation of marginal land, and deforestation; future plans to build a dam and road bordering the nature reserve pose other threats. Proposed management plans for the Makalu-Barun Nature Park (established in November 1991) and Conservation Area include a division of the park into nature reserve areas free of human activity, protected areas which permit traditional land use, and special sites and trail for tourists and religious pilgrims. The conservation area will act as a buffer for the park and provide economic opportunities; further subdivisions include land use for biodiversity protection, community forest and pasture, agroforestry, and agriculture and settlement. Efforts will be made to increase the welfare of women and local people; proposed projects include the introduction of higher milk-producing animals for stall feeding. Also proposed is a cultural and natural history museum. 70% of the project's resources will be directed to local community participation in consultation and park maintenance. The project is a model of how conservation and protection of natural resources can coexist with local economic development and participation; an integration of preservation of biological diversity, mountain wisdom, and the value of local people as resources for conservation. PMID:12285834

Pepall, J; Khanal, P

1992-10-01

316

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.

317

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

318

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

319

Triage Framework for Resource Conservation in a Speaker Identification System  

Microsoft Academic Search

We present a novel framework for triaging (prioritizing and discarding) data to conserve resources for a speaker identification (SID) system. Our work is motivated by applications that require a SID system to process an overwhelming volume of audio data. We design a triage filter whose goal is to conserve recognizer resources while preserving relevant content. We propose triage methods that

A. Jairam; E. Singer; D. A. Reynolds

2007-01-01

320

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

321

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

322

Documenting biogeographical patterns of African timber species using herbarium records: a conservation perspective based on native trees from Angola.  

PubMed

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

323

Populations of Lobaria pulmonaria (L.) Hoffm. in the Cansiglio Regional Forest (Veneto, Pre-Alps, north-east Italy): Distribution, diversity and conservation issues  

Microsoft Academic Search

The distribution of the epiphytic macrolichen Lobaria pulmonaria (L.) Hoffm. was surveyed in the Regional Forest of Cansiglio, extending over 3,500 ha in the eastern part of the Veneto Pre-Alps (north-east Italy). Data on the main characteristics of the forest sites and on Lobaria trees were collected with the aim to evaluate the main ecological factors, related to forest composition

J. Nascimbene; G. Caniglia; M. Nicli; M. Dalle Vedove

2006-01-01

324

Understanding biological conservation strategies: a molecular-genetic approach to the case of myrtle ( Myrtus communis L.) in two Italian regions: Sardinia and Calabria  

Microsoft Academic Search

Myrtle (Myrtus communis L.), a shrub widespread in the Mediterranean area, is the only species belonging to the Myrtaceae family growing in Europe.\\u000a The pharmacological and aromatic properties of myrtle have caused a growing interest in this plant. The use of myrtle as an\\u000a aromatic plant is traditionally established in the Italian regions of Sardinia and Calabria, where it is

Caterina Agrimonti; Roberto Bianchi; Alberto Bianchi; Mauro Ballero; Ferruccio Poli; Nelson Marmiroli

2007-01-01

325

Wet and Wonderful: The World's Largest Wetlands Are Conservation Priorities  

NSDL National Science Digital Library

Wetlands perform many essential ecosystem servicesâÂÂcarbon storage, flood control, maintenance of biodiversity, fish production, and aquifer recharge, among othersâÂÂservices that have increasingly important global consequences. Like biodiversity hotspots and frontier forests, the world's largest wetlands are now mapped and described by an international team of scientists, highlighting their conservation importance at the global scale. We explore current understanding of some ecosystem services wetlands provide. We selected four of these wetlands (the largest peatland, West Siberian Lowland; the largest floodplain, Amazon River Basin; the least-known wetland, Congo River Basin; and the most heavily developed wetland, Mississippi River Basin), and we illustrate their diversity, emphasizing values and lessons for thinking big in terms of conservation goals. Recognizing the global significance of these wetlands is an important first step toward forging global conservation solutions. Each of the world's largest wetlands requires a basinwide sustainable management strategy built on new institutional frameworksâÂÂat international, national, and regional levelsâÂÂto ensure provision of their vital services.

Paul Keddy (Southeastern Louisiana University;Dept of Biological Sciences)

2009-01-01

326

Genome Trees from Conservation Profiles  

PubMed Central

The concept of the genome tree depends on the potential evolutionary significance in the clustering of species according to similarities in the gene content of their genomes. In this respect, genome trees have often been identified with species trees. With the rapid expansion of genome sequence data it becomes of increasing importance to develop accurate methods for grasping global trends for the phylogenetic signals that mutually link the various genomes. We therefore derive here the methodological concept of genome trees based on protein conservation profiles in multiple species. The basic idea in this derivation is that the multi-component “presence-absence” protein conservation profiles permit tracking of common evolutionary histories of genes across multiple genomes. We show that a significant reduction in informational redundancy is achieved by considering only the subset of distinct conservation profiles. Beyond these basic ideas, we point out various pitfalls and limitations associated with the data handling, paving the way for further improvements. As an illustration for the methods, we analyze a genome tree based on the above principles, along with a series of other trees derived from the same data and based on pair-wise comparisons (ancestral duplication-conservation and shared orthologs). In all trees we observe a sharp discrimination between the three primary domains of life: Bacteria, Archaea, and Eukarya. The new genome tree, based on conservation profiles, displays a significant correspondence with classically recognized taxonomical groupings, along with a series of departures from such conventional clusterings. PMID:16362074

Tekaia, Fredj; Yeramian, Edouard

2005-01-01

327

40 CFR 262.86 - Provisions relating to recognized traders.  

Code of Federal Regulations, 2010 CFR

... STANDARDS APPLICABLE TO GENERATORS OF HAZARDOUS WASTE Transfrontier Shipments of Hazardous Waste for Recovery within the OECD § 262.86 Provisions relating to recognized traders. (a) A recognized trader who takes physical custody of a...

2010-07-01

328

76 FR 10500 - Nationally Recognized Testing Laboratories Fees  

Federal Register 2010, 2011, 2012, 2013

...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

329

Recognizing scientific artifacts in biomedical literature.  

PubMed

Today's search engines and digital libraries offer little or no support for discovering those scientific artifacts (hypotheses, supporting/contradicting statements, or findings) that form the core of scientific written communication. Consequently, we currently have no means of identifying central themes within a domain or to detect gaps between accepted knowledge and newly emerging knowledge as a means for tracking the evolution of hypotheses from incipient phases to maturity or decline. We present a hybrid Machine Learning approach using an ensemble of four classifiers, for recognizing scientific artifacts (ie, hypotheses, background, motivation, objectives, and findings) within biomedical research publications, as a precursory step to the general goal of automatically creating argumentative discourse networks that span across multiple publications. The performance achieved by the classifiers ranges from 15.30% to 78.39%, subject to the target class. The set of features used for classification has led to promising results. Furthermore, their use strictly in a local, publication scope, ie, without aggregating corpus-wide statistics, increases the versatility of the ensemble of classifiers and enables its direct applicability without the necessity of re-training. PMID:23645987

Groza, Tudor; Hassanzadeh, Hamed; Hunter, Jane

2013-01-01

330

Overview: recognizing the problem of magnesium deficiency  

SciTech Connect

The magnesium content of the usual American diet is less than the recommended dietary allowance. Excesses of some macro- and micro-nutrients interact with Mg, increasing its requirements. Marginal deficiency of Mg is not associated with hypomagnesemia, is not characterized by typical manifestations, as is thus difficult to diagnose. Serum or plasma Mg levels are held within narrow limits unless tissue levels are very low, or renal function is poor. Vulnerability to Mg deficiency increases during growth and development, pregnancy, when under physical or psychological stress, and during illness or its treatment that interferes with absorption or causes loss of Mg. Evidence of biochemical changes of early Mg deficiency is rarely sought, although the roles of Mg in many enzyme systems are recognized. The effects of Mg deficiency on metabolism, even in disorders caused by vitamin dependencies in which Mg is a co-factor, are largely unexplored. Deficiency of Mg is diagnosed confidently when the laboratory reports hypomagnesemia in patients with convulsions or arrhythmias. Without these signs, Mg levels are not often ordered, even in the presence of neuromuscular irritability such as respond to Mg repletion. Because Mg supplementation or Mg-sparing drugs protect against premature or ectopic heart beats and sudden death, to which diuretic-treated hypertensive patients are at risk, it is increasingly being advised that their Mg status be determined.

Seelig, M.S.

1988-01-01

331

Artificial Immune System for Recognizing Patterns  

NASA Technical Reports Server (NTRS)

A method of recognizing or classifying patterns is based on an artificial immune system (AIS), which includes an algorithm and a computational model of nonlinear dynamics inspired by the behavior of a biological immune system. The method has been proposed as the theoretical basis of the computational portion of a star-tracking system aboard a spacecraft. In that system, a newly acquired star image would be treated as an antigen that would be matched by an appropriate antibody (an entry in a star catalog). The method would enable rapid convergence, would afford robustness in the face of noise in the star sensors, would enable recognition of star images acquired in any sensor or spacecraft orientation, and would not make an excessive demand on the computational resources of a typical spacecraft. Going beyond the star-tracking application, the AIS-based pattern-recognition method is potentially applicable to pattern- recognition and -classification processes for diverse purposes -- for example, reconnaissance, detecting intruders, and mining data.

Huntsberger, Terrance

2005-01-01

332

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 plane to determine whether a particular target is present in the field of view. Preferably, a temporal pattern is imaged in the output plane with a optical detector having a plurality of pixels and a correlation coefficient for each pixel is determined by accumulating the intensity and intensity-square of each pixel. The orbiting of the constant response caused by the filter rotation is also preferably eliminated either by the use of two orthogonal mirrors pivoted correspondingly to the rotation of the filter or the attaching of a refracting wedge to the filter to remove the offset angle. Detection is preferably performed of the temporal pattern in the output plane at a plurality of different angles with angular separation sufficient to decorrelate successive frames. 1 fig.

Ochoa, E.; Schils, G.F.; Sweeney, D.W.

1987-09-15

333

Recognizing Scientific Artifacts in Biomedical Literature  

PubMed Central

Today’s search engines and digital libraries offer little or no support for discovering those scientific artifacts (hypotheses, supporting/contradicting statements, or findings) that form the core of scientific written communication. Consequently, we currently have no means of identifying central themes within a domain or to detect gaps between accepted knowledge and newly emerging knowledge as a means for tracking the evolution of hypotheses from incipient phases to maturity or decline. We present a hybrid Machine Learning approach using an ensemble of four classifiers, for recognizing scientific artifacts (ie, hypotheses, background, motivation, objectives, and findings) within biomedical research publications, as a precursory step to the general goal of automatically creating argumentative discourse networks that span across multiple publications. The performance achieved by the classifiers ranges from 15.30% to 78.39%, subject to the target class. The set of features used for classification has led to promising results. Furthermore, their use strictly in a local, publication scope, ie, without aggregating corpus-wide statistics, increases the versatility of the ensemble of classifiers and enables its direct applicability without the necessity of re-training. PMID:23645987

Groza, Tudor; Hassanzadeh, Hamed; Hunter, Jane

2013-01-01

334

Escherichia coli fimbriae recognizing sialyl galactosides.  

PubMed Central

Fimbriae recognizing sialyl galactosides (S fimbriae) were purified from an Escherichia coli strain. The S fimbriae were morphologically identical to type 1 and P fimbriae of E. coli and showed a hemagglutination that was abolished when erythrocytes were treated with neuraminidase. Hemagglutination by the purified fimbriae was inhibited by orosomucoid but not by its desialylated derivative. Of the oligosaccharides tested, sialyl-(alpha 2-3)-lactose and sialyl-(alpha 2-3)-N-acetyllactosamine had the strongest inhibitory activities. It was concluded that S fimbriae have the strongest affinity for (alpha 2-3)-linked sialyl galactosides. In the enzyme-linked immunosorbent assay, the hyperimmune serum to the S fimbriae reacted strongly with the homologous antigen but not with type 1, P, or nonhemagglutinating KS71C fimbriae of E. coli. Analogously, the hyperimmune sera to the other E. coli fimbriae did not react with the purified S fimbriae. The immunoprecipitation assay showed that S fimbriae on different E. coli serotypes shared immunological cross-reactivity. Images PMID:6146600

Korhonen, T K; Väisänen-Rhen, V; Rhen, M; Pere, A; Parkkinen, J; Finne, J

1984-01-01

335

Escherichia coli fimbriae recognizing sialyl galactosides.  

PubMed

Fimbriae recognizing sialyl galactosides (S fimbriae) were purified from an Escherichia coli strain. The S fimbriae were morphologically identical to type 1 and P fimbriae of E. coli and showed a hemagglutination that was abolished when erythrocytes were treated with neuraminidase. Hemagglutination by the purified fimbriae was inhibited by orosomucoid but not by its desialylated derivative. Of the oligosaccharides tested, sialyl-(alpha 2-3)-lactose and sialyl-(alpha 2-3)-N-acetyllactosamine had the strongest inhibitory activities. It was concluded that S fimbriae have the strongest affinity for (alpha 2-3)-linked sialyl galactosides. In the enzyme-linked immunosorbent assay, the hyperimmune serum to the S fimbriae reacted strongly with the homologous antigen but not with type 1, P, or nonhemagglutinating KS71C fimbriae of E. coli. Analogously, the hyperimmune sera to the other E. coli fimbriae did not react with the purified S fimbriae. The immunoprecipitation assay showed that S fimbriae on different E. coli serotypes shared immunological cross-reactivity. PMID:6146600

Korhonen, T K; Väisänen-Rhen, V; Rhen, M; Pere, A; Parkkinen, J; Finne, J

1984-08-01

336

Recognizing Disguised Faces: Human and Machine Evaluation  

PubMed Central

Face verification, though an easy task for humans, is a long-standing open research area. This is largely due to the challenging covariates, such as disguise and aging, which make it very hard to accurately verify the identity of a person. This paper investigates human and machine performance for recognizing/verifying disguised faces. Performance is also evaluated under familiarity and match/mismatch with the ethnicity of observers. The findings of this study are used to develop an automated algorithm to verify the faces presented under disguise variations. We use automatically localized feature descriptors which can identify disguised face patches and account for this information to achieve improved matching accuracy. The performance of the proposed algorithm is evaluated on the IIIT-Delhi Disguise database that contains images pertaining to 75 subjects with different kinds of disguise variations. The experiments suggest that the proposed algorithm can outperform a popular commercial system and evaluates them against humans in matching disguised face images. PMID:25029188

Dhamecha, Tejas Indulal; Singh, Richa; Vatsa, Mayank; Kumar, Ajay

2014-01-01

337

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 attempt to quantify the variations between the calculations of I and L* of those models. The deviation between the results given by the models depends on particle starting position geocentric distance, pitch angle and magnetospheric conditions. Using the 3-D tracer we attempt to map the areas in the Earth's magnetosphere where I and L* can be assumed to be conserved by monitoring the constancy of I for energetic proton propagating forwards and backwards in time. These areas are found to be centered on the noon area and their size also depends on particle starting position geocentric distance, pitch angle and magnetospheric conditions.

Konstantinidis, K.; Sarris, T.

2014-09-01

338

Building Collections: Recognizing and Appreciating Differences  

ERIC Educational Resources Information Center

A huge world exists outside the family. When youngsters enter school, they meet children from diverse and unfamiliar backgrounds--regional, ethnic, religious, and racial. Often there is confusion, mistrust, and apprehension. In the eyes of a child, being different is not always a good thing. Parents and teachers bear the burden of discussing…

Krapp, Joanna Vergona

2004-01-01

339

Structural Diversity in Conserved Regions Like the DRY-Motif among Viral 7TM Receptors—A Consequence of Evolutionary Pressure?  

PubMed Central

Several herpes- and poxviruses have captured chemokine receptors from their hosts and modified these to their own benefit. The human and viral chemokine receptors belong to class A 7 transmembrane (TM) receptors which are characterized by several structural motifs like the DRY-motif in TM3 and the C-terminal tail. In the DRY-motif, the arginine residue serves important purposes by being directly involved in G protein coupling. Interestingly, among the viral receptors there is a greater diversity in the DRY-motif compared to their endogenous receptor homologous. The C-terminal receptor tail constitutes another regulatory region that through a number of phosphorylation sites is involved in signaling, desensitization, and internalization. Also this region is more variable among virus-encoded 7TM receptors compared to human class A receptors. In this review we will focus on these two structural motifs and discuss their role in viral 7TM receptor signaling compared to their endogenous counterparts. PMID:22899926

Jensen, Ann-Sofie Mølleskov; Sparre-Ulrich, Alexander Hovard; Davis-Poynter, Nicholas; Rosenkilde, Mette Marie

2012-01-01

340

Conservation successes at micro-, meso- and macroscales.  

PubMed

Although large-scale biodiversity declines are ongoing, certain conservation actions have made a positive difference. Rates of extinction and endangerment of vertebrate species, for instance, have probably been reduced via conservation interventions. Such conservation actions operate at different spatial scales. Habitat preservation and endangered species recovery are examples of conservation successes at microscales. Mesoscale conservation includes regional cooperation among neighboring countries that has arrested population declines of endangered species, such as mountain gorillas. At macroscales, public pressure on multinational corporations has sometimes resulted in their abandoning environmentally damaging practices or suppliers with poor environmental records. Overall, conservation projects such as these need more long-term funding and greater political and popular support, and must also include provisions to evaluate and document their outcomes. As we discuss here, a focus on conservation successes achieved at different scales can help to promote these aims and guide future conservation victories. PMID:21824677

Sodhi, Navjot S; Butler, Rhett; Laurance, William F; Gibson, Luke

2011-11-01

341

Conservative groupoids recognize only regular languages Martin Beaudry1 Danny Dub2 Maxime Dub2  

E-print Network

de Sherbrooke". Buses from Sherbrooke to other cities (Montreal, Quebec City, Ottawa etc.) You need to see schedule and fares. To go to Quebec City: Student fares: one way ticket: 33,43$; return ticket: 60

Latendresse, Mario

342

Linkage mapping in sheep and deer identifies a conserved pecora ruminant linkage group orthologous to two regions of HSA16 and a portion of HSA7Q  

SciTech Connect

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 of 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. One locus from the long arm of human chromosome 16 is also present, demonstrating a previously unknown rearrangement between human and ruminant chromosomes. There is no significant difference in marker order and distances between the two linkage groups, implying that this linkage pattern was present in the genome of the common ancestor of the pecora ruminants. 35 refs., 1 fig., 2 tabs.

Broom, J.E.; Tate, M.L. [Univ. of Otago, Dunedin (New Zealand)] [Univ. of Otago, Dunedin (New Zealand); Dodds, K.G. [AgResearch, Mosgiel (New Zealand)] [AgResearch, Mosgiel (New Zealand)

1996-05-01

343

Sequence conservation in the C-terminal region of spider silk proteins (Spidroin) from Nephila clavipes (Tetragnathidae) and Araneus bicentenarius (Araneidae).  

PubMed

The polymerase chain reaction (PCR) has been used to amplify the portion of the Spidroin 1 gene that codes for the C-terminal part of the silk protein of the spider Nephila clavipes. Along with some substitution mutations of minor consequence, the PCR-derived sequence reveals an additional base missing from the previously published Nephila Spidroin 1 sequence. Comparison of the PCR-derived sequence with the equivalent region of Spidroin 2 indicates that the insertion of this single base results in greatly increased similarity in the resulting amino acid sequences of Spidroin 1 and Spidroin 2 (75% over 97 amino acids). The same PCR primers also amplified a fragment of the same length from Araneus bicentenarius. This sequence is also very similar to Spidroin 1 of Nephila (71% over 238 bases excluding the PCR primers, which translates into 76% over 79 amino acids). PMID:8120021

Beckwitt, R; Arcidiacono, S

1994-03-01

344

Region- and cell type-selective expression of the evolutionarily conserved Nolz-1/zfp503 gene in the developing mouse hindbrain.  

PubMed

Nolz-1/Zfp503, a zinc finger-containing gene, is a mammalian member of the SP1-related nocA/elb/tlp-1 gene family. Previous studies have shown that Nolz-1 homologs are important for patterning the rhombomeres in zebrafish hindbrain. We therefore studied the expression pattern of Nolz-1 in the developing mouse hindbrain. Nolz-1 mRNA expression was detected in the prospective rhombomere 3, 5 and caudal regions as early as E8.75. After E11.5, Nolz-1-positive cells were organized as distinct cell clusters, and they were largely non-overlapped with either Pax2-positive or Phox2b-positive domains. Most interestingly, we found that Nolz-1 was specifically expressed by Phox2b-negative/Isl1/2-positive somatic motor neurons, but not by Phox2b-positive/Isl1/2-positive branchial and visceral motor neurons, suggesting that Nolz-1 may regulate development of somatic motor neurons in the hindbrain. In addition to be expressed in differentiating post-mitotic neurons, Nolz-1 was also expressed by progenitor cells in the ventricular zone located in the dorsal part of aqueduct and the alar plates of hindbrain, which suggests a regulatory role of Nolz-1 in the germinal zone. Taken together, based on its domain- and cell type-selective pattern, Nolz-1 may involve in regulation of various developmental processes, including regional patterning and cell-type specification and differentiation in the developing mouse hindbrain. PMID:21945624

Chang, Sunny Li-Yun; Yan, Yu-Ting; Shi, Yan-Ling; Liu, Ya-Chi; Takahashi, Hiroshi; Liu, Fu-Chin

2011-12-01

345

Recognizing the importance of tropical forests in limiting rainfall-induced debris flows  

EPA Science Inventory

Worldwide concern for continuing loss of montane forest cover in the tropics usually focuses on adverse ecological consequences. Less recognized, but equally important to inhabitants of these affected regions, is an increasing susceptibility to rainfall-induced debris flows and t...

346

Recognizing and modeling variable drawdown due to evapotranspiration in a semiarid riparian zone considering  

E-print Network

Recognizing and modeling variable drawdown due to evapotranspiration in a semiarid riparian zone January 2013; published 25 February 2013. [1] Riparian zones in semiarid regions often exhibit high rates. ET at the Boise Hydrogeophysical Research Site (BHRS), a riparian zone in a temperate, semiarid

Barrash, Warren

347

Kgagodi Basin: The first impact structure recognized in Botswana  

NASA Astrophysics Data System (ADS)

The 3.4 km wide, so-called Kgagodi Basin structure, which is centered at longitude 27o34.4' E and latitude 22o 28.6' S in eastern Botswana, has been confirmed as a meteorite impact structure. This crater structure was first recognized through geophysical analysis; now, we confirm its impact origin by the recognition of shock metamorphosed material in samples from a drill core obtained close to the crater rim. The structure formed in Archean granitoid basement overlain and intruded by Karoo dolerite. The crater yielded a gravity model consistent with a simple bowl-shape crater form. The drill core extends to a depth of 274 m and comprises crater fill sediments to a depth of 158 m. Impact breccia was recovered only between 158 and 165 m depth, below which locally brecciated basement granitoids grade into fractured and eventually undeformed crystalline basement, from ~250 m depth. Shock metamorphic effects were only found in granitoid clasts in the narrow breccia zone. This breccia is classified as suevitic impact breccia due to the presence of melt and glass fragments, at a very small abundance. The shocked grains are exclusively derived from granitoid target material. Shock effects include multiple sets of planar deformation features in quartz and feldspar; diaplectic quartz, and partially and completely isotropized felsic minerals, and rare melt fragments were encountered. Abundances of some siderophile elements and especially, Ir, in suevitic breccia samples are significantly elevated compared to the contents in the target rocks, which provides evidence for the presence of a small meteoritic component. Kgagodi is the first impact structure recognized in the region of the Kalahari Desert in southern Africa. Based on lithological and first palynological evidence, the age of the Kgagodi structure is tentatively assigned to the upper Cretaceous to early Tertiary interval. Thus, the crater fill has the potential to provide a long record of paleoclimatic conditions.

Brandt, D.; Holmes, H.; Reimold, W. U.; Paya, B. K.; Koeberl, C.; Hancox, P. J.

2002-12-01

348

HIV-1 conserved elements p24CE DNA vaccine induces humoral immune responses with broad epitope recognition in macaques.  

PubMed

To target immune responses towards invariable regions of the virus, we engineered DNA-based immunogens encoding conserved elements (CE) of HIV-1 p24gag. This conserved element vaccine is designed to avoid decoy epitopes by focusing responses to critical viral elements. We previously reported that vaccination of macaques with p24CE DNA induced robust cellular immune responses to CE that were not elicited upon wild type p55gag DNA vaccination. p24CE DNA priming followed by p55gag DNA boost provided a novel strategy to increase the magnitude and breadth of the cellular immune responses to HIV-1 Gag, including the induction of strong, multifunctional T-cell responses targeting epitopes within CE. Here, we examined the humoral responses induced upon p24CE DNA or p55gag DNA vaccination in macaques and found that although both vaccines induced robust p24gag binding antibody responses, the responses induced by p24CE DNA showed a unique broad range of linear epitope recognition. In contrast, antibodies elicited by p55gag DNA vaccine failed to recognize p24CE protein and did not recognize linear epitopes spanning the CE. Interestingly, boosting of p24CE DNA primed animals with p55gag DNA resulted in augmentation of antibodies able to recognize p24gag as well as the p24CE proteins, thereby inducing broadest immunity. Our results indicate that an effectively directed vaccine strategy that includes priming with the conserved element vaccine followed by boost with the complete immunogen induces broad cellular and humoral immunity focused on the conserved regions of the virus. This novel and effective strategy to broaden responses could be applied against other antigens of highly diverse pathogens. PMID:25338098

Kulkarni, Viraj; Valentin, Antonio; Rosati, Margherita; Rolland, Morgane; Mullins, James I; Pavlakis, George N; Felber, Barbara K

2014-01-01

349

HIV-1 Conserved Elements p24CE DNA Vaccine Induces Humoral Immune Responses with Broad Epitope Recognition in Macaques  

PubMed Central

To target immune responses towards invariable regions of the virus, we engineered DNA-based immunogens encoding conserved elements (CE) of HIV-1 p24gag. This conserved element vaccine is designed to avoid decoy epitopes by focusing responses to critical viral elements. We previously reported that vaccination of macaques with p24CE DNA induced robust cellular immune responses to CE that were not elicited upon wild type p55gag DNA vaccination. p24CE DNA priming followed by p55gag DNA boost provided a novel strategy to increase the magnitude and breadth of the cellular immune responses to HIV-1 Gag, including the induction of strong, multifunctional T-cell responses targeting epitopes within CE. Here, we examined the humoral responses induced upon p24CE DNA or p55gag DNA vaccination in macaques and found that although both vaccines induced robust p24gag binding antibody responses, the responses induced by p24CE DNA showed a unique broad range of linear epitope recognition. In contrast, antibodies elicited by p55gag DNA vaccine failed to recognize p24CE protein and did not recognize linear epitopes spanning the CE. Interestingly, boosting of p24CE DNA primed animals with p55gag DNA resulted in augmentation of antibodies able to recognize p24gag as well as the p24CE proteins, thereby inducing broadest immunity. Our results indicate that an effectively directed vaccine strategy that includes priming with the conserved element vaccine followed by boost with the complete immunogen induces broad cellular and humoral immunity focused on the conserved regions of the virus. This novel and effective strategy to broaden responses could be applied against other antigens of highly diverse pathogens. PMID:25338098

Kulkarni, Viraj; Valentin, Antonio; Rosati, Margherita; Rolland, Morgane; Mullins, James I.; Pavlakis, George N.; Felber, Barbara K.

2014-01-01

350

EXECUTIVE SUMMARY A Review of Water Conservation Planning for the  

E-print Network

EXECUTIVE SUMMARY A Review of Water Conservation Planning for the Atlanta, Georgia Region (August asked the Pacific Institute to review the region's water conservation plans, including potential water that the Metropolitan North Georgia Water Planning Dis- trict's Water Supply and Water Conservation Plan may

351

Superior Control of HIV-1 Replication by CD8+ T Cells Targeting Conserved Epitopes: Implications for HIV Vaccine Design  

PubMed Central

A successful HIV vaccine will likely induce both humoral and cell-mediated immunity, however, the enormous diversity of HIV has hampered the development of a vaccine that effectively elicits both arms of the adaptive immune response. To tackle the problem of viral diversity, T cell-based vaccine approaches have focused on two main strategies (i) increasing the breadth of vaccine-induced responses or (ii) increasing vaccine-induced responses targeting only conserved regions of the virus. The relative extent to which set-point viremia is impacted by epitope-conservation of CD8+ T cell responses elicited during early HIV-infection is unknown but has important implications for vaccine design. To address this question, we comprehensively mapped HIV-1 CD8+ T cell epitope-specificities in 23 ART-naïve individuals during early infection and computed their conservation score (CS) by three different methods (prevalence, entropy and conseq) on clade-B and group-M sequence alignments. The majority of CD8+ T cell responses were directed against variable epitopes (p<0.01). Interestingly, increasing breadth of CD8+ T cell responses specifically recognizing conserved epitopes was associated with lower set-point viremia (r?=?- 0.65, p?=?0.009). Moreover, subjects possessing CD8+ T cells recognizing at least one conserved epitope had 1.4 log10 lower set-point viremia compared to those recognizing only variable epitopes (p?=?0.021). The association between viral control and the breadth of conserved CD8+ T cell responses may be influenced by the method of CS definition and sequences used to determine conservation levels. Strikingly, targeting variable versus conserved epitopes was independent of HLA type (p?=?0.215). The associations with viral control were independent of functional avidity of CD8+ T cell responses elicited during early infection. Taken together, these data suggest that the next-generation of T-cell based HIV-1 vaccines should focus on strategies that can elicit CD8+ T cell responses to multiple conserved epitopes of HIV-1. PMID:23741326

Kunwar, Pratima; Hawkins, Natalie; Dinges, Warren L.; Liu, Yi; Gabriel, Erin E.; Swan, David A.; Stevens, Claire E.; Maenza, Janine; Collier, Ann C.; Mullins, James I.; Hertz, Tomer; Yu, Xuesong; Horton, Helen

2013-01-01

352

Comparative Analysis of the Mitochondrial Genomes of Callitettixini Spittlebugs (Hemiptera: Cercopidae) Confirms the Overall High Evolutionary Speed of the AT-Rich Region but Reveals the Presence of Short Conservative Elements at the Tribal Level  

PubMed Central

The present study compares the mitochondrial genomes of five species of the spittlebug tribe Callitettixini (Hemiptera: Cercopoidea: Cercopidae) from eastern Asia. All genomes of the five species sequenced are circular double-stranded DNA molecules and range from 15,222 to 15,637 bp in length. They contain 22 tRNA genes, 13 protein coding genes (PCGs) and 2 rRNA genes and share the putative ancestral gene arrangement of insects. The PCGs show an extreme bias of nucleotide and amino acid composition. Significant differences of the substitution rates among the different genes as well as the different codon position of each PCG are revealed by the comparative evolutionary analyses. The substitution speeds of the first and second codon position of different PCGs are negatively correlated with their GC content. Among the five species, the AT-rich region features great differences in length and pattern and generally shows a 2–5 times higher substitution rate than the fastest PCG in the mitochondrial genome, atp8. Despite the significant variability in length, short conservative segments were identified in the AT-rich region within Callitettixini, although absent from the other groups of the spittlebug superfamily Cercopoidea. PMID:25285442

Liu, Jie; Bu, Cuiping; Wipfler, Benjamin; Liang, Aiping

2014-01-01

353

Molluscan life and death assemblages of a sheltered lagoon in the northern Red Sea: Implications for paleoecology, regional diversity and conservation  

NASA Astrophysics Data System (ADS)

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. In addition, death assemblages (DAs) also preserve important information on regional diversity which is not available from single censuses of the life assemblages (LAs). Most case studies on LD agreement were performed in temperate environments. 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) of a sheltered lagoon in the northern Red Sea, which is under increasing anthropogenic pressure from tourism. A total of 3,566 molluscs from nine tidal flat and nine sublittoral stations were analyzed for species composition and distribution of living and dead molluscs. Of 97 recorded species, one potamidid gastropod dominated strongly and another 4 species were numerically abundant. There were many more dead (70.3%) than living individuals, with large differences between gastropods (57.5% dead) and bivalves (95.5% dead), and between the intertidal (49.3% dead) and the subtidal (96.2% dead). The mean number of species per sample is lower in the intertidal than in the subtidal, and this difference is much higher in the death assemblage than in the life assemblage. Distinct assemblages characterized intertidal and sublittoral habitats, however, and the distribution and abundance of empty shells generally corresponded to that of the living species. 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.

Zuschin, Martin; Gützer, Claudia

2014-05-01

354

Afrotherian Conservation  

E-print Network

w members: I do not think Professor Jonathan Kingdon needs any introduction! Dr. Thomas Lehmann from the Transvaal Museum joined us as an authority on aardvarks and Dr. Andrew Baker of the Philadelphia Zoo agreed to give us his expertise on captive afrotheres, especially sengis and aardvarks (see issue No. 3 of our newsletter). WELCOME to these new members! The complete membership list is attached at the end of the newsletter. As this issue of Afrotherian Conservation goes to press, we are waiting for news as to whether Jon Benstead, Link Olson, Daniel Rakotondravony, and Erika Ranoarivony will be successful in obtaining a Chicago Board of Trade grant, through the Chicago Zoological Society, for their proposal on the web-footed tenrec in Madagascar. With the GMA, Red List update, and new quadrennial behind us we have two main activities that need our focus. First, our web site needs attention, including finishing the golden mole and tenrec pages, and updating the taxonomy, Red List s

Newsletter Of The; Galen Rathbun; R. W. Yarnell; D. M. Scott; Moles G. B. Rathbun; L. Rathbun; F. Kachel; U. Zeller; V Besnard

2006-01-01

355

The Mathematical Formula Recognizing System Based On Web Service  

Microsoft Academic Search

This paper focused on mathematical expression recognizing, we have designed online handwriting recognizing systems of mathematical expressions, MatheWriter and Embedded-MatheWriter, which have succeeded to be embedded in Office (like Word) and mobile equipments (like PDA). The paper expounds the system structure and basic functions of recognition system. On the basis of these studies, it also expounds the recognizing technology of

Qi Xiangwei; Yusup Abaydulla

2009-01-01

356

46 CFR 160.077-9 - Recognized laboratory.  

Code of Federal Regulations, 2010 CFR

...HOMELAND SECURITY (CONTINUED) EQUIPMENT, CONSTRUCTION, AND MATERIALS: SPECIFICATIONS AND APPROVAL LIFESAVING EQUIPMENT Hybrid Inflatable Personal Flotation Devices § 160.077-9 Recognized laboratory. (a) A manufacturer seeking...

2010-10-01

357

Wetland Loss and Biodiversity Conservation  

Microsoft Academic Search

Most species of wetland-dependent organisms live in multiple local populations sustained through occasional migration. Retention of minimum wetland densities in human-dominated landscapes is funda- mental to conserving these organisms. An analysis of wetland mosaics was performed for two regions of the northeastern United States to assess the degree to which historical wetland loss alters the metrics of wetland mosaics and

James P. Gibbs

2000-01-01

358

Conservation International: Biodiversity Hotspots  

NSDL National Science Digital Library

From Conservation International, this Biodiversity Hotspots site (first reported on in the October 18, 2002 NSDL Scout Report for Life Sciences) "was re-launched in 2005 with completely updated information as presented in the new book _Hotspots Revisited_." The updated Hotspots website features profiles of more than 30 ecologically important areas of the world. Hotspots are categorized under five world regions including South America, Africa, North and Central America, Europe and Central Asia, and Asia-Pacific. Site visitors will find profiles about such Hotspots as the Himalaya, Mediterranean Basin, Horn of Africa, Tropical Andes, Madrean Pine-Oak Woodlands, Sundaland, and more. In addition to regional profiles, the site offers a number of helpful resources such as a Terrestrial Vertebrate Species Database, a Glossary, Maps, and related References.

359

75 FR 50777 - Final Comprehensive Conservation Plan; John Hay National Wildlife Refuge, Merrimack County, NH  

Federal Register 2010, 2011, 2012, 2013

...emphasize habitat for priority bird species of conservation concern in the Bird Conservation Region 14 and Partners...Hampshire Wildlife Action Plan, Birds of Conservation Concern 2008...route for the John Hay II Forest Ecology Trail to allow visitors to...

2010-08-17

360

Two DNA-binding factors recognize specific sequences at silencers, upstream activating sequences, autonomously replicating sequences, and telomeres in Saccharomyces cerevisiae  

SciTech Connect

Two DNA-binding factors from Saccharomyces cerevisiae have been characterized, GRFI (general regulatory factor I) and ABFI (ARS-binding factor I), that recognize specific sequences within diverse genetic elements. GRFI bound to sequences at the negative regulatory elements (silencers) of the silent mating type loci HML E and HMR E and to the upstream activating sequence (UAS) required for transcription of the MAT ..cap alpha.. genes. A putative conserved UAS located at genes involved in translation (RPG box) was also recognized by GRFI. In addition, GRFI bound with high affinity to sequences within the (C/sub 1-3/A)-repeat region at yeast telomeres. Binding sites for GRFI with the highest affinity appeared to be of the form 5'-(A/G)(A/C)ACCCAN NCA(T/C)(T/C)-3', where N is any nucleotide. ABFI-binding sites were located next to autonomously replicating sequences (ARSs) at controlling elements of the silent mating type loci HMR E, HMR I, and HML I and were associated with ARS1, ARS2, and the 2..mu..m plasmid ARS. Two tandem ABFI binding sites were found between the HIS3 and DED1 genes, several kilobase pairs from any ARS, indicating that ABFI-binding sites are not restricted to ARSs. The sequences recognized by AFBI showed partial dyad-symmetry and appeared to be variations of the consensus 5'-TATCATTNNNNACGA-3'. GRFI and ABFI were both abundant DNA-binding factors and did not appear to be encoded by the SIR genes, whose product are required for repression of the silent mating type loci. Together, these results indicate that both GRFI and ABFI play multiple roles within the cell.

Buchman, A.R.; Kimmerly, W.J.; Rine, J.; Kornberg, R.D.

1988-01-01

361

Recognizing Sights, Smells, and Sounds with Gnostic Fields  

PubMed Central

Mammals rely on vision, audition, and olfaction to remotely sense stimuli in their environment. Determining how the mammalian brain uses this sensory information to recognize objects has been one of the major goals of psychology and neuroscience. Likewise, researchers in computer vision, machine audition, and machine olfaction have endeavored to discover good algorithms for stimulus classification. Almost 50 years ago, the neuroscientist Jerzy Konorski proposed a theoretical model in his final monograph in which competing sets of “gnostic” neurons sitting atop sensory processing hierarchies enabled stimuli to be robustly categorized, despite variations in their presentation. Much of what Konorski hypothesized has been remarkably accurate, and neurons with gnostic-like properties have been discovered in visual, aural, and olfactory brain regions. Surprisingly, there have not been any attempts to directly transform his theoretical model into a computational one. Here, I describe the first computational implementation of Konorski's theory. The model is not domain specific, and it surpasses the best machine learning algorithms on challenging image, music, and olfactory classification tasks, while also being simpler. My results suggest that criticisms of exemplar-based models of object recognition as being computationally intractable due to limited neural resources are unfounded. PMID:23365648

Kanan, Christopher

2013-01-01

362

Kortright Centre for Conservation: Water Theme.  

ERIC Educational Resources Information Center

One of a series of four reports on specific conservation themes, this report (on water) is intended to consolidate techniques which will best communicate the legislation, role, objectives, and practices of the Metropolitan Toronto and Region Conservation Authority in land and water management: to retain the physical characteristics of the land in…

Foster, Allan

363

Teaching for a World Conservation Strategy.  

ERIC Educational Resources Information Center

The World Conservation Strategy calls upon international, national, and regional efforts to balance development with conservation of the world's living resources (e.g., forests, water, farmland, coastal resources). Environmental educators must inform themselves, establish adequate teacher training programs, and develop curriculum materials to…

Kirk, John J.

1982-01-01

364

Adoption of conservation agriculture in Europe  

Microsoft Academic Search

According to KASSA findings, conservation agriculture is less adopted in Europe compared to other adopting regions and, reduced tillage is more common than no-tillage and cover crops. Currently, it is not popularised and it is less researched. The lack of knowledge on conservation agriculture systems and their management and, the absence of dynamic and effective innovation systems make it difficult

Rabah Lahmar

2010-01-01

365

Water conservation programs  

SciTech Connect

The paper discusses three water conservation programs: statewide water conservation efforts, a 5-point program of the City of Albuquerque, and the program for recycling wastewater by the Intel Corporation. Water conservation programs depend largely on public education programs. Albuquerque`s program, for example, includes development of a K-12th grade curriculum on water conservation, live theater performances promoting conservation for elementary school children, and collaboration with existing community organizations to promote water conservation.

Darilek, A. [New Mexico State Engineer Office, Santa Fe, NM (United States). Water Conservation Program; Witherspoon, J. [City of Albuquerque, NM (United States). Public Works Dept.; Hutchinson, D.L. [Intel Corp., Rio Rancho, NM (United States)

1995-12-31

366

Energy Conservation Renewable Energy  

E-print Network

Energy Conservation Renewable Energy The Future at Rutgers University Facilities & Capital Planning ti ? R bl EWhy Conservation? Renewable Energy · Climate control reduces green house gases · Reduces

Delgado, Mauricio

367

Joint Attention and Dynamics Repertoire in Coupled Dynamical Recognizers  

E-print Network

Joint Attention and Dynamics Repertoire in Coupled Dynamical Recognizers Takashi Ikegami the sensitivity by referring to Trevarthen's double monitor experiments. 1 Intersubjectivity and Joint Atten- tion Here in this paper, we propose a simulation study of joint attention via coupled dynamical recognizers

Ikegami, Takashi

368

A simple O(mn) algorithm for recognizing Hamming graphs  

E-print Network

A simple O(mn) algorithm for recognizing Hamming graphs W. Imrich Institut fË?ur Mathematik und to design a simple O(mn) algorithm for recognizing Hamming graphs. 1 Introduction All graphs considered be embedded isometrically in a Cartesian product of complete graphs are called Hamming graphs. Interest

Klavzar, Sandi

369

Recognizing Hamming graphs in linear time and space Wilfried Imrich  

E-print Network

Recognizing Hamming graphs in linear time and space Wilfried Imrich Department of Mathematics, PEF University of Maribor Koroska cesta 160 2000 Maribor Slovenia Abstract Hamming graphs are present an algorithm recognizing Hamming graphs in linear time and space. This improves a previous

Klavzar, Sandi

370

Recognizing Hamming graphs in linear time and space Wilfried Imrich  

E-print Network

Recognizing Hamming graphs in linear time and space Wilfried Imrich Department of Mathematics of Mathematics, PEF University of Maribor KoroŸska cesta 160 2000 Maribor Slovenia Abstract Hamming graphs are present an algorithm recognizing Hamming graphs in linear time and space. This improves a previous

Klavzar, Sandi

371

A simple O(mn) algorithm for recognizing Hamming graphs  

E-print Network

A simple O(mn) algorithm for recognizing Hamming graphs W. Imrich Institut f¨ur Mathematik und to design a simple O(mn) algorithm for recognizing Hamming graphs. 1 Introduction All graphs considered be embedded isometrically in a Cartesian product of complete graphs are called Hamming graphs. Interest

Klavzar, Sandi

372

When Do Infants Begin Recognizing Familiar Words in Sentences?  

ERIC Educational Resources Information Center

Previous studies have shown that by 11 but not by 10 months infants recognize words that have become familiar from everyday life independently of the experimental setting. This study explored the ability of 10-, 11-, and 12- month-old infants to recognize familiar words in sentential context, without experimental training. The headturn preference…

DePaolis, Rory A.; Vihman, Marilyn M.; Keren-Portnoy, Tamar

2014-01-01

373

38 CFR 17.199 - Inspection of recognized State homes.  

Code of Federal Regulations, 2010 CFR

...2010-07-01 false Inspection of recognized State homes. 17.199 Section 17.199 Pensions...Aid to States for Care of Veterans in State Homes § 17.199 Inspection of recognized State homes. Representatives of the Department of...

2010-07-01

374

Comparison of risk of local-regional recurrence after mastectomy or breast conservation therapy for patients treated with neoadjuvant chemotherapy and radiation stratified according to a prognostic index score  

SciTech Connect

Purpose: We previously developed a prognostic index that stratified patients treated with breast conservation therapy (BCT) after neoadjuvant chemotherapy into groups with different risks for local-regional recurrence (LRR). The purpose of this study was to compare the rates of LRR as a function of prognostic index score for patients treated with BCT or mastectomy plus radiation after neoadjuvant chemotherapy. Methods and Materials: We retrospectively analyzed 815 patients treated with neoadjuvant chemotherapy, surgery, and radiation. Patients were assigned an index score from 0 to 4 and given 1 point for the presence of each factor: clinical N2 to N3 disease, lymphovascular invasion, pathologic size >2 cm, and multifocal residual disease. Results: The 10-year LRR rates were very low and similar between the mastectomy and BCT groups for patients with an index score of 0 or 1. For patients with a score of 2, LRR trended lower for those treated with mastectomy vs. BCT (12% vs. 28%, p = 0.28). For patients with a score of 3 to 4, LRR was significantly lower for those treated with mastectomy vs. BCT (19% vs. 61%, p = 0.009). Conclusions: This analysis suggests that BCT can provide excellent local-regional treatment for the vast majority of patients after neoadjuvant chemotherapy. For the few patients with a score of 3 to 4, LRR was >60% after BCT and was <20% with mastectomy. If these findings are confirmed in larger randomized studies, the prognostic index may be useful in helping to select the type of surgical treatment for patients treated with neoadjuvant chemotherapy, surgery, and radiation.

Huang, Eugene H. [Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX (United States); Strom, Eric A. [Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX (United States); Perkins, George H. [Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX (United States); Oh, Julia L. [Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX (United States); Chen, Allen M. [Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX (United States); Meric-Bernstam, Funda [Department of Surgical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX (United States); Hunt, Kelly K. [Department of Surgical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX (United States); Sahin, Aysegul A. [Department of Pathology, University of Texas M.D. Anderson Cancer Center, Houston, TX (United States); Hortobagyi, Gabriel N. [Department of Breast Medical Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX (United States); Buchholz, Thomas A. [Department of Radiation Oncology, University of Texas M.D. Anderson Cancer Center, Houston, TX (United States)]. E-mail: tbuchhol@mdanderson.org

2006-10-01

375

The ?11A of promoter DNA and two conserved amino acids in the melting region of ?70 both directly affect the rate limiting step in formation of the stable RNA polymerase-promoter complex, but they do not necessarily interact  

PubMed Central

Formation of the stable, strand separated, ‘open’ complex between RNA polymerase and a promoter involves DNA melting of approximately 14 base pairs. The likely nucleation site is the highly conserved ?11A base in the non-template strand of the ?10 promoter region. Amino acid residues Y430 and W433 on the ?70 subunit of the RNA polymerase participate in the strand separation. The roles of ?11A and of the Y430 and W433 were addressed by employing synthetic consensus promoters containing base analog and other substitutions at ?11 in the non-template strand, and ?70 variants bearing amino acid substitutions at positions 430 and 433. Substitutions for ?11A and for Y430 and W433 in ?70 have small or no effects on formation of the initial RNA polymerase-promoter complex, but exert their effects on subsequent steps on the way to formation of the open complex. As substitutions for Y430 and W433 also affect open complex formation on promoter DNA lacking the ?11A base, it is concluded that these amino acid residues have other (or additional) roles, not involving the ?11A. The effects of the substitutions at ?11A of the promoter and Y430 and W433 of ?70 are cumulative. PMID:17567604

Schroeder, Lisa A.; Choi, Ae-Jin; deHaseth, Pieter L.

2007-01-01

376

Conservation of position-specific gene expression in axolotl limb skin.  

PubMed

Urodele amphibians can regenerate their limbs after amputation. After amputation, undifferentiated cells appear on the amputation plane and form regeneration blastema. A limb blastema recreates a complete replica of the original limb. It is well known that disturbance of the location of limb tissues prior to amputation perturbs limb patterning, suggesting that different intact limb tissues carry different location information despite their identical appearance. The cause of such differences in intact tissues remains unknown. In this study, we found that Lmx1b, Tbx2, and Tbx3 genes, which are expressed in developing limb in a region specific manner, remained detectable in a mature axolotl limb. Furthermore, those position-specific gene expression patterns were conserved in mature limbs. Treatment with retinoic acid (RA), which is known to have ventralizing activity, changed Lmx1b expression in intact dorsal skin and dorsal character to ventral, indicating that conserved Lmx1b expression was due to the dorsal character and not leaky gene expression. Furthermore, we found that such conserved gene expression was rewritable in regeneration blastemas. These results suggest that axolotl limb cells can recognize their locations and maintain limbness via conserved expression profiles of developmental genes. PMID:24410490

Satoh, Akira; Makanae, Aki

2014-01-01

377

Antibody Recognition of a Highly Conserved Influenza Virus Epitope  

SciTech Connect

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

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

2009-05-21

378

The human G1m1 allotype associates with CD4+ T-cell responsiveness to a highly conserved IgG1 constant region peptide and confers an asparaginyl endopeptidase cleavage site.  

PubMed

The human G1m1 allotype comprises two amino acids, D12 and L14, in the CH3 domain of IGHG1. Although the G1m1 allotype is prevalent in human populations, ~40% of Caucasiods are homozygous for the nG1m1 allotype corresponding to E12 and M14. Peptides derived from the G1m1 region were tested for their ability to induce CD4+ T-cell proliferative responses in vitro. A peptide immediately downstream from the G1m1 sequence was recognized by CD4+ T cells in a large percentage of donors (peptide CH3??-??). CD4+ T-cell proliferative responses to CH3??-?? were found at an increased frequency in nG1m1 homozygous donors. Homozygous nG1m1 donors possessing the HLA-DRB1*07 allele displayed the highest magnitudes of proliferation. CD4+ T cells from donors homozygous for nG1m1 proliferated to G1m1-carrying Fc-fragment proteins, whereas CD4+ T cells from G1m1 homozygous donors did not. The G1m1 sequence creates an enzymatic cleavage site for asparaginyl endopeptidase in vitro. Proteolytic activity at D12 may allow the presentation of the CH3??-?? peptide, which in turn may result in the establishment of tolerance to this peptide in G1m1-positive donors. Homozygous nG1m1 patients may be more likely to develop CD4+ T-cell-mediated immune responses to therapeutic antibodies carrying the G1m1 allotype. PMID:21326320

Stickler, M M; Reddy, A; Xiong, J M; Hinton, P R; DuBridge, R; Harding, F A

2011-04-01

379

The human G1m1 allotype associates with CD4+ T-cell responsiveness to a highly conserved IgG1 constant region peptide and confers an asparaginyl endopeptidase cleavage site  

PubMed Central

The human G1m1 allotype comprises two amino acids, D12 and L14, in the CH3 domain of IGHG1. Although the G1m1 allotype is prevalent in human populations, ?40% of Caucasiods are homozygous for the nG1m1 allotype corresponding to E12 and M14. Peptides derived from the G1m1 region were tested for their ability to induce CD4+ T-cell proliferative responses in vitro. A peptide immediately downstream from the G1m1 sequence was recognized by CD4+ T cells in a large percentage of donors (peptide CH315?29). CD4+ T-cell proliferative responses to CH315?29 were found at an increased frequency in nG1m1 homozygous donors. Homozygous nG1m1 donors possessing the HLA-DRB1*07 allele displayed the highest magnitudes of proliferation. CD4+ T cells from donors homozygous for nG1m1 proliferated to G1m1-carrying Fc-fragment proteins, whereas CD4+ T cells from G1m1 homozygous donors did not. The G1m1 sequence creates an enzymatic cleavage site for asparaginyl endopeptidase in vitro. Proteolytic activity at D12 may allow the presentation of the CH315?29 peptide, which in turn may result in the establishment of tolerance to this peptide in G1m1-positive donors. Homozygous nG1m1 patients may be more likely to develop CD4+ T-cell-mediated immune responses to therapeutic antibodies carrying the G1m1 allotype. PMID:21326320

Stickler, M M; Reddy, A; Xiong, J M; Hinton, P R; DuBridge, R; Harding, F A

2011-01-01

380

Conservation Planning for Ecosystem Services  

PubMed Central

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 and opportunities for aligning conservation goals for biodiversity with six ecosystem services (carbon storage, flood control, forage production, outdoor recreation, crop pollination, and water provision) in the Central Coast ecoregion of California, United States. We found weak positive and some weak negative associations between the priority areas for biodiversity conservation and the flows of the six ecosystem services across the ecoregion. Excluding the two agriculture-focused services—crop pollination and forage production—eliminates all negative correlations. We compared the degree to which four contrasting conservation network designs protect biodiversity and the flow of the six services. We found that biodiversity conservation protects substantial collateral flows of services. Targeting ecosystem services directly can meet the multiple ecosystem services and biodiversity goals more efficiently but cannot substitute for targeted biodiversity protection (biodiversity losses of 44% relative to targeting biodiversity alone). Strategically targeting only biodiversity plus the four positively associated services offers much promise (relative biodiversity losses of 7%). Here we present an initial analytical framework for integrating biodiversity and ecosystem services in conservation planning and illustrate its application. We found that although there are important potential trade-offs between conservation for biodiversity and for ecosystem services, a systematic planning framework offers scope for identifying valuable synergies. PMID:17076586

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

2006-01-01

381

Conservation planning for ecosystem services.  

PubMed

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 and opportunities for aligning conservation goals for biodiversity with six ecosystem services (carbon storage, flood control, forage production, outdoor recreation, crop pollination, and water provision) in the Central Coast ecoregion of California, United States. We found weak positive and some weak negative associations between the priority areas for biodiversity conservation and the flows of the six ecosystem services across the ecoregion. Excluding the two agriculture-focused services-crop pollination and forage production-eliminates all negative correlations. We compared the degree to which four contrasting conservation network designs protect biodiversity and the flow of the six services. We found that biodiversity conservation protects substantial collateral flows of services. Targeting ecosystem services directly can meet the multiple ecosystem services and biodiversity goals more efficiently but cannot substitute for targeted biodiversity protection (biodiversity losses of 44% relative to targeting biodiversity alone). Strategically targeting only biodiversity plus the four positively associated services offers much promise (relative biodiversity losses of 7%). Here we present an initial analytical framework for integrating biodiversity and ecosystem services in conservation planning and illustrate its application. We found that although there are important potential trade-offs between conservation for biodiversity and for ecosystem services, a systematic planning framework offers scope for identifying valuable synergies. PMID:17076586

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

2006-10-01

382

Conservation of Intrinsic Disorder in Protein Domains and Families: II. Functions of Conserved Disorder†  

PubMed Central

Regions of conserved disorder prediction (CDP) were found in protein domains from all available InterPro member databases, although with varying frequency. These CDP regions were found in proteins from all kingdoms of life, including viruses. However, eukaryotes had one order of magnitude more proteins containing long disordered regions than did archaea and bacteria. Sequence conservation in CDP regions varied, but was on average slightly lower than in regions of conserved order. In some cases disordered regions evolve faster than ordered regions, in others they evolve slower, and in the rest they evolve at roughly the same rate. A variety of functions were found to be associated with domains containing conserved disorder. The most common were DNA/RNA binding, and protein binding. Many ribosomal proteins also were found to contain conserved disordered regions. Other functions identified included membrane translocation and amino acid storage for germination. Due to limitations of current knowledge as well as the methodology used for this work, it was not determined whether or not these functions were directly associated with the predicted disordered region. However, the functions associated with conserved disorder in this work are in agreement with the functions found in other studies to correlate to disordered regions. We have established that intrinsic disorder may be more common in bacterial and archaeal proteins than previously thought, but this disorder is likely to be used for different purposes than in eukaryotic proteins, as well as occurring in shorter stretches of protein. Regions of predicted disorder were found to be conserved within a large number of protein families and domains. Although many think of such conserved domains as being ordered, in fact a significant number of them contain regions of disorder that are likely to be crucial to their function. PMID:16602696

Chen, Jessica Walton; Romero, Pedro; Uversky, Vladimir N.; Dunker, A. Keith

2008-01-01

383

Non-random Escape Pathways from a Broadly Neutralizing Human Monoclonal Antibody Map to a Highly Conserved Region on the Hepatitis C Virus E2 Glycoprotein Encompassing Amino Acids 412–423  

PubMed Central

A challenge for hepatitis C virus (HCV) vaccine development is to define epitopes that are able to elicit protective antibodies against this highly diverse virus. The E2 glycoprotein region located at residues 412–423 is conserved and antibodies to 412–423 have broadly neutralizing activities. However, an adaptive mutation, N417S, is associated with a glycan shift in a variant that cannot be neutralized by a murine but by human monoclonal antibodies (HMAbs) against 412–423. To determine whether HCV escapes from these antibodies, we analyzed variants that emerged when cell culture infectious HCV virions (HCVcc) were passaged under increasing concentrations of a specific HMAb, HC33.1. Multiple nonrandom escape pathways were identified. Two pathways occurred in the context of an N-glycan shift mutation at N417T. At low antibody concentrations, substitutions of two residues outside of the epitope, N434D and K610R, led to variants having improved in vitro viral fitness and reduced sensitivity to HC33.1 binding and neutralization. At moderate concentrations, a S419N mutation occurred within 412–423 in escape variants that have greatly reduced sensitivity to HC33.1 but compromised viral fitness. Importantly, the variants generated from these pathways differed in their stability. N434D and K610R-associated variants were stable and became dominant as the virions were passaged. The S419N mutation reverted back to N419S when immune pressure was reduced by removing HC33.1. At high antibody concentrations, a mutation at L413I was observed in variants that were resistant to HC33.1 neutralization. Collectively, the combination of multiple escape pathways enabled the virus to persist under a wide range of antibody concentrations. Moreover, these findings pose a different challenge to vaccine development beyond the identification of highly conserved epitopes. It will be necessary for a vaccine to induce high potency antibodies that prevent the formation of escape variants, which can co-exist with lower potency or levels of neutralizing activities. PMID:25122476

Keck, Zhen-yong; Angus, Allan G. N.; Wang, Wenyan; Lau, Patrick; Wang, Yong; Gatherer, Derek; Patel, Arvind H.; Foung, Steven K. H.

2014-01-01

384

LAND & WATER CONSERVATION PROGRAM  

E-print Network

and resources in a geographic area Promote conservation of these natural features and resources Guide ________________________________________________________________________ Preparing a Conservation Plan INTRODUCTION Conservation of land, water and other natural features and resources is a priority for many New Hampshire communities. In order to implement conservation projects

New Hampshire, University of

385

PREVENTIVE CONSERVATION: A CONCEPT SUITED TO THE CONSERVATION OF EARTHEN  

E-print Network

PREVENTIVE CONSERVATION: A CONCEPT SUITED TO THE CONSERVATION OF EARTHEN ARCHITECTURAL HERITAGE and Construction Key words: Preventive conservation, traditional conservation practices, risk reduction, heritage management Abstract The concept of "preventive conservation" is relatively old as it has already been

Paris-Sud XI, Université de

386

3-minute diagnosis: Researchers develop new method to recognize pathogens  

SciTech Connect

Imagine knowing precisely why you feel sick ... before the doctor's exam is over. Lawrence Livermore researcher Reg Beer and his engineering colleagues have developed a new method to recognize disease-causing pathogens quicker than ever before.

Beer, Reg

2014-01-06

387

37 CFR 11.15 - Refusal to recognize a practitioner.  

Code of Federal Regulations, 2011 CFR

37 Patents, Trademarks, and Copyrights 1 2011-07-01 2011-07-01...11.15 Patents, Trademarks, and Copyrights UNITED STATES PATENT AND TRADEMARK...Trademarks, and Other Non-Patent Law § 11.15 Refusal to recognize...

2011-07-01

388

3-minute diagnosis: Researchers develop new method to recognize pathogens  

ScienceCinema

Imagine knowing precisely why you feel sick ... before the doctor's exam is over. Lawrence Livermore researcher Reg Beer and his engineering colleagues have developed a new method to recognize disease-causing pathogens quicker than ever before.

Beer, Reg

2014-05-30

389

Drinking to Excess: Recognize and Treat Alcohol Problems  

MedlinePLUS

... disclaimer . Subscribe Drinking to Excess Recognize and Treat Alcohol Problems Some people enjoy an occasional glass of ... while watching a football game. Most people drink alcohol moderately, within their limits. Others overdo it occasionally. ...

390

ADEQUACY OF DISINFECTION FOR CONTROL OF NEWLY RECOGNIZED WATERBORNE PATHOGENS  

EPA Science Inventory

Agents recently recognized as causes or potential causes of waterborne outbreaks include pathogenic bacteria (Campylobacter jejuni, Yersinia enterocoliticia), viruses (rotavirus, Norwalk virus and other poorly defined viral agents) and Giardia lamblia, a protozoan agent. Although...

391

Consumers Learning To Recognize High-Value Health Care Providers  

MedlinePLUS

... salud para tà Newsletters Events Newsroom Navigating the Health Care System Advice Columns from Dr. Carolyn Clancy Former ... 3 2012 Consumers Learning To Recognize High-Value Health Care Providers By Carolyn M. Clancy, M.D. As ...

392

(WR121 -New Delivery Models) RECOGNIZES WHEN INFORMATION  

E-print Network

(WR121 - New Delivery Models) RECOGNIZES WHEN INFORMATION IS NEEDED Delivery Models) FINDS INFORMATION EFFICIENTLY: Successful learners know that knowledge to design effective search strategies (WR121 - New Delivery Models) LEARNS

Tullos, Desiree

393

Development of forest-conservation area network in estonia  

Microsoft Academic Search

In the Estonian new forest policy an effort has been given on formulation of the biodiversity assessment of forest communities and plans for developing forest conservation area network representative to all forests in this region. There are also discussed problems in connection with selection of conservation areas and social aspects of forest conservation ideas. As maintaining of particular area outside

Henn Korjus; Kaili Viilma

394

In vitro binding of Sorghum bicolor transcription factors ABI4 and ABI5 to a conserved region of a GA 2-OXIDASE promoter: possible role of this interaction in the expression of seed dormancy  

PubMed Central

The precise adjustment of the timing of dormancy release according to final grain usage is still a challenge for many cereal crops. Grain sorghum [Sorghum bicolor (L.) Moench] shows wide intraspecific variability in dormancy level and susceptibility to pre-harvest sprouting (PHS). Both embryo sensitivity to abscisic acid (ABA) and gibberellin (GA) metabolism play an important role in the expression of dormancy of the developing sorghum grain. In previous works, it was shown that, simultaneously with a greater embryo sensitivity to ABA and higher expression of SbABA-INSENSITIVE 4 (SbABI4) and SbABA-INSENSITIVE 5 (SbABI5), dormant grains accumulate less active GA4 due to a more active GA catabolism. In this work, it is demonstrated that the ABA signalling components SbABI4 and SbABI5 interact in vitro with a fragment of the SbGA 2-OXIDASE 3 (SbGA2ox3) promoter containing an ABA-responsive complex (ABRC). Both transcription factors were able to bind the promoter, although not simultaneously, suggesting that they might compete for the same cis-acting regulatory sequences. A biological role for these interactions in the expression of dormancy of sorghum grains is proposed: either SbABI4 and/or SbABI5 activate transcription of the SbGA2ox3 gene in vivo and promote SbGA2ox3 protein accumulation; this would result in active degradation of GA4, thus preventing germination of dormant grains. A comparative analysis of the 5?-regulatory region of GA2oxs from both monocots and dicots is also presented; conservation of the ABRC in closely related GA2oxs from Brachypodium distachyon and rice suggest that these species might share the same regulatory mechanism as proposed for grain sorghum. PMID:24151305

Cantoro, Renata

2013-01-01

395

Rectangles and Squares Recognized by Two-Dimensional Automata  

Microsoft Academic Search

We consider sets of rectangles and squares recognized by deterministic and non-deterministic two-dimensional finite-state automata. We show that NFAs are strictly more powerful than DFAs, even for pictures over a one-symbol alphabet. In the process, we show that the pitcure languages recognized by NFAs are not closed under complement, resolving a long-standing open question. We also show that NFAs can

Jarkko Kari; Cristopher Moore

2000-01-01

396

Zoning invariant holistic recognizer for hybrid recognition of handwriting  

Microsoft Academic Search

As human handwriting is immensely variable, no single recognition approachappears capable of uniformly good performance. Combining results of multiplerecognition approaches gives improved recognition rates. Recognizers used in such ahybrid approach need to be different, so that their results are complementary.Segmentation-based and wholistic recognition approaches are methods which aredifferent in principle.This paper describes a wholistic recognizer developed for use in a

Robert K. Powalka; Nasser Sherkat; Robert J. Whitrow

1995-01-01

397

The impact of isolated tumor cells on loco-regional recurrence in breast cancer patients treated with breast-conserving treatment or mastectomy without post-mastectomy radiation therapy.  

PubMed

To compare the outcome of patients with invasive breast cancer, who had isolated tumor cells (ITC) in sentinel lymph nodes, pN0(i+), to patients with histologically negative nodes, pN0. We retrospectively studied 1,273 patients diagnosed with T1-T3 breast cancer from 1999 to 2009. Patients were divided into 2 populations: 807 patients treated with breast-conserving surgery (BCS) and radiotherapy (RT), 85(10.5 %) with pN0(i+) and 722(89.5 %) with pN0. And the other population had 466 patients treated with mastectomy without post-mastectomy radiation therapy (PMRT), 80(17.2 %) with pN0(i+),and 386(82.8 %)with pN0. All patients underwent sentinel node biopsy, and the presence of ITC was determined. Patients with axillary dissection only or neoadjuvant chemotherapy were excluded. Among the 1,273 patients studied; 87.3 % received adjuvant systemic therapy. Kaplan-Meier, Cox regression, and log-rank statistical tests were used. Median patient age was 55.7 years. Median follow-up was 69.5 months. The 5- and 10-year cumulative incidence of Loco-regional recurrence (LRR) for patients treated with BCS and RT was 1.6 and 3.5 % for 85 pN0(i+) patients, and 2.4 and 5 % for 722 pN0 patients, respectively. For patients treated with mastectomy without PMRT, 5- and 10-year LRR rates were 2.8 and 2.8 % for 80 pN0(i+) patients, and 1.8 and 3 % for 386 pN0 patients, respectively. There were no statistically significant differences in LRR (p = 0.9), distant recurrence (p = 0.3) ,and overall survival (p = 0.5) among all groups. On multivariate analysis, ITC were not associated with increased risk of LRR, distant recurrence and overall survival. Grade (p = 0.003) and systemic therapy (p = 0.02) were statistically significantly associated with risk of LRR. Sentinel node ITC have no significant impact on LRR, distant recurrence and overall survival in breast cancer patients. Additional treatments such as axillary dissection, chemotherapy, or regional radiation should not be given solely based on the presence of sentinel node ITC. PMID:24952906

Keruakous, Amany R; Sadek, Betro T; Shenouda, Mina N; Niemierko, Andrzej; Abi Raad, Rita F; Specht, Michelle; Smith, Barbara L; Taghian, Alphonse G

2014-07-01

398

Applying molecular genetic tools to the conservation and action plan for the critically endangered Far Eastern leopard ( Panthera pardus orientalis)  

Microsoft Academic Search

A role for molecular genetic approaches in conservation of endangered taxa is now commonly recognized. Because conservation genetic analyses provide essential insights on taxonomic status, recent evolutionary history and current health of endangered taxa, they are considered in nearly all conservation programs. Genetic analyses of the critically endangered Far Eastern, or Amur leopard, Panthera pardus orientalis, have been done recently

Olga Uphyrkina; Stephen J. O'Brien

2003-01-01

399

Nonstereotyped Lymphoma B-cell Receptors Recognize Vimentin as a Shared Autoantigen  

PubMed Central

Antigen activation of the B-cell receptor (BCR) may play a role in the pathogenesis of human follicular lymphoma (FL) and other B-cell malignancies. However, the nature of the antigen(s) recognized by tumor BCRs has not been well studied. Here, we used unbiased approaches to demonstrate that 42 (19.35%) of 217 tested FL immunoglobulins (Igs) recognized vimentin as a shared autoantigen. The epitope was localized to the N-terminal region of vimentin for all vimentin-reactive tumor Igs. We confirmed specific binding to vimentin by using recombinant vimentin and by performing competitive inhibition studies. Furthermore, using indirect immunofluorescence staining, we showed that the vimentin-reactive tumor Igs colocalized with an anti-vimentin monoclonal antibody in HEp-2 cells. The reactivity to N-terminal vimentin of IgG FL Igs was significantly higher than that of IgM FL Igs (30.4% vs. 10%; P=0.0022). However, vimentin-reactive FL Igs did not share complimentarity determining region 3 motifs and were not homologous. Vimentin was expressed in the T-cell rich regions of FL, suggesting that vimentin is available for binding with tumor BCRs within the tumor microenvironment. Vimentin was also frequently recognized by mantle cell lymphoma and multiple myeloma Igs. Our results demonstrate that vimentin is a shared autoantigen recognized by nonstereotyped FL BCRs and by the Igs of mantle cell lymphoma and multiple myeloma and suggest that vimentin may play a role in the pathogenesis of multiple B-cell malignancies. These findings may lead to better understanding of the biology and natural history of FL and other B cell malignancies. PMID:23536634

Cha, Soung-Chul; Qin, Hong; Kannan, Shibichakravarthy; Rawal, Seema; Watkins, Leticia S.; Baio, Flavio E.; Wu, Weiguo; Ong, Juliana; Wei, Jinsong; Kwak, Benjamin; Kim, Sang; Popescu, Michael S.; Paick, Daniel S.; Kim, Kunhwa; Luong, Amber; Davis, Richard E; Schroeder, Harry W.; Kwak, Larry W.; Neelapu, Sattva S.

2013-01-01

400

NATURAL RESOURCES CONSERVATION FOREST ECOLOGY & CONSERVATION  

E-print Network

NATURAL RESOURCES CONSERVATION FOREST ECOLOGY & CONSERVATION For students entering after 8 oriented towards natural resources, e.g., GEO-SCI 360 Economic Geography; REGIONPL 574 City Planning; NRC ____________________ Senior Year NRC 526 Silviculture (EOY even) 4 NRC 540 Forest Resources Mgt. 4 Land/mgt./resource elective

Massachusetts at Amherst, University of

401

The African Conservation Foundation  

NSDL National Science Digital Library

This portal provides in-depth information about conservation issues and initiatives in Africa. The online searchable databases and forums showcase, promote and provide background information on almost 300 conservation organisations and protected area institutions across the continent. The African Conservation Foundation (ACF) is primarily concerned with education and capacity building in Africa in the areas of environment and conservation. Its mission is to support and link African conservation initiatives, groups and NGOs, with the aim of strengthening their capacity, building partnerships and promoting effective communication and co-ordination of conservation efforts.

Terry Harnwell

2001-08-15

402

Incorporating climate change into systematic conservation planning  

USGS Publications Warehouse

The principles of systematic conservation planning are now widely used by governments and non-government organizations alike to develop biodiversity conservation plans for countries, states, regions, and ecoregions. Many of the species and ecosystems these plans were designed to conserve are now being affected by climate change, and there is a critical need to incorporate new and complementary approaches into these plans that will aid species and ecosystems in adjusting to potential climate change impacts. We propose five approaches to climate change adaptation that can be integrated into existing or new biodiversity conservation plans: (1) conserving the geophysical stage, (2) protecting climatic refugia, (3) enhancing regional connectivity, (4) sustaining ecosystem process and function, and (5) capitalizing on opportunities emerging in response to climate change. We discuss both key assumptions behind each approach and the trade-offs involved in using the approach for conservation planning. We also summarize additional data beyond those typically used in systematic conservation plans required to implement these approaches. A major strength of these approaches is that they are largely robust to the uncertainty in how climate impacts may manifest in any given region.

Groves, Craig R.; Game, Edward T.; Anderson, Mark G.; Cross, Molly; Enquist, Carolyn; Ferdana, Zach; Girvetz, Evan; Gondor, Anne; Hall, Kimberly R.; Higgins, Jonathan; Marshall, Rob; Popper, Ken; Schill, Steve; Shafer, Sarah L.

2012-01-01

403

Characterizing fish community diversity across Virginia landscapes: Prerequisite for conservation  

USGS Publications Warehouse

The number of community types occurring within landscapes is an important, but often unprotected, component of biological diversity. Generally applicable protocols for characterizing community diversity need to be developed to facilitate conservation. We used several multivariate techniques to analyze geographic variation in the composition of fish communities in Virginia streams. We examined relationships between community composition and six landscape variables: drainage basin, physiography, stream order, elevation, channel slope, and map coordinates. We compared patterns at two scales (statewide and subdrainage-specific) to assess sensitivity of community classification to spatial scale. We also compared patterns based on characterizing communities by species composition vs. ecological composition. All landscape variables explained significant proportions of the variance in community composition. Statewide, they explained 32% of the variance in species composition and 48% of the variance in ecological composition. Typical communities in each drainage or physiography were statistically distinctive. Communities in different combinations of drainage, physiography, and stream size were even more distinctive, but composition was strongly spatially autocorrelated. Ecological similarity and species similarity of community pairs were strongly related, but replacement by ecologically similar species was common among drainage-physiography combinations. Landscape variables explained significant proportions of variance in community composition within selected subdrainages, but proportions were less than at the statewide scale, and the explanatory power of individual variables varied considerably among subdrainages. Community variation within subdrainages appeared to be much more closely related to environmental variation than to replacement among ecologically similar species. Our results suggest that taxonomic and ecological characterizations of community composition are complementary; both are useful in a conservation context. Landscape features such as drainage, physiography, and water body size generally may provide a basis for assessing aquatic community diversity, especially in regions where the biota is poorly known. Systematic conservation of community types would be a major advance relative to most current conservation programs, which typically focus narrowly on populations of imperiled species. More effective conservation of aquatic biodiversity will require new approaches that recognize the value of both species and assemblages, and that emphasize protection of key landscape-scale processes.

Angermeier, P.L.; Winston, M.R.

1999-01-01

404

Recognizing articulatory gestures from speech for robust speech recognition.  

PubMed

Studies have shown that supplementary articulatory information can help to improve the recognition rate of automatic speech recognition systems. Unfortunately, articulatory information is not directly observable, necessitating its estimation from the speech signal. This study describes a system that recognizes articulatory gestures from speech, and uses the recognized gestures in a speech recognition system. Recognizing gestures for a given utterance involves recovering the set of underlying gestural activations and their associated dynamic parameters. This paper proposes a neural network architecture for recognizing articulatory gestures from speech and presents ways to incorporate articulatory gestures for a digit recognition task. The lack of natural speech database containing gestural information prompted us to use three stages of evaluation. First, the proposed gestural annotation architecture was tested on a synthetic speech dataset, which showed that the use of estimated tract-variable-time-functions improved gesture recognition performance. In the second stage, gesture-recognition models were applied to natural speech waveforms and word recognition experiments revealed that the recognized gestures can improve the noise-robustness of a word recognition system. In the final stage, a gesture-based Dynamic Bayesian Network was trained and the results indicate that incorporating gestural information can improve word recognition performance compared to acoustic-only systems. PMID:22423722

Mitra, Vikramjit; Nam, Hosung; Espy-Wilson, Carol; Saltzman, Elliot; Goldstein, Louis

2012-03-01

405

Conservation and Reading Readiness  

ERIC Educational Resources Information Center

Conservation is positively correlated with reading readiness and intelligence. Suggests that conservation is worthy of attention by primary teachers as a predictor of the child's readiness for learning to read. (ST)

Brekke, Beverly W.; And Others

1973-01-01

406

The Conservator's Studio  

NSDL National Science Digital Library

Produced by the Seattle Art Museum, this online resource explores the Art Conservator's profession, showing you 4 paintings through a conservator's eyes. The exhibit begins with an overview of the profession.

Museum, Seattle A.

407

Anthropological Objects Conservation  

NSDL National Science Digital Library

This online article introduces students to the Objects Conservation Laboratory run by the museum's Anthropology Division. It discusses the main activities of the lab's conservators what that process involves.

408

Waterbird Conservation for the Americas : The North American Waterbird Conservation Plan, Version 1  

USGS Publications Warehouse

This Plan provides an overarching framework and guide for conserving waterbirds. It sets forth goals and priorities for waterbirds in all habitats from the Canadian Arctic to the offshore islands of Venezuela, from Bermuda to the U.S. Pacific Islands, at nesting sites, during annual migrations and during nonbreeding periods. It advocates continent-wide monitoring; provides an impetus for regional conservation planning; proposes national, provincial, state, and other local conservation planning and action; and creates a larger context within which local habitat conservation can nest. Taken together, we hope that these activities will assure healthy populations and habitats for the waterbirds of the Americas.

Kushlan, J.A.; Steinkamp, M.J.; Parsons, K.C.; Capp, J.; Cruz, M.A.; Coulter, M.; Davidson, I.J.; Dickson, L.; Edelson, N.; Elliot, R.; Erwin, R.M.; Hatch, S.; Kress, S.; Milko, R.; Miller, S.; Mills, K.; Paul, R.; Phillips, R.; Saliva, J.E.; Syderman, B.; Trapp, J.L.; Wheeler, J.; Wohl, K.

2002-01-01

409

The IgG Fc contains distinct Fc receptor (FcR) binding sites: the leukocyte receptors Fc gamma RI and Fc gamma RIIa bind to a region in the Fc distinct from that recognized by neonatal FcR and protein A.  

PubMed

The CH2-CH3 interface of the IgG Fc domain contains the binding sites for a number of Fc receptors including Staphylococcal protein A and the neonatal Fc receptor (FcRn). It has recently been proposed that the CH2-CH3 interface also contains the principal binding site for an isoform of the low affinity IgG Fc receptor II (Fc gamma RIIb). The Fc gamma RI and Fc gamma RII binding sites have previously been mapped to the lower hinge and the adjacent surface of the CH2 domain although contributions of the CH2-CH3 interface to binding have been suggested. This study addresses the question whether the CH2-CH3 interface plays a role in the interaction of IgG with Fc gamma RI and Fc gamma RIIa. We demonstrate that recombinant soluble murine Fc gamma RI and human Fc gamma RIIa did not compete with protein A and FcRn for binding to IgG, and that the CH2-CH3 interface therefore appears not to be involved in Fc gamma RI and Fc gamma RIIa binding. The importance of the lower hinge was confirmed by introducing mutations in the proposed binding site (LL234,235AA) which abrogated binding of recombinant soluble Fc gamma RIIa to human IgG1. We conclude that the lower hinge and the adjacent region of the CH2 domain of IgG Fc is critical for the interaction between Fc gamma RIIa and human IgG, whereas contributions of the CH2-CH3 interface appear to be insignificant. PMID:10799893

Wines, B D; Powell, M S; Parren, P W; Barnes, N; Hogarth, P M

2000-05-15

410

The Ocean Conservancy  

NSDL National Science Digital Library

Learn about the Ocean Conservancy's conservation projects, the latest news in marine conservation, how to get involved, and more. Read over the current issues the Ocean Conservancy is working on, such as by catch, invasive species, and overfishing. Explore the "Fish and Wildlife" link for pictures and information on threatened and endangered animals; and read past and current issues of Blue Planet Magazine, OC's quarterly publication.

411

Natural Resources Conservation Service: Backyard Conservation  

NSDL National Science Digital Library

The Natural Resources Conservation Service, a division of the U.S. Department of Agriculture, has a feature on their website on backyard conservation. Conservation practices used on agricultural land throughout the country have been adapted for the smaller scale of backyards. Not only can visitors download and print out a 28-page booklet in English or Spanish, but they can also download and print out eight tip sheets on backyard conversation. Information on how to order the free above-mentioned material, through the mail, is also provided. Using the link in the middle of the page, "See More Tips and Topics on Backyard Conservation", visitors can read over 30 archived tips and topics, including "Invite a Toad to Dinner", "Selecting the Right Tree", and "Dream Yard". For teachers, the link "Backyard Conservation Lesson Plans" in the middle of the page provides a variety of lesson plans. Some of the lessons included are "Team Flight", which is about birds; "Growing Native", which is about native plant communities; and "Backyard Conservation and Local Laws", which is about how community laws may help or hinder backyard conservation efforts. A mock city council hearing is the final activity of the lesson.

412

The conservation and divergence of telomeric structures, effects, and functions  

E-print Network

The conservation and divergence of telomeric structures, effects, and functions H. W. Bass Sciences Telomeres are specialized eukaryotic structures at the ends of linear chromosomes, recognized, the recognition that telomeres play a critical role in aging and cancer has resulted in a great deal of excitement

Bass, Hank W.

413

Approaches to Expand NGO Natural Resource Conservation Program Outreach  

Microsoft Academic Search

Nongovernmental organizations (NGOs) are widely recognized for their success in designing and implementing locally effective natural resource conservation programs. However, most NGOs are small, scattered organizations that do not generate large-scale change. Some try to expand their operations, yet in the process lose the very attributes that fostered their local successes. This article examines how NGOs successfully achieve large-scale outreach,

Scott J. Josiah

2001-01-01

414

From conservation genetics to conservation genomics.  

PubMed

Although the application of population and evolutionary genetic theory and methods to address issues of conservation relevance has a long history, the formalization of conservation genetics as a research field is still relatively recent. One of the periodic catalysts for increased research effort in the field has been advances in molecular technologies, leading to an increasingly wider variety of molecular markers for application in conservation genetic studies. To date, genetic methods have been applied in conservation biology primarily as selectively neutral molecular tools for resolving questions of conservation relevance. However, there has been renewed interest in complementing the analysis of neutral markers with the assessment of loci that may be directly involved in responses to processes such as environmental change, with a view to identifying the genes involved in them. These kinds of studies are now possible due to the increase in availability of genomic resources for nonmodel organisms, and there will likely be an even more rapid increase in the near future due to the advent of new ultrahigh throughput-sequencing technologies. This review considers the implications of the most recent developments in genomic technologies and their potential for contributing to the conservation of populations and species. Three "conservation genomics" case studies are presented (Atlantic salmon, Salmo sala; the butterfly, Melitaea cinxia; and the California condor, Gymnogyps californianus) in order to demonstrate the diversity of applications now possible. While it is clear that genomics approaches in conservation will not replace other tried-and-true methods, these recent developments open up an exciting new range of possibilities that will enable further diversification of the application of genomics in conservation biology. PMID:19432656

Primmer, Craig R

2009-04-01

415

Introduction to Conservation Genetics  

Microsoft Academic Search

Introduction to Conservation Genetics written by R. Frankham, J.D. Ballou, and D.A. Briscoe, is a comprehensive introductory text that provides an enlightening synthesis of data and theory from ecology, population genetics, evolution, and conservation biology. The book focuses on the science of conservation genetics and is appealing in its general lack of overt advocacy, while the final section provides meaningful

R. Frankham; J. D. Ballou; D. A. Briscoe; Alec R. Lindsay

2002-01-01

416

Global Biodiversity Conservation Priorities  

E-print Network

irreplaceability/vulnerability framework of systematic conservation planning. Most of the templates prioritize, results, impacts, and challenges of these prioritizations of conservation practice within the theoretical so within the framework of conservation planning (10). We review the published concepts and methods

Wilmers, Chris

417

Global Biodiversity Conservation Priorities  

Microsoft Academic Search

The location of and threats to biodiversity are distributed unevenly, so prioritization is essential to minimize biodiversity loss. To address this need, biodiversity conservation organizations have proposed nine templates of global priorities over the past decade. Here, we review the concepts, methods, results, impacts, and challenges of these prioritizations of conservation practice within the theoretical irreplaceability\\/vulnerability framework of systematic conservation

T. M. Brooks; R. A. Mittermeier; G. A. B. da Fonseca; J. Gerlach; M. Hoffmann; J. F. Lamoreux; C. G. Mittermeier; J. D. Pilgrim; A. S. L. Rodrigues

2006-01-01

418

Building robust conservation plans.  

PubMed

Systematic conservation planning optimizes trade-offs between biodiversity conservation and human activities by accounting for socioeconomic costs while aiming to achieve prescribed conservation objectives. However, the most cost-efficient conservation plan can be very dissimilar to any other plan achieving the set of conservation objectives. This is problematic under conditions of implementation uncertainty (e.g., if all or part of the plan becomes unattainable). We determined through simulations of parallel implementation of conservation plans and habitat loss the conditions under which optimal plans have limited chances of implementation and where implementation attempts would fail to meet objectives. We then devised a new, flexible method for identifying conservation priorities and scheduling conservation actions. This method entails generating a number of alternative plans, calculating the similarity in site composition among all plans, and selecting the plan with the highest density of neighboring plans in similarity space. We compared our method with the classic method that maximizes cost efficiency with synthetic and real data sets. When implementation was uncertain-a common reality-our method provided higher likelihood of achieving conservation targets. We found that ?, a measure of the shortfall in objectives achieved by a conservation plan if the plan could not be implemented entirely, was the main factor determining the relative performance of a flexibility enhanced approach to conservation prioritization. Our findings should help planning authorities prioritize conservation efforts in the face of uncertainty about future condition and availability of sites. PMID:25362995

Visconti, Piero; Joppa, Lucas

2014-10-31

419

Biodiversity and Conservation Research  

NSDL National Science Digital Library

The Center for Biodiversity and Conservation (CBC) at the American Museum of Natural History aims to "integrate scientific research, education, and outreach so that people, themselves major catalysts in the rapid loss of biodiversity, will become participants in its conservation." The CBC currently conducts biodiversity conservation research in the Bahamas, Bolivia, Madagascar, Vietnam, and in metropolitan New York.

420

Multispecies Conservation Planning  

E-print Network

CHAPTER 3 Multispecies Conservation Planning on U.S. Federal Lands Barry R. Noon, Kevin S. McKelvey, and Brett G. Dickson Numerous laws directly, or indirectly, mandate the conservation of all species that govern the use of these same lands that are in conflict with a goal of maximizing the conservation

421

Scanning the Conservation Horizon  

E-print Network

.S. Geological Survey Fundamental Science Practices. Scanning the Conservation Horizon is available online at Sciences Evan Girvetz, The Nature Conservancy Patty Glick, National Wildlife Federation John GrossScanning the Conservation Horizon A Guide to Climate Change Vulnerability Assessment #12;Scanning

422

Loss of a Conserved N-Linked Glycosylation Site in the Simian Immunodeficiency Virus Envelope Glycoprotein V2 Region Enhances Macrophage Tropism by Increasing CD4-Independent Cell-to-Cell Transmission  

PubMed Central

ABSTRACT Human immunodeficiency virus (HIV) and simian immunodeficiency virus (SIV) strains differ in their capacity to replicate in macrophages, but mechanisms underlying these differences are not fully understood. Here, we identify a highly conserved N-linked glycosylation site (N173 in SIV, corresponding to N160 in HIV) in the V2 region of the SIV envelope glycoprotein (Env) as a novel determinant of macrophage tropism and characterize mechanisms underlying this phenotype. Loss of the N173 glycosylation site in the non-macrophage-tropic SIVmac239 by introducing an N173Q mutation enhanced viral replication and multinucleated giant cell formation upon infection of rhesus macrophages, while the addition of N173 to SIVmac251 had the opposite effect. The removal of N173 in SIVmac239 enhanced CD4-independent cell-to-cell transmission to CCR5-expressing cells. SIVmac239 with N173Q mediated CD4-independent cell-cell fusion but could not infect CD4-negative cells in single-round infections. Thus, CD4-independent phenotypes were detected only in the context of cell-to-cell contact. Similar results were obtained in SIVmac251 with and without N173. N173 decreased the neutralization sensitivity of SIVmac251 but had no effect on the neutralization sensitivity of SIVmac239. The N173Q mutation had no effect on SIVmac239 binding to CD4 in Biacore assays, coimmunoprecipitation assays, and enzyme-linked immunosorbent assays (ELISAs). These findings suggest that the loss of the N173 N-linked glycosylation site increases SIVmac239 replication in macrophages by enhancing CD4-independent cell-to-cell virus transmission through CCR5-mediated fusion. This mechanism may facilitate the escape of macrophage-tropic viruses from neutralizing antibodies while promoting spreading infection by these viruses in vivo. IMPORTANCE In this study, we identify a genetic determinant in the viral envelope (N173) that increases replication and spreading infection of SIV strains in macrophages by enhancing cell-to-cell virus transmission. This effect is explained by a novel mechanism involving increased cell-to-cell fusion in the absence of CD4, the primary receptor that normally mediates virus entry. The same genetic determinant also affects the sensitivity of these viruses to inhibition by neutralizing antibodies. Most macrophage-tropic HIV/SIV strains are known to be neutralization sensitive. Together, these findings suggest that this efficient mode of virus transmission may facilitate the escape of macrophage-tropic viruses from neutralizing antibodies while promoting spreading infection by these viruses to cells expressing little or no CD4 in vivo. PMID:24554659

Yen, Po-Jen; Herschhorn, Alon; Haim, Hillel; Salas, Ignacio; Gu, Christopher; Sodroski, Joseph

2014-01-01

423

Safety and Tolerability of Conserved Region Vaccines Vectored by Plasmid DNA, Simian Adenovirus and Modified Vaccinia Virus Ankara Administered to Human Immunodeficiency Virus Type 1-Uninfected Adults in a Randomized, Single-Blind Phase I Trial  

PubMed Central

Trial Design HIV-1 vaccine development has advanced slowly due to viral antigenic diversity, poor immunogenicity and recently, safety concerns associated with human adenovirus serotype-5 vectors. To tackle HIV-1 variation, we designed a unique T-cell immunogen HIVconsv from functionally conserved regions of the HIV-1 proteome, which were presented to the immune system using a heterologous prime-boost combination of plasmid DNA, a non-replicating simian (chimpanzee) adenovirus ChAdV-63 and a non-replicating poxvirus, modified vaccinia virus Ankara. A block-randomized, single-blind, placebo-controlled phase I trial HIV-CORE 002 administered for the first time candidate HIV-1- vaccines or placebo to 32 healthy HIV-1/2-uninfected adults in Oxford, UK and elicited high frequencies of HIV-1-specific T cells capable of inhibiting HIV-1 replication in vitro. Here, detail safety and tolerability of these vaccines are reported. Methods Local and systemic reactogenicity data were collected using structured interviews and study-specific diary cards. Data on all other adverse events were collected using open questions. Serum neutralizing antibody titres to ChAdV-63 were determined before and after vaccination. Results Two volunteers withdrew for vaccine-unrelated reasons. No vaccine-related serious adverse events or reactions occurred during 190 person-months of follow-up. Local and systemic events after vaccination occurred in 27/32 individuals and most were mild (severity grade 1) and predominantly transient (<48 hours). Myalgia and flu-like symptoms were more strongly associated with MVA than ChAdV63 or DNA vectors and more common in vaccine recipients than in placebo. There were no intercurrent HIV-1 infections during follow-up. 2/24 volunteers had low ChAdV-63-neutralizing titres at baseline and 7 increased their titres to over 200 with a median (range) of 633 (231-1533) post-vaccination, which is of no safety concern. Conclusions These data demonstrate safety and good tolerability of the pSG2.HIVconsv DNA, ChAdV63.HIVconsv and MVA.HIVconsv vaccines and together with their high immunogenicity support their further development towards efficacy studies. Trial Registration ClinicalTrials.gov NCT01151319 PMID:25007091

Hayton, Emma-Jo; Rose, Annie; Ibrahimsa, Umar; Del Sorbo, Mariarosaria; Capone, Stefania; Crook, Alison; Black, Antony P.; Dorrell, Lucy; Hanke, Tomáš

2014-01-01

424

Postprocessing statistical language models for handwritten Chinese character recognizer.  

PubMed

Two statistical language models have been investigated on their effectiveness in upgrading the accuracy of a Chinese character recognizer. The baseline model is one of lexical analytic nature which segments a sequence of character images according to the maximum matching of words with consideration of word binding forces. A model of bigram statistics of word-classes is then investigated and compared against the baseline model in terms of recognition rate improvement on the image recognizer. On the average, the baseline language model improves the recognition rate by about 7% while the bigram statistics model upgrades it by about 10% PMID:18252301

Wong, P K; Chan, C

1999-01-01

425

Conservation Education: Strategic Plan To Advance Environmental Literacy. 2007-2012. FS-879  

ERIC Educational Resources Information Center

Since its establishment in 1905, the Forest Service has recognized a role and responsibility to educate people about management and conservation of American forests and grasslands. The Forest Service provides expertise in science, land management, and outdoor experiences as the foundation for environmental literacy efforts. Many conservation

US Department of Agriculture, 2007

2007-01-01

426

Fibrinogen {alpha} genes: Conservation of bipartite transcripts and carboxy-terminal-extended {alpha} subunits in vertebrates  

SciTech Connect

All three well-studied subunits of the clotting protein fibrinogen ({alpha}, {beta}, {gamma}) share N-terminal structural homologies, but until recently only the {beta} and {gamma} chains were recognized as having similar globular C-termini. With the discovery of an extra exon in the human fibrinogen {alpha} gene (exon VI), a minor form of the {alpha} subunit ({alpha}{sub E}) with an extended {beta}- and {gamma}-like C-terminus has been identified. In the present study, the polymerase chain reaction has been used to identify sequences that encode counterparts to {alpha}{sub E} in chicken, rabbit, rat, and baboon. The basic six-exon structure of the fibrinogen {alpha} genes is shown to be conserved among mammals and birds, as are the intron positions. Bipartite transcripts - still bearing an intron prior to the last exon - are found among the products of the various vertebrate fibrinogen {alpha} genes. The last exon represents the largest conserved segment of the gene and, in each species examined, encodes exactly 236 amino acids. The C-termini of these {alpha}{sub E} chains align without a single gap and are between 76 and 99% identical. Since the exon VI-encoded domain of {alpha}{sub E} is as well conserved as the corresponding regions of the {beta} and {gamma} chains, it follows that it is equally important and that {alpha}{sub E}-fibrinogen plays a vital, if as-yet unrecognized physiological role. 21 refs., 7 figs., 1 tab.

Fu, Y.; Cao, Y.; Hertzberg, K.M.; Grieninger, G. [Lindsley F. Kimball Research Inst. of the New York Blood Center, NY (United States)] [Lindsley F. Kimball Research Inst. of the New York Blood Center, NY (United States)

1995-11-01

427

Exactly conservative integrators  

SciTech Connect

Traditional numerical discretizations of conservative s