Sample records for identifying conserved regions

  1. Delineating Focus Areas for Bird Conservation in the Central Hardwoods Bird Conservation Region

    Treesearch

    Jane A. Fitzgerald; C. Diane True; David D. Diamond; Troy Ettel; Laurel Moore; Timothy A. Nigh; Shawchyi Vorisek; Greg Wathen

    2005-01-01

    This paper reports on a process used to identify landscape-scale focus areas for the conservation of priority grassland, grass-shrubland, wetland and forest-woodland birds in the Central Hardwoods Bird Conservation Region (CHBCR). The areas were delineated by biologists and other technical staff of partner agencies and organizations in the CHBCR with the use of...

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

    PubMed Central

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

    2013-01-01

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

  3. Flexible risk metrics for identifying and monitoring conservation-priority species

    USGS Publications Warehouse

    Stanton, Jessica C.; Semmens, Brice X.; McKann, Patrick C.; Will, Tom; Thogmartin, Wayne E.

    2016-01-01

    Region-specific conservation programs should have objective, reliable metrics for species prioritization and progress evaluation that are customizable to the goals of a program, easy to comprehend and communicate, and standardized across time. Regional programs may have vastly different goals, spatial coverage, or management agendas, and one-size-fits-all schemes may not always be the best approach. We propose a quantitative and objective framework for generating metrics for prioritizing species that is straightforward to implement and update, customizable to different spatial resolutions, and based on readily available time-series data. This framework is also well-suited to handling missing-data and observer error. We demonstrate this approach using North American Breeding Bird Survey (NABBS) data to identify conservation priority species from a list of over 300 landbirds across 33 bird conservation regions (BCRs). To highlight the flexibility of the framework for different management goals and timeframes we calculate two different metrics. The first identifies species that may be inadequately monitored by NABBS protocols in the near future (TMT, time to monitoring threshold), and the other identifies species likely to decline significantly in the near future based on recent trends (TPD, time to percent decline). Within the individual BCRs we found up to 45% (mean 28%) of the species analyzed had overall declining population trajectories, which could result in up to 37 species declining below a minimum NABBS monitoring threshold in at least one currently occupied BCR within the next 50 years. Additionally, up to 26% (mean 8%) of the species analyzed within the individual BCRs may decline by 30% within the next decade. Conservation workers interested in conserving avian diversity and abundance within these BCRs can use these metrics to plan alternative monitoring schemes or highlight the urgency of those populations experiencing the fastest declines. However, this

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

    PubMed Central

    Lessmann, Janeth; Muñoz, Jesús; Bonaccorso, Elisa

    2014-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  6. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment

    PubMed Central

    2013-01-01

    Background Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. Results In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Conclusion Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering

  7. Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.

    PubMed

    Nagar, Anurag; Hahsler, Michael

    2013-01-01

    Next Generation Sequencing techniques are producing enormous amounts of biological sequence data and analysis becomes a major computational problem. Currently, most analysis, especially the identification of conserved regions, relies heavily on Multiple Sequence Alignment and its various heuristics such as progressive alignment, whose run time grows with the square of the number and the length of the aligned sequences and requires significant computational resources. In this work, we present a method to efficiently discover regions of high similarity across multiple sequences without performing expensive sequence alignment. The method is based on approximating edit distance between segments of sequences using p-mer frequency counts. Then, efficient high-throughput data stream clustering is used to group highly similar segments into so called quasi-alignments. Quasi-alignments have numerous applications such as identifying species and their taxonomic class from sequences, comparing sequences for similarities, and, as in this paper, discovering conserved regions across related sequences. In this paper, we show that quasi-alignments can be used to discover highly similar segments across multiple sequences from related or different genomes efficiently and accurately. Experiments on a large number of unaligned 16S rRNA sequences obtained from the Greengenes database show that the method is able to identify conserved regions which agree with known hypervariable regions in 16S rRNA. Furthermore, the experiments show that the proposed method scales well for large data sets with a run time that grows only linearly with the number and length of sequences, whereas for existing multiple sequence alignment heuristics the run time grows super-linearly. Quasi-alignment-based algorithms can detect highly similar regions and conserved areas across multiple sequences. Since the run time is linear and the sequences are converted into a compact clustering model, we are able to

  8. Combining endangered plants and animals as surrogates to identify priority conservation areas in Yunnan, China

    PubMed Central

    Yang, Feiling; Hu, Jinming; Wu, Ruidong

    2016-01-01

    Suitable surrogates are critical for identifying optimal priority conservation areas (PCAs) to protect regional biodiversity. This study explored the efficiency of using endangered plants and animals as surrogates for identifying PCAs at the county level in Yunnan, southwest China. We ran the Dobson algorithm under three surrogate scenarios at 75% and 100% conservation levels and identified four types of PCAs. Assessment of the protection efficiencies of the four types of PCAs showed that endangered plants had higher surrogacy values than endangered animals but that the two were not substitutable; coupled endangered plants and animals as surrogates yielded a higher surrogacy value than endangered plants or animals as surrogates; the plant-animal priority areas (PAPAs) was the optimal among the four types of PCAs for conserving both endangered plants and animals in Yunnan. PAPAs could well represent overall species diversity distribution patterns and overlap with critical biogeographical regions in Yunnan. Fourteen priority units in PAPAs should be urgently considered as optimizing Yunnan’s protected area system. The spatial pattern of PAPAs at the 100% conservation level could be conceptualized into three connected conservation belts, providing a valuable reference for optimizing the layout of the in situ protected area system in Yunnan. PMID:27538537

  9. Combining endangered plants and animals as surrogates to identify priority conservation areas in Yunnan, China

    NASA Astrophysics Data System (ADS)

    Yang, Feiling; Hu, Jinming; Wu, Ruidong

    2016-08-01

    Suitable surrogates are critical for identifying optimal priority conservation areas (PCAs) to protect regional biodiversity. This study explored the efficiency of using endangered plants and animals as surrogates for identifying PCAs at the county level in Yunnan, southwest China. We ran the Dobson algorithm under three surrogate scenarios at 75% and 100% conservation levels and identified four types of PCAs. Assessment of the protection efficiencies of the four types of PCAs showed that endangered plants had higher surrogacy values than endangered animals but that the two were not substitutable; coupled endangered plants and animals as surrogates yielded a higher surrogacy value than endangered plants or animals as surrogates; the plant-animal priority areas (PAPAs) was the optimal among the four types of PCAs for conserving both endangered plants and animals in Yunnan. PAPAs could well represent overall species diversity distribution patterns and overlap with critical biogeographical regions in Yunnan. Fourteen priority units in PAPAs should be urgently considered as optimizing Yunnan’s protected area system. The spatial pattern of PAPAs at the 100% conservation level could be conceptualized into three connected conservation belts, providing a valuable reference for optimizing the layout of the in situ protected area system in Yunnan.

  10. Identifying Conservation and Restoration Priorities for Saproxylic and Old-Growth Forest Species: A Case Study in Switzerland

    NASA Astrophysics Data System (ADS)

    Lachat, Thibault; Bütler, Rita

    2009-07-01

    Saproxylic (dead-wood-associated) and old-growth species are among the most threatened species in European forest ecosystems, as they are susceptible to intensive forest management. Identifying areas with particular relevant features of biodiversity is of prime concern when developing species conservation and habitat restoration strategies and in optimizing resource investments. We present an approach to identify regional conservation and restoration priorities even if knowledge on species distribution is weak, such as for saproxylic and old-growth species in Switzerland. Habitat suitability maps were modeled for an expert-based selection of 55 focal species, using an ecological niche factor analyses (ENFA). All the maps were then overlaid, in order to identify potential species’ hotspots for different species groups of the 55 focal species (e.g., birds, fungi, red-listed species). We found that hotspots for various species groups did not correspond. Our results indicate that an approach based on “richness hotspots” may fail to conserve specific species groups. We hence recommend defining a biodiversity conservation strategy prior to implementing conservation/restoration efforts in specific regions. The conservation priority setting of the five biogeographical regions in Switzerland, however, did not differ when different hotspot definitions were applied. This observation emphasizes that the chosen method is robust. Since the ENFA needs only presence data, this species prediction method seems to be useful for any situation where the species distribution is poorly known and/or absence data are lacking. In order to identify priorities for either conservation or restoration efforts, we recommend a method based on presence data only, because absence data may reflect factors unrelated to species presence.

  11. Identifying conservation and restoration priorities for saproxylic and old-growth forest species: a case study in Switzerland.

    PubMed

    Lachat, Thibault; Bütler, Rita

    2009-07-01

    Saproxylic (dead-wood-associated) and old-growth species are among the most threatened species in European forest ecosystems, as they are susceptible to intensive forest management. Identifying areas with particular relevant features of biodiversity is of prime concern when developing species conservation and habitat restoration strategies and in optimizing resource investments. We present an approach to identify regional conservation and restoration priorities even if knowledge on species distribution is weak, such as for saproxylic and old-growth species in Switzerland. Habitat suitability maps were modeled for an expert-based selection of 55 focal species, using an ecological niche factor analyses (ENFA). All the maps were then overlaid, in order to identify potential species' hotspots for different species groups of the 55 focal species (e.g., birds, fungi, red-listed species). We found that hotspots for various species groups did not correspond. Our results indicate that an approach based on "richness hotspots" may fail to conserve specific species groups. We hence recommend defining a biodiversity conservation strategy prior to implementing conservation/restoration efforts in specific regions. The conservation priority setting of the five biogeographical regions in Switzerland, however, did not differ when different hotspot definitions were applied. This observation emphasizes that the chosen method is robust. Since the ENFA needs only presence data, this species prediction method seems to be useful for any situation where the species distribution is poorly known and/or absence data are lacking. In order to identify priorities for either conservation or restoration efforts, we recommend a method based on presence data only, because absence data may reflect factors unrelated to species presence.

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

    PubMed Central

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

    1990-01-01

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

  13. Integrated Migratory Bird Planning in the Lower Great Lakes/St. Lawrence Plain Bird Conservation Region

    Treesearch

    Chuck Hayes; Andrew Milliken; Randy Dettmers; Kevin Loftus; Brigitte Collins; Isabelle Ringuet

    2005-01-01

    The Atlantic Coast and Eastern Habitat Joint Ventures hosted two international planning workshops to begin the process of integrating bird conservation strategies under the North American Bird Conservation Initiative in the Lower Great Lakes/St. Lawrence Plain Bird Conservation Region. The workshops identified priority species and habitats, delineated focus areas,...

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

    PubMed Central

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

    2015-01-01

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

  15. Exploring spatial patterns of vulnerability for diverse biodiversity descriptors in regional conservation planning.

    PubMed

    Vimal, Ruppert; Pluvinet, Pascal; Sacca, Céline; Mazagol, Pierre-Olivier; Etlicher, Bernard; Thompson, John D

    2012-03-01

    In this study, we developed a multi-criteria assessment of spatial variability of the vulnerability of three different biodiversity descriptors: sites of high conservation interest by virtue of the presence of rare or remarkable species, extensive areas of high ecological integrity, and landscape diversity in grid cells across an entire region. We assessed vulnerability in relation to (a) direct threats in and around sites to a distance of 2 km associated with intensive agriculture, building and road infrastructure and (b) indirect effects of human population density on a wider scale (50 km). The different combinations of biodiversity and threat indicators allowed us to set differential priorities for biodiversity conservation and assess their spatial variation. For example, with this method we identified sites and grid cells which combined high biodiversity with either high threat values or low threat values for the three different biodiversity indicators. In these two classes the priorities for conservation planning will be different, reduce threat values in the former and restrain any increase in the latter. We also identified low priority sites (low biodiversity with either high or low threats). This procedure thus allows for the integration of a spatial ranking of vulnerability into priority setting for regional conservation planning. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. Plant conservation priorities of Xinjiang region, China

    NASA Astrophysics Data System (ADS)

    Li, L. P.; Cui, W. H.; Wang, T.; Tian, S.; Xing, W. J.; Yin, L. K.; Abdusalih, N.; Jiang, Y. M.

    2017-02-01

    As an important region in the Silk Road, Xinjiang is getting a good chance of developing economy. However at the same time, its natural environment is facing a big challenge. To better protect the plant diversity, it is urgent to make a thorough conservation plan. With a full database of vascular and medicinal plant distributions and nature reserve plant lists and boundaries in Xinjiang of China, we analysed the plant diversity hotspots, protection gaps and proposed the plant conservation priorities of this region. Differed from the widely accepted viewpoints that lots of plants were not included in nature reserves, we found that most of the plants ( > 90%) were actually included in the current nature reserves. We believe that compared with establishing more nature reserves, improving the management of the existing ones is also important. Furthermore, the very few unprotected plants ( < 10%) were distributed mostly in the regions of Aletai, Tacheng, Zhaosu, Manasi, Qitai and Hetian which could be the future conservation priorities.

  17. Identifying and prioritizing ungulate migration routes for landscape-level conservation

    USGS Publications Warehouse

    Sawyer, H.; Kauffman, M.J.; Nielson, R.M.; Horne, J.S.

    2009-01-01

    As habitat loss and fragmentation increase across ungulate ranges, identifying and prioritizing migration routes for conservation has taken on new urgency. Here we present a general framework using the Brownian bridge movement model (BBMM) that: (1) provides a probabilistic estimate of the migration routes of a sampled population, (2) distinguishes between route segments that function as stopover sites vs. those used primarily as movement corridors, and (3) prioritizes routes for conservation based upon the proportion of the sampled population that uses them. We applied this approach to a migratory mule deer (Odocoileus hemionus) population in a pristine area of southwest Wyoming, USA, where 2000 gas wells and 1609 km of pipelines and roads have been proposed for development. Our analysis clearly delineated where migration routes occurred relative to proposed development and provided guidance for on-the-ground conservation efforts. Mule deer migration routes were characterized by a series of stopover sites where deer spent most of their time, connected by movement corridors through which deer moved quickly. Our findings suggest management strategies that differentiate between stopover sites and movement corridors may be warranted. Because some migration routes were used by more mule deer than others, proportional level of use may provide a reasonable metric by which routes can be prioritized for conservation. The methods we outline should be applicable to a wide range of species that inhabit regions where migration routes are threatened or poorly understood. ?? 2009 by the Ecological Society of America.

  18. Identifying and prioritizing ungulate migration routes for landscape-level conservation

    USGS Publications Warehouse

    Sawyer, Hall; Kauffman, Matthew J.; Nielson, Ryan M.; Horne, Jon S.

    2009-01-01

    As habitat loss and fragmentation increase across ungulate ranges, identifying and prioritizing migration routes for conservation has taken on new urgency. Here we present a general framework using the Brownian bridge movement model (BBMM) that: (1) provides a probabilistic estimate of the migration routes of a sampled population, (2) distinguishes between route segments that function as stopover sites vs. those used primarily as movement corridors, and (3) prioritizes routes for conservation based upon the proportion of the sampled population that uses them. We applied this approach to a migratory mule deer (Odocoileus hemionus) population in a pristine area of southwest Wyoming, USA, where 2000 gas wells and 1609 km of pipelines and roads have been proposed for development. Our analysis clearly delineated where migration routes occurred relative to proposed development and provided guidance for on-the-ground conservation efforts. Mule deer migration routes were characterized by a series of stopover sites where deer spent most of their time, connected by movement corridors through which deer moved quickly. Our findings suggest management strategies that differentiate between stopover sites and movement corridors may be warranted. Because some migration routes were used by more mule deer than others, proportional level of use may provide a reasonable metric by which routes can be prioritized for conservation. The methods we outline should be applicable to a wide range of species that inhabit regions where migration routes are threatened or poorly understood.

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

    PubMed

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

    2012-03-01

    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.

  20. Analysis of ecological context for identifying vegetation and animal conservation planning foci: An example from the arid South-western USA

    USGS Publications Warehouse

    Hamazaki, T.; Thompson, B.C.; Locke, B.A.; Boykin, K.G.

    2003-01-01

    In developing conservation strategies, it is important to maximize effects of conservation within a specified land tract and to maximize conservation effects on surrounding area (ecological context). The authors proposed two criteria to select biotic entities for conservation foci: (1) the relative occurrence of fauna or flora in a tract is greater than that of an ecological context region; and (2) occurrence of the fauna or flora is relatively limited in the ecological context region. Using extensive spatial data on vegetation and wildlife habitat distribution, the authors identified strategic vegetation and fauna conservation foci for the 400 000 ha Fort Bliss military reservation in New Mexico and Texas relative to a 164 km radius ecological context region intersecting seven ecological zones and the predicted habitat distribution of 616 animal species. The authors set two specific criteria: (1) predicted area of a species' occurrence is 5% (Fort Bliss is 4.2% of the region). These criteria selected one vegetation class and 40 animal species. Further, these vegetation and animal foci were primarily located in two areas of Fort Bliss. Sensitivity analyses with other analytical radii corroborated the context radius used. Conservation of the two areas and associated taxa will maximize the contribution of Fort Bliss's conservation efforts in its ecological proximity. This relatively simple but information-rich process represents economical and defensible preliminary contextual analysis for detailed conservation planning.

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

    USGS Publications Warehouse

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

    2005-01-01

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

  2. The C-terminal region of Ge-1 presents conserved structural features required for P-body localization.

    PubMed

    Jinek, Martin; Eulalio, Ana; Lingel, Andreas; Helms, Sigrun; Conti, Elena; Izaurralde, Elisa

    2008-10-01

    The removal of the 5' cap structure by the DCP1-DCP2 decapping complex irreversibly commits eukaryotic mRNAs to degradation. In human cells, the interaction between DCP1 and DCP2 is bridged by the Ge-1 protein. Ge-1 contains an N-terminal WD40-repeat domain connected by a low-complexity region to a conserved C-terminal domain. It was reported that the C-terminal domain interacts with DCP2 and mediates Ge-1 oligomerization and P-body localization. To understand the molecular basis for these functions, we determined the three-dimensional crystal structure of the most conserved region of the Drosophila melanogaster Ge-1 C-terminal domain. The region adopts an all alpha-helical fold related to ARM- and HEAT-repeat proteins. Using structure-based mutants we identified an invariant surface residue affecting P-body localization. The conservation of critical surface and structural residues suggests that the C-terminal region adopts a similar fold with conserved functions in all members of the Ge-1 protein family.

  3. Conservation of hot regions in protein-protein interaction in evolution.

    PubMed

    Hu, Jing; Li, Jiarui; Chen, Nansheng; Zhang, Xiaolong

    2016-11-01

    The hot regions of protein-protein interactions refer to the active area which formed by those most important residues to protein combination process. With the research development on protein interactions, lots of predicted hot regions can be discovered efficiently by intelligent computing methods, while performing biology experiments to verify each every prediction is hardly to be done due to the time-cost and the complexity of the experiment. This study based on the research of hot spot residue conservations, the proposed method is used to verify authenticity of predicted hot regions that using machine learning algorithm combined with protein's biological features and sequence conservation, though multiple sequence alignment, module substitute matrix and sequence similarity to create conservation scoring algorithm, and then using threshold module to verify the conservation tendency of hot regions in evolution. This research work gives an effective method to verify predicted hot regions in protein-protein interactions, which also provides a useful way to deeply investigate the functional activities of protein hot regions. Copyright © 2016. Published by Elsevier Inc.

  4. Identifying core habitat and connectivity for focal species in the interior cedar-hemlock forest of North America to complete a conservation area design

    Treesearch

    Lance Craighead; Baden Cross

    2007-01-01

    To identify the remaining areas of the Interior Cedar- Hemlock Forest of North America and prioritize them for conservation planning, the Craighead Environmental Research Institute has developed a 2-scale method for mapping critical habitat utilizing 1) a broad-scale model to identify important regional locations as the basis for a Conservation Area Design (CAD), and 2...

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

    NASA Astrophysics Data System (ADS)

    Clerici, Nicola; Vogt, Peter

    2013-04-01

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

  6. Effectiveness of conservation easements in agricultural regions.

    PubMed

    Braza, Mark

    2017-08-01

    Conservation easements are a standard technique for preventing habitat loss, particularly in agricultural regions with extensive cropland cultivation, yet little is known about their effectiveness. I developed a spatial econometric approach to propensity-score matching and used the approach to estimate the amount of habitat loss prevented by a grassland conservation easement program of the U.S. federal government. I used a spatial autoregressive probit model to predict tract enrollment in the easement program as of 2001 based on tract agricultural suitability, habitat quality, and spatial interactions among neighboring tracts. Using the predicted values from the model, I matched enrolled tracts with similar unenrolled tracts to form a treatment group and a control group. To measure the program's impact on subsequent grassland loss, I estimated cropland cultivation rates for both groups in 2014 with a second spatial probit model. Between 2001 and 2014, approximately 14.9% of control tracts were cultivated and 0.3% of treated tracts were cultivated. Therefore, approximately 14.6% of the protected land would have been cultivated in the absence of the program. My results demonstrate that conservation easements can significantly reduce habitat loss in agricultural regions; however, the enrollment of tracts with low cropland suitability may constrain the amount of habitat loss they prevent. My results also show that spatial econometric models can improve the validity of control groups and thereby strengthen causal inferences about program effectiveness in situations when spatial interactions influence conservation decisions. © 2017 Society for Conservation Biology.

  7. Scale-dependent complementarity of climatic velocity and environmental diversity for identifying priority areas for conservation under climate change.

    PubMed

    Carroll, Carlos; Roberts, David R; Michalak, Julia L; Lawler, Joshua J; Nielsen, Scott E; Stralberg, Diana; Hamann, Andreas; Mcrae, Brad H; Wang, Tongli

    2017-11-01

    As most regions of the earth transition to altered climatic conditions, new methods are needed to identify refugia and other areas whose conservation would facilitate persistence of biodiversity under climate change. We compared several common approaches to conservation planning focused on climate resilience over a broad range of ecological settings across North America and evaluated how commonalities in the priority areas identified by different methods varied with regional context and spatial scale. Our results indicate that priority areas based on different environmental diversity metrics differed substantially from each other and from priorities based on spatiotemporal metrics such as climatic velocity. Refugia identified by diversity or velocity metrics were not strongly associated with the current protected area system, suggesting the need for additional conservation measures including protection of refugia. Despite the inherent uncertainties in predicting future climate, we found that variation among climatic velocities derived from different general circulation models and emissions pathways was less than the variation among the suite of environmental diversity metrics. To address uncertainty created by this variation, planners can combine priorities identified by alternative metrics at a single resolution and downweight areas of high variation between metrics. Alternately, coarse-resolution velocity metrics can be combined with fine-resolution diversity metrics in order to leverage the respective strengths of the two groups of metrics as tools for identification of potential macro- and microrefugia that in combination maximize both transient and long-term resilience to climate change. Planners should compare and integrate approaches that span a range of model complexity and spatial scale to match the range of ecological and physical processes influencing persistence of biodiversity and identify a conservation network resilient to threats operating at

  8. Development of a landscape integrity model framework to support regional conservation planning.

    PubMed

    Walston, Leroy J; Hartmann, Heidi M

    2018-01-01

    Land managers increasingly rely upon landscape assessments to understand the status of natural resources and identify conservation priorities. Many of these landscape planning efforts rely on geospatial models that characterize the ecological integrity of the landscape. These general models utilize measures of habitat disturbance and human activity to map indices of ecological integrity. We built upon these modeling frameworks by developing a Landscape Integrity Index (LII) model using geospatial datasets of the human footprint, as well as incorporation of other indicators of ecological integrity such as biodiversity and vegetation departure. Our LII model serves as a general indicator of ecological integrity in a regional context of human activity, biodiversity, and change in habitat composition. We also discuss the application of the LII framework in two related coarse-filter landscape conservation approaches to expand the size and connectedness of protected areas as regional mitigation for anticipated land-use changes.

  9. Development of a landscape integrity model framework to support regional conservation planning

    PubMed Central

    Hartmann, Heidi M.

    2018-01-01

    Land managers increasingly rely upon landscape assessments to understand the status of natural resources and identify conservation priorities. Many of these landscape planning efforts rely on geospatial models that characterize the ecological integrity of the landscape. These general models utilize measures of habitat disturbance and human activity to map indices of ecological integrity. We built upon these modeling frameworks by developing a Landscape Integrity Index (LII) model using geospatial datasets of the human footprint, as well as incorporation of other indicators of ecological integrity such as biodiversity and vegetation departure. Our LII model serves as a general indicator of ecological integrity in a regional context of human activity, biodiversity, and change in habitat composition. We also discuss the application of the LII framework in two related coarse-filter landscape conservation approaches to expand the size and connectedness of protected areas as regional mitigation for anticipated land-use changes. PMID:29614093

  10. Identifying designatable units for intraspecific conservation prioritization: a hierarchical approach applied to the lake whitefish species complex (Coregonus spp.)

    PubMed Central

    Mee, Jonathan A; Bernatchez, Louis; Reist, Jim D; Rogers, Sean M; Taylor, Eric B

    2015-01-01

    The concept of the designatable unit (DU) affords a practical approach to identifying diversity below the species level for conservation prioritization. However, its suitability for defining conservation units in ecologically diverse, geographically widespread and taxonomically challenging species complexes has not been broadly evaluated. The lake whitefish species complex (Coregonus spp.) is geographically widespread in the Northern Hemisphere, and it contains a great deal of variability in ecology and evolutionary legacy within and among populations, as well as a great deal of taxonomic ambiguity. Here, we employ a set of hierarchical criteria to identify DUs within the Canadian distribution of the lake whitefish species complex. We identified 36 DUs based on (i) reproductive isolation, (ii) phylogeographic groupings, (iii) local adaptation and (iv) biogeographic regions. The identification of DUs is required for clear discussion regarding the conservation prioritization of lake whitefish populations. We suggest conservation priorities among lake whitefish DUs based on biological consequences of extinction, risk of extinction and distinctiveness. Our results exemplify the need for extensive genetic and biogeographic analyses for any species with broad geographic distributions and the need for detailed evaluation of evolutionary history and adaptive ecological divergence when defining intraspecific conservation units. PMID:26029257

  11. Using a distribution and conservation status weighted hotspot approach to identify areas in need of conservation action to benefit Idaho bird species

    USGS Publications Warehouse

    Haines, Aaron M.; Leu, Matthias; Svancara, Leona K.; Wilson, Gina; Scott, J. Michael

    2010-01-01

    Identification of biodiversity hotspots (hereafter, hotspots) has become a common strategy to delineate important areas for wildlife conservation. However, the use of hotspots has not often incorporated important habitat types, ecosystem services, anthropogenic activity, or consistency in identifying important conservation areas. The purpose of this study was to identify hotspots to improve avian conservation efforts for Species of Greatest Conservation Need (SGCN) in the state of Idaho, United States. We evaluated multiple approaches to define hotspots and used a unique approach based on weighting species by their distribution size and conservation status to identify hotspot areas. All hotspot approaches identified bodies of water (Bear Lake, Grays Lake, and American Falls Reservoir) as important hotspots for Idaho avian SGCN, but we found that the weighted approach produced more congruent hotspot areas when compared to other hotspot approaches. To incorporate anthropogenic activity into hotspot analysis, we grouped species based on their sensitivity to specific human threats (i.e., urban development, agriculture, fire suppression, grazing, roads, and logging) and identified ecological sections within Idaho that may require specific conservation actions to address these human threats using the weighted approach. The Snake River Basalts and Overthrust Mountains ecological sections were important areas for potential implementation of conservation actions to conserve biodiversity. Our approach to identifying hotspots may be useful as part of a larger conservation strategy to aid land managers or local governments in applying conservation actions on the ground.

  12. Analysis of evolutionary conservation patterns and their influence on identifying protein functional sites.

    PubMed

    Fang, Chun; Noguchi, Tamotsu; Yamana, Hayato

    2014-10-01

    Evolutionary conservation information included in position-specific scoring matrix (PSSM) has been widely adopted by sequence-based methods for identifying protein functional sites, because all functional sites, whether in ordered or disordered proteins, are found to be conserved at some extent. However, different functional sites have different conservation patterns, some of them are linear contextual, some of them are mingled with highly variable residues, and some others seem to be conserved independently. Every value in PSSMs is calculated independently of each other, without carrying the contextual information of residues in the sequence. Therefore, adopting the direct output of PSSM for prediction fails to consider the relationship between conservation patterns of residues and the distribution of conservation scores in PSSMs. In order to demonstrate the importance of combining PSSMs with the specific conservation patterns of functional sites for prediction, three different PSSM-based methods for identifying three kinds of functional sites have been analyzed. Results suggest that, different PSSM-based methods differ in their capability to identify different patterns of functional sites, and better combining PSSMs with the specific conservation patterns of residues would largely facilitate the prediction.

  13. RNA expression in a cartilaginous fish cell line reveals ancient 3′ noncoding regions highly conserved in vertebrates

    PubMed Central

    Forest, David; Nishikawa, Ryuhei; Kobayashi, Hiroshi; Parton, Angela; Bayne, Christopher J.; Barnes, David W.

    2007-01-01

    We have established a cartilaginous fish cell line [Squalus acanthias embryo cell line (SAE)], a mesenchymal stem cell line derived from the embryo of an elasmobranch, the spiny dogfish shark S. acanthias. Elasmobranchs (sharks and rays) first appeared >400 million years ago, and existing species provide useful models for comparative vertebrate cell biology, physiology, and genomics. Comparative vertebrate genomics among evolutionarily distant organisms can provide sequence conservation information that facilitates identification of critical coding and noncoding regions. Although these genomic analyses are informative, experimental verification of functions of genomic sequences depends heavily on cell culture approaches. Using ESTs defining mRNAs derived from the SAE cell line, we identified lengthy and highly conserved gene-specific nucleotide sequences in the noncoding 3′ UTRs of eight genes involved in the regulation of cell growth and proliferation. Conserved noncoding 3′ mRNA regions detected by using the shark nucleotide sequences as a starting point were found in a range of other vertebrate orders, including bony fish, birds, amphibians, and mammals. Nucleotide identity of shark and human in these regions was remarkably well conserved. Our results indicate that highly conserved gene sequences dating from the appearance of jawed vertebrates and representing potential cis-regulatory elements can be identified through the use of cartilaginous fish as a baseline. Because the expression of genes in the SAE cell line was prerequisite for their identification, this cartilaginous fish culture system also provides a physiologically valid tool to test functional hypotheses on the role of these ancient conserved sequences in comparative cell biology. PMID:17227856

  14. Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.

    PubMed

    Amaral, Paulo P; Leonardi, Tommaso; Han, Namshik; Viré, Emmanuelle; Gascoigne, Dennis K; Arias-Carrasco, Raúl; Büscher, Magdalena; Pandolfini, Luca; Zhang, Anda; Pluchino, Stefano; Maracaja-Coutinho, Vinicius; Nakaya, Helder I; Hemberg, Martin; Shiekhattar, Ramin; Enright, Anton J; Kouzarides, Tony

    2018-03-15

    The mammalian genome is transcribed into large numbers of long noncoding RNAs (lncRNAs), but the definition of functional lncRNA groups has proven difficult, partly due to their low sequence conservation and lack of identified shared properties. Here we consider promoter conservation and positional conservation as indicators of functional commonality. We identify 665 conserved lncRNA promoters in mouse and human that are preserved in genomic position relative to orthologous coding genes. These positionally conserved lncRNA genes are primarily associated with developmental transcription factor loci with which they are coexpressed in a tissue-specific manner. Over half of positionally conserved RNAs in this set are linked to chromatin organization structures, overlapping binding sites for the CTCF chromatin organiser and located at chromatin loop anchor points and borders of topologically associating domains (TADs). We define these RNAs as topological anchor point RNAs (tapRNAs). Characterization of these noncoding RNAs and their associated coding genes shows that they are functionally connected: they regulate each other's expression and influence the metastatic phenotype of cancer cells in vitro in a similar fashion. Furthermore, we find that tapRNAs contain conserved sequence domains that are enriched in motifs for zinc finger domain-containing RNA-binding proteins and transcription factors, whose binding sites are found mutated in cancers. This work leverages positional conservation to identify lncRNAs with potential importance in genome organization, development and disease. The evidence that many developmental transcription factors are physically and functionally connected to lncRNAs represents an exciting stepping-stone to further our understanding of genome regulation.

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

    PubMed Central

    McClellan, Catherine M.; Brereton, Tom; Dell'Amico, Florence; Johns, David G.; Cucknell, Anna-C.; Patrick, Samantha C.; Penrose, Rod; Ridoux, Vincent; Solandt, Jean-Luc; Stephan, Eric; Votier, Stephen C.; Williams, Ruth; Godley, Brendan J.

    2014-01-01

    The temperate waters of the North-Eastern Atlantic have a long history of maritime resource richness and, as a result, the European Union is endeavouring to maintain regional productivity and biodiversity. At the intersection of these aims lies potential conflict, signalling the need for integrated, cross-border management approaches. This paper focuses on the marine megafauna of the region. This guild of consumers was formerly abundant, but is now depleted and protected under various national and international legislative structures. We present a meta-analysis of available megafauna datasets using presence-only distribution models to characterise suitable habitat and identify spatially-important regions within the English Channel and southern bight of the North Sea. The integration of studies from dedicated and opportunistic observer programmes in the United Kingdom and France provide a valuable perspective on the spatial and seasonal distribution of various taxonomic groups, including large pelagic fishes and sharks, marine mammals, seabirds and marine turtles. The Western English Channel emerged as a hotspot of biodiversity for megafauna, while species richness was low in the Eastern English Channel. Spatial conservation planning is complicated by the highly mobile nature of marine megafauna, however they are important components of the marine environment and understanding their distribution is a first crucial step toward their inclusion into marine ecosystem management. PMID:24586985

  16. Nucleosome exclusion from the interspecies-conserved central AT-rich region of the Ars insulator.

    PubMed

    Takagi, Haruna; Inai, Yuta; Watanabe, Shun-ichiro; Tatemoto, Sayuri; Yajima, Mamiko; Akasaka, Koji; Yamamoto, Takashi; Sakamoto, Naoaki

    2012-01-01

    The Ars insulator is a boundary element identified in the upstream region of the arylsulfatase (HpArs) gene in the sea urchin, Hemicentrotus pulcherrimus, and possesses the ability to both block enhancer-promoter communications and protect transgenes from silent chromatin. To understand the molecular mechanism of the Ars insulator, we investigated the correlation between chromatin structure, DNA structure and insulator activity. Nuclease digestion of nuclei isolated from sea urchin embryos revealed the presence of a nuclease-hypersensitive site within the Ars insulator. Analysis of micrococcal nuclease-sensitive sites in the Ars insulator, reconstituted with nucleosomes, showed the exclusion of nucleosomes from the central AT-rich region. Furthermore, the central AT-rich region in naked DNA was sensitive to nucleotide base modification by diethylpyrocarbonate (DEPC). These observations suggest that non-B-DNA structures in the central AT-rich region may inhibit nucleosomal formation, which leads to nuclease hypersensitivity. Furthermore, comparison of nucleotide sequences between the HpArs gene and its ortholog in Strongylocentrotus purpuratus revealed that the central AT-rich region of the Ars insulator is conserved, and this conserved region showed significant enhancer blocking activity. These results suggest that the central AT-rich nucleosome-free region plays an important role in the function of the Ars insulator.

  17. Social Network Analysis Identifies Key Participants in Conservation Development.

    PubMed

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

    2018-05-01

    Understanding patterns of participation in private lands conservation, which is often implemented voluntarily by individual citizens and private organizations, could improve its effectiveness at combating biodiversity loss. We used social network analysis (SNA) to examine participation in conservation development (CD), a private land conservation strategy that clusters houses in a small portion of a property while preserving the remaining land as protected open space. Using data from public records for six counties in Colorado, USA, we compared CD participation patterns among counties and identified actors that most often work with others to implement CDs. We found that social network characteristics differed among counties. The network density, or proportion of connections in the network, varied from fewer than 2 to nearly 15%, and was higher in counties with smaller populations and fewer CDs. Centralization, or the degree to which connections are held disproportionately by a few key actors, was not correlated strongly with any county characteristics. Network characteristics were not correlated with the prevalence of wildlife-friendly design features in CDs. The most highly connected actors were biological and geological consultants, surveyors, and engineers. Our work demonstrates a new application of SNA to land-use planning, in which CD network patterns are examined and key actors are identified. For better conservation outcomes of CD, we recommend using network patterns to guide strategies for outreach and information dissemination, and engaging with highly connected actor types to encourage widespread adoption of best practices for CD design and stewardship.

  18. Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding.

    PubMed

    Silla, Toomas; Kepp, Katrin; Tai, E Shyong; Goh, Liang; Davila, Sonia; Catela Ivkovic, Tina; Calin, George A; Voorhoeve, P Mathijs

    2014-01-01

    Ultra-conserved genes or elements (UCGs/UCEs) in the human genome are extreme examples of conservation. We characterized natural variations in 2884 UCEs and UCGs in two distinct populations; Singaporean Chinese (n = 280) and Italian (n = 501) by using a pooled sample, targeted capture, sequencing approach. We identify, with high confidence, in these regions the abundance of rare SNVs (MAF<0.5%) of which 75% is not present in dbSNP137. UCEs association studies for complex human traits can use this information to model expected background variation and thus necessary power for association studies. By combining our data with 1000 Genome Project data, we show in three independent datasets that prevalent UCE variants (MAF>5%) are more often found in relatively less-conserved nucleotides within UCEs, compared to rare variants. Moreover, prevalent variants are less likely to overlap transcription factor binding site. Using SNPfold we found no significant influence of RNA secondary structure on UCE conservation. All together, these results suggest UCEs are not under selective pressure as a stretch of DNA but are under differential evolutionary pressure on the single nucleotide level.

  19. Waterbird conservation planning in the northern prairie and parkland region: Integration across borders and with other bird conservation initiatives

    Treesearch

    Neal D. Niemuth; Gerard W. Beyersbergen; Michael R. Norton

    2005-01-01

    The Northern Prairie and Parkland Region contain millions of wetland basins, which harbor large proportions of the populations of many North American waterbird species, several of which are of high conservation concern. However, knowledge of waterbirds in the region is limited, and there has been little direction for waterbird conservation planning or management. The...

  20. Augmenting Chinese hamster genome assembly by identifying regions of high confidence.

    PubMed

    Vishwanathan, Nandita; Bandyopadhyay, Arpan A; Fu, Hsu-Yuan; Sharma, Mohit; Johnson, Kathryn C; Mudge, Joann; Ramaraj, Thiruvarangan; Onsongo, Getiria; Silverstein, Kevin A T; Jacob, Nitya M; Le, Huong; Karypis, George; Hu, Wei-Shou

    2016-09-01

    Chinese hamster Ovary (CHO) cell lines are the dominant industrial workhorses for therapeutic recombinant protein production. The availability of genome sequence of Chinese hamster and CHO cells will spur further genome and RNA sequencing of producing cell lines. However, the mammalian genomes assembled using shot-gun sequencing data still contain regions of uncertain quality due to assembly errors. Identifying high confidence regions in the assembled genome will facilitate its use for cell engineering and genome engineering. We assembled two independent drafts of Chinese hamster genome by de novo assembly from shotgun sequencing reads and by re-scaffolding and gap-filling the draft genome from NCBI for improved scaffold lengths and gap fractions. We then used the two independent assemblies to identify high confidence regions using two different approaches. First, the two independent assemblies were compared at the sequence level to identify their consensus regions as "high confidence regions" which accounts for at least 78 % of the assembled genome. Further, a genome wide comparison of the Chinese hamster scaffolds with mouse chromosomes revealed scaffolds with large blocks of collinearity, which were also compiled as high-quality scaffolds. Genome scale collinearity was complemented with EST based synteny which also revealed conserved gene order compared to mouse. As cell line sequencing becomes more commonly practiced, the approaches reported here are useful for assessing the quality of assembly and potentially facilitate the engineering of cell lines. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  1. 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...

  2. Identifying taxonomic and functional surrogates for spring biodiversity conservation.

    PubMed

    Jyväsjärvi, Jussi; Virtanen, Risto; Ilmonen, Jari; Paasivirta, Lauri; Muotka, Timo

    2018-02-27

    Surrogate approaches are widely used to estimate overall taxonomic diversity for conservation planning. Surrogate taxa are frequently selected based on rarity or charisma, whereas selection through statistical modeling has been applied rarely. We used boosted-regression-tree models (BRT) fitted to biological data from 165 springs to identify bryophyte and invertebrate surrogates for taxonomic and functional diversity of boreal springs. We focused on these 2 groups because they are well known and abundant in most boreal springs. The best indicators of taxonomic versus functional diversity differed. The bryophyte Bryum weigelii and the chironomid larva Paratrichocladius skirwithensis best indicated taxonomic diversity, whereas the isopod Asellus aquaticus and the chironomid Macropelopia spp. were the best surrogates of functional diversity. In a scoring algorithm for priority-site selection, taxonomic surrogates performed only slightly better than random selection for all spring-dwelling taxa, but they were very effective in representing spring specialists, providing a distinct improvement over random solutions. However, the surrogates for taxonomic diversity represented functional diversity poorly and vice versa. When combined with cross-taxon complementarity analyses, surrogate selection based on statistical modeling provides a promising approach for identifying groundwater-dependent ecosystems of special conservation value, a key requirement of the EU Water Framework Directive. © 2018 Society for Conservation Biology.

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

    PubMed

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

    2015-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

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

    PubMed

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

    2016-10-01

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

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

    PubMed

    Anderson, Elizabeth P; Maldonado-Ocampo, Javier A

    2011-02-01

    The tropical Andes harbor an extraordinarily varied concentration of species in a landscape under increasing pressure from human activities. Conservation of the region's native plants and animals has received considerable international attention, but the focus has been on terrestrial biota. The conservation of freshwater fauna, particularly the conservation of fishes, has not been emphasized. Tropical Andean fishes are among the most understudied vertebrates in the world. We estimate that between 400 and 600 fish species inhabit the diverse aquatic environments in the region. Nearly 40% of these species are endemic. Tropical Andean fishes are vulnerable to ongoing environmental changes related to deforestation, water withdrawals, water pollution, species introductions, and hydropower development. Additionally, their distributions and population dynamics may be affected by hydrologic alterations and warmer water temperatures associated with projected climate change. Presently, at least three species are considered extinct, some populations are endangered, and some species are likely to decline or disappear. The long-term persistence of tropical Andean fishes will depend on greater consideration of freshwater systems in regional conservation initiatives. ©2010 Society for Conservation Biology.

  7. CORAL: aligning conserved core regions across domain families.

    PubMed

    Fong, Jessica H; Marchler-Bauer, Aron

    2009-08-01

    Homologous protein families share highly conserved sequence and structure regions that are frequent targets for comparative analysis of related proteins and families. Many protein families, such as the curated domain families in the Conserved Domain Database (CDD), exhibit similar structural cores. To improve accuracy in aligning such protein families, we propose a profile-profile method CORAL that aligns individual core regions as gap-free units. CORAL computes optimal local alignment of two profiles with heuristics to preserve continuity within core regions. We benchmarked its performance on curated domains in CDD, which have pre-defined core regions, against COMPASS, HHalign and PSI-BLAST, using structure superpositions and comprehensive curator-optimized alignments as standards of truth. CORAL improves alignment accuracy on core regions over general profile methods, returning a balanced score of 0.57 for over 80% of all domain families in CDD, compared with the highest balanced score of 0.45 from other methods. Further, CORAL provides E-values to aid in detecting homologous protein families and, by respecting block boundaries, produces alignments with improved 'readability' that facilitate manual refinement. CORAL will be included in future versions of the NCBI Cn3D/CDTree software, which can be downloaded at http://www.ncbi.nlm.nih.gov/Structure/cdtree/cdtree.shtml. Supplementary data are available at Bioinformatics online.

  8. Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome

    PubMed Central

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

    2013-01-01

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

  9. Identifying species conservation strategies to reduce disease-associated declines

    USGS Publications Warehouse

    Gerber, Brian D.; Converse, Sarah J.; Muths, Erin L.; Crockett, Harry J.; Mosher, Brittany A.; Bailey, Larissa L.

    2018-01-01

    Emerging infectious diseases (EIDs) are a salient threat to many animal taxa, causing local and global extinctions, altering communities and ecosystem function. The EID chytridiomycosis is a prominent driver of amphibian declines, which is caused by the fungal pathogen Batrachochytrium dendrobatidis (Bd). To guide conservation policy, we developed a predictive decision-analytic model that combines empirical knowledge of host-pathogen metapopulation dynamics with expert judgment regarding effects of management actions, to select from potential conservation strategies. We apply our approach to a boreal toad (Anaxyrus boreas boreas) and Bd system, identifying optimal strategies that balance tradeoffs in maximizing toad population persistence and landscape-level distribution, while considering costs. The most robust strategy is expected to reduce the decline of toad breeding sites from 53% to 21% over 50 years. Our findings are incorporated into management policy to guide conservation planning. Our online modeling application provides a template for managers of other systems challenged by EIDs.

  10. Characterization of chromosomal regions conserved in Yersinia pseudotuberculosis and lost by Yersinia pestis.

    PubMed

    Pouillot, Flavie; Fayolle, Corinne; Carniel, Elisabeth

    2008-10-01

    The transformation of the enteropathogenic bacterium Yersinia pseudotuberculosis into the plague bacillus, Yersinia pestis, has been accompanied by extensive genetic loss. This study focused on chromosomal regions conserved in Y. pseudotuberculosis and lost during its transformation into Y. pestis. An extensive PCR screening of 78 strains of the two species identified five regions (R1 to R5) and four open reading frames (ORFs; orf1 to orf4) that were conserved in Y. pseudotuberculosis and absent from Y. pestis. Their conservation in Y. pseudotuberculosis suggests a positive selective pressure and a role during the life cycle of this species. Attempts to delete two ORFs (orf3 and orf4) from the chromosome of strain IP32953 were unsuccessful, indicating that they are essential for its viability. The seven remaining loci were individually deleted from the IP32953 chromosome, and the ability of each mutant to grow in vitro and to kill mice upon intragastric infection was evaluated. Four loci (orf1, R2, R4, and R5) were not required for optimal growth or virulence of Y. pseudotuberculosis. In contrast, orf2, encoding a putative pseudouridylate synthase involved in RNA stability, was necessary for the optimal growth of IP32953 at 37 degrees C in a chemically defined medium (M63S). Deletion of R1, a region predicted to encode the methionine salvage pathway, altered the mutant pathogenicity, suggesting that the availability of free methionine is severely restricted in vivo. R3, a region composed mostly of genes of unknown functions, was necessary for both optimal growth of Y. pseudotuberculosis at 37 degrees C in M63S and for virulence. Therefore, despite their loss in Y. pestis, five of the nine Y. pseudotuberculosis-specific chromosomal loci studied play a role in the survival, growth, or virulence of this species.

  11. Seabird Conservation Planning in the Pacific Region

    Treesearch

    Kyra L. Mills; Maura Naughton; Gregg Elliott

    2005-01-01

    The North Pacific is a highly productive marine area, sustaining millions of resident and migratory marine birds. These birds are faced with a variety of threats, both on land, where they breed and roost, and at sea, where they forage for food. Several seabird conservation plans are currently underway in this region. The U. S. Fish and Wildlife Service (USFWS) Pacific...

  12. Identifying all moiety conservation laws in genome-scale metabolic networks.

    PubMed

    De Martino, Andrea; De Martino, Daniele; Mulet, Roberto; Pagnani, Andrea

    2014-01-01

    The stoichiometry of a metabolic network gives rise to a set of conservation laws for the aggregate level of specific pools of metabolites, which, on one hand, pose dynamical constraints that cross-link the variations of metabolite concentrations and, on the other, provide key insight into a cell's metabolic production capabilities. When the conserved quantity identifies with a chemical moiety, extracting all such conservation laws from the stoichiometry amounts to finding all non-negative integer solutions of a linear system, a programming problem known to be NP-hard. We present an efficient strategy to compute the complete set of integer conservation laws of a genome-scale stoichiometric matrix, also providing a certificate for correctness and maximality of the solution. Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism. Convergence to the full set of moiety conservation laws in each case is achieved in extremely reduced computing times. In addition, we uncover a scaling relation that links the size of the independent pool basis to the number of metabolites, for which we present an analytical explanation.

  13. Roles of the conserved cytoplasmic region and non-conserved carboxy-terminal region of SecE in Escherichia coli protein translocase.

    PubMed

    Kontinen, V P; Yamanaka, M; Nishiyama, K; Tokuda, H

    1996-06-01

    SecE, an essential membrane component of the Escherichia coli protein translocase, consists of 127 amino acid residues. Only a part of the second putative cytoplasmic region comprising some 13 residues is essential for the SecE function as long as the proper topological arrangement is retained. The Trp84 and Pro85 residues of this region are conserved in all eubacterial SecE homologues. The conservation of positively charged residues corresponding to Arg80 and Lys81 is also substantial. We deleted or replaced these residues to assess their roles in the SecE function. Deletion of the Arg80-Lys81 dipeptide did not abolish the SecE function whereas that of Trp84 or Pro85 caused a loss of the function. Strikingly, however, replacement of Pro85 with either Gly, Ser, or Ala, and that of Trp84 with Lys did not abolish the SecE function. These results indicate that the strong conservation of these residues does not reflect their obligatory requirement for the SecE function. A chimeric SecE possessing the cytoplasmic region of the E. coli SecE and the following region of the Bacillus subtilis SecE was able to form the translocation machinery together with SecA, SecY, and SecG. Although a Leu to Arg mutation at position 108 has been thought to cause a loss of signal recognition fidelity and thereby suppress a signal sequence defect, the same mutation at position 111 caused a complete loss of the function. The levels of SecY and SecG in the secEcsE501 mutant, which expresses SecE at a decreased level and is sensitive to low temperature, increased upon the expression of functional SecE derivatives, irrespective of the site of mutation, suggesting that the levels of SecY and SecG are co-operatively determined by the level of functional, but not non-functional, SecE. Based on these results, the SecE function in the translocase is discussed.

  14. In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites

    PubMed Central

    2016-01-01

    Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus. Our results provide insight into pigment phenotypes in pythons. PMID:27698666

  15. In Silico Analysis of Gene Expression Network Components Underlying Pigmentation Phenotypes in the Python Identified Evolutionarily Conserved Clusters of Transcription Factor Binding Sites.

    PubMed

    Irizarry, Kristopher J L; Bryden, Randall L

    2016-01-01

    Color variation provides the opportunity to investigate the genetic basis of evolution and selection. Reptiles are less studied than mammals. Comparative genomics approaches allow for knowledge gained in one species to be leveraged for use in another species. We describe a comparative vertebrate analysis of conserved regulatory modules in pythons aimed at assessing bioinformatics evidence that transcription factors important in mammalian pigmentation phenotypes may also be important in python pigmentation phenotypes. We identified 23 python orthologs of mammalian genes associated with variation in coat color phenotypes for which we assessed the extent of pairwise protein sequence identity between pythons and mouse, dog, horse, cow, chicken, anole lizard, and garter snake. We next identified a set of melanocyte/pigment associated transcription factors (CREB, FOXD3, LEF-1, MITF, POU3F2, and USF-1) that exhibit relatively conserved sequence similarity within their DNA binding regions across species based on orthologous alignments across multiple species. Finally, we identified 27 evolutionarily conserved clusters of transcription factor binding sites within ~200-nucleotide intervals of the 1500-nucleotide upstream regions of AIM1, DCT, MC1R, MITF, MLANA, OA1, PMEL, RAB27A, and TYR from Python bivittatus . Our results provide insight into pigment phenotypes in pythons.

  16. SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments.

    PubMed

    Ajawatanawong, Pravech; Atkinson, Gemma C; Watson-Haigh, Nathan S; Mackenzie, Bryony; Baldauf, Sandra L

    2012-07-01

    Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.

  17. Functionally conserved cis-regulatory elements of COL18A1 identified through zebrafish transgenesis.

    PubMed

    Kague, Erika; Bessling, Seneca L; Lee, Josephine; Hu, Gui; Passos-Bueno, Maria Rita; Fisher, Shannon

    2010-01-15

    Type XVIII collagen is a component of basement membranes, and expressed prominently in the eye, blood vessels, liver, and the central nervous system. Homozygous mutations in COL18A1 lead to Knobloch Syndrome, characterized by ocular defects and occipital encephalocele. However, relatively little has been described on the role of type XVIII collagen in development, and nothing is known about the regulation of its tissue-specific expression pattern. We have used zebrafish transgenesis to identify and characterize cis-regulatory sequences controlling expression of the human gene. Candidate enhancers were selected from non-coding sequence associated with COL18A1 based on sequence conservation among mammals. Although these displayed no overt conservation with orthologous zebrafish sequences, four regions nonetheless acted as tissue-specific transcriptional enhancers in the zebrafish embryo, and together recapitulated the major aspects of col18a1 expression. Additional post-hoc computational analysis on positive enhancer sequences revealed alignments between mammalian and teleost sequences, which we hypothesize predict the corresponding zebrafish enhancers; for one of these, we demonstrate functional overlap with the orthologous human enhancer sequence. Our results provide important insight into the biological function and regulation of COL18A1, and point to additional sequences that may contribute to complex diseases involving COL18A1. More generally, we show that combining functional data with targeted analyses for phylogenetic conservation can reveal conserved cis-regulatory elements in the large number of cases where computational alignment alone falls short. Copyright 2009 Elsevier Inc. All rights reserved.

  18. A freshwater biodiversity hotspot under pressure - assessing threats and identifying conservation needs for ancient Lake Ohrid

    NASA Astrophysics Data System (ADS)

    Kostoski, G.; Albrecht, C.; Trajanovski, S.; Wilke, T.

    2010-07-01

    activities, and ongoing research on conservation and raising of public awareness. Following this summary, we evaluate the status quo and future of Lake Ohrid and its biota. Given the number of identified threats, it is clear that only concerted international action can stop or at least slow down further degradation of Lake Ohrid and the creeping biodiversity crisis already evident. A comprehensive conservation strategy should include measures that result in an immediate reduction of pollution, particularly with phosphorous, in order to slow down the ongoing eutrophication process. The existing watershed management should become more effective. Implementation and particularly with a view to the enforcement of national laws should be enhanced. Increased research on the lakes' limnology, biodiversity, and conservation management practices are necessary. The latter research should identify conservation priorities. Public awareness should be enhanced. Facing these parallel needs to protect the unique biodiversity of Lake Ohrid, we suggest urging (a) implementation and enforcement of the General Management Plan that would ensure long-term integrated and sustainable use of the lake and its watershed, (b) scientific studies on ecology, biodiversity and effects of human impact, (c) the establishment of Core Conservation areas (CCA), including underwater reserves, and (d) Coastal Zone Management (CZM) areas that would constitute buffer zones for the CCA around the lake. These activities should, among others, ultimately lead to a trans-boundary major conservation area of the Ohrid-Prespa region that would allow long-term integration of both humans and nature.

  19. A freshwater biodiversity hotspot under pressure - assessing threats and identifying conservation needs for ancient Lake Ohrid

    NASA Astrophysics Data System (ADS)

    Kostoski, G.; Albrecht, C.; Trajanovski, S.; Wilke, T.

    2010-12-01

    conservation activities, and ongoing research on conservation and raising of public awareness. Following this summary, we evaluate the status quo and future of Lake Ohrid and its biota. A comprehensive conservation strategy should include measures that result in an immediate reduction of nutrient input, particularly with phosphorus, in order to slow down the ongoing eutrophication process. The existing watershed management should become more effective. Implementation and particularly with a view to the enforcement of national laws should be enhanced. Increased research on the lakes' limnology, biodiversity, and conservation management practices are necessary. The latter research should identify conservation priorities. Public awareness should be enhanced. Facing these parallel needs to protect the unique biodiversity of Lake Ohrid, we suggest urging (a) implementation and enforcement of the General Management Plan that would ensure long-term integrated and sustainable use of the lake and its watershed, (b) scientific studies on ecology, biodiversity and effects of human impact, (c) the establishment of Core Conservation areas (CCA), including underwater reserves, and (d) Coastal Zone Management (CZM) areas that would constitute buffer zones for the CCAs around the lake. Given the number of identified threats, it is clear that only concerted international action can stop or at least slow down further degradation of Lake Ohrid and the creeping biodiversity crisis already evident. All conservation activities should, among others, ultimately lead to a trans-boundary major conservation area of the Ohrid-Prespa region that would allow long-term integration of both humans and nature.

  20. Identifying conservation priorities and management strategies based on ecosystem services to improve urban sustainability in Harbin, China.

    PubMed

    Qu, Yi; Lu, Ming

    2018-01-01

    Rapid urbanization and agricultural development has resulted in the degradation of ecosystems, while also negatively impacting ecosystem services (ES) and urban sustainability. Identifying conservation priorities for ES and applying reasonable management strategies have been found to be effective methods for mitigating this phenomenon. The purpose of this study is to propose a comprehensive framework for identifying ES conservation priorities and associated management strategies for these planning areas. First, we incorporated 10 ES indicators within a systematic conservation planning (SCP) methodology in order to identify ES conservation priorities with high irreplaceability values based on conservation target goals associated with the potential distribution of ES indicators. Next, we assessed the efficiency of the ES conservation priorities for meeting the designated conservation target goals. Finally, ES conservation priorities were clustered into groups using a K-means clustering analysis in an effort to identify the dominant ES per location before formulating management strategies. We effectively identified 12 ES priorities to best represent conservation target goals for the ES indicators. These 12 priorities had a total areal coverage of 13,364 km 2 representing 25.16% of the study area. The 12 priorities were further clustered into five significantly different groups ( p -values between groups < 0.05), which helped to refine management strategies formulated to best enhance ES across the study area. The proposed method allows conservation and management plans to easily adapt to a wide variety of quantitative ES target goals within urban and agricultural areas, thereby preventing urban and agriculture sprawl and guiding sustainable urban development.

  1. Identifying conservation priorities and management strategies based on ecosystem services to improve urban sustainability in Harbin, China

    PubMed Central

    2018-01-01

    Rapid urbanization and agricultural development has resulted in the degradation of ecosystems, while also negatively impacting ecosystem services (ES) and urban sustainability. Identifying conservation priorities for ES and applying reasonable management strategies have been found to be effective methods for mitigating this phenomenon. The purpose of this study is to propose a comprehensive framework for identifying ES conservation priorities and associated management strategies for these planning areas. First, we incorporated 10 ES indicators within a systematic conservation planning (SCP) methodology in order to identify ES conservation priorities with high irreplaceability values based on conservation target goals associated with the potential distribution of ES indicators. Next, we assessed the efficiency of the ES conservation priorities for meeting the designated conservation target goals. Finally, ES conservation priorities were clustered into groups using a K-means clustering analysis in an effort to identify the dominant ES per location before formulating management strategies. We effectively identified 12 ES priorities to best represent conservation target goals for the ES indicators. These 12 priorities had a total areal coverage of 13,364 km2 representing 25.16% of the study area. The 12 priorities were further clustered into five significantly different groups (p-values between groups < 0.05), which helped to refine management strategies formulated to best enhance ES across the study area. The proposed method allows conservation and management plans to easily adapt to a wide variety of quantitative ES target goals within urban and agricultural areas, thereby preventing urban and agriculture sprawl and guiding sustainable urban development. PMID:29682412

  2. Conservation genomics of anadromous Atlantic salmon across its North American range: outlier loci identify the same patterns of population structure as neutral loci.

    PubMed

    Moore, Jean-Sébastien; Bourret, Vincent; Dionne, Mélanie; Bradbury, Ian; O'Reilly, Patrick; Kent, Matthew; Chaput, Gérald; Bernatchez, Louis

    2014-12-01

    Anadromous Atlantic salmon (Salmo salar) is a species of major conservation and management concern in North America, where population abundance has been declining over the past 30 years. Effective conservation actions require the delineation of conservation units to appropriately reflect the spatial scale of intraspecific variation and local adaptation. Towards this goal, we used the most comprehensive genetic and genomic database for Atlantic salmon to date, covering the entire North American range of the species. The database included microsatellite data from 9142 individuals from 149 sampling locations and data from a medium-density SNP array providing genotypes for >3000 SNPs for 50 sampling locations. We used neutral and putatively selected loci to integrate adaptive information in the definition of conservation units. Bayesian clustering with the microsatellite data set and with neutral SNPs identified regional groupings largely consistent with previously published regional assessments. The use of outlier SNPs did not result in major differences in the regional groupings, suggesting that neutral markers can reflect the geographic scale of local adaptation despite not being under selection. We also performed assignment tests to compare power obtained from microsatellites, neutral SNPs and outlier SNPs. Using SNP data substantially improved power compared to microsatellites, and an assignment success of 97% to the population of origin and of 100% to the region of origin was achieved when all SNP loci were used. Using outlier SNPs only resulted in minor improvements to assignment success to the population of origin but improved regional assignment. We discuss the implications of these new genetic resources for the conservation and management of Atlantic salmon in North America. © 2014 John Wiley & Sons Ltd.

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

    USGS Publications Warehouse

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

    2012-01-01

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

  4. A Genome-Wide Association Study Identifies Multiple Regions Associated with Head Size in Catfish

    PubMed Central

    Geng, Xin; Liu, Shikai; Yao, Jun; Bao, Lisui; Zhang, Jiaren; Li, Chao; Wang, Ruijia; Sha, Jin; Zeng, Peng; Zhi, Degui; Liu, Zhanjiang

    2016-01-01

    Skull morphology is fundamental to evolution and the biological adaptation of species to their environments. With aquaculture fish species, head size is also important for economic reasons because it has a direct impact on fillet yield. However, little is known about the underlying genetic basis of head size. Catfish is the primary aquaculture species in the United States. In this study, we performed a genome-wide association study using the catfish 250K SNP array with backcross hybrid catfish to map the QTL for head size (head length, head width, and head depth). One significantly associated region on linkage group (LG) 7 was identified for head length. In addition, LGs 7, 9, and 16 contain suggestively associated regions for head length. For head width, significantly associated regions were found on LG9, and additional suggestively associated regions were identified on LGs 5 and 7. No region was found associated with head depth. Head size genetic loci were mapped in catfish to genomic regions with candidate genes involved in bone development. Comparative analysis indicated that homologs of several candidate genes are also involved in skull morphology in various other species ranging from amphibian to mammalian species, suggesting possible evolutionary conservation of those genes in the control of skull morphologies. PMID:27558670

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

    USGS Publications Warehouse

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

    2016-01-01

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

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

    PubMed

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

    2016-07-05

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

  7. A cross-species bi-clustering approach to identifying conserved co-regulated genes.

    PubMed

    Sun, Jiangwen; Jiang, Zongliang; Tian, Xiuchun; Bi, Jinbo

    2016-06-15

    A growing number of studies have explored the process of pre-implantation embryonic development of multiple mammalian species. However, the conservation and variation among different species in their developmental programming are poorly defined due to the lack of effective computational methods for detecting co-regularized genes that are conserved across species. The most sophisticated method to date for identifying conserved co-regulated genes is a two-step approach. This approach first identifies gene clusters for each species by a cluster analysis of gene expression data, and subsequently computes the overlaps of clusters identified from different species to reveal common subgroups. This approach is ineffective to deal with the noise in the expression data introduced by the complicated procedures in quantifying gene expression. Furthermore, due to the sequential nature of the approach, the gene clusters identified in the first step may have little overlap among different species in the second step, thus difficult to detect conserved co-regulated genes. We propose a cross-species bi-clustering approach which first denoises the gene expression data of each species into a data matrix. The rows of the data matrices of different species represent the same set of genes that are characterized by their expression patterns over the developmental stages of each species as columns. A novel bi-clustering method is then developed to cluster genes into subgroups by a joint sparse rank-one factorization of all the data matrices. This method decomposes a data matrix into a product of a column vector and a row vector where the column vector is a consistent indicator across the matrices (species) to identify the same gene cluster and the row vector specifies for each species the developmental stages that the clustered genes co-regulate. Efficient optimization algorithm has been developed with convergence analysis. This approach was first validated on synthetic data and compared

  8. Identifying Conservation Successes, Failures and Future Opportunities; Assessing Recovery Potential of Wild Ungulates and Tigers in Eastern Cambodia

    PubMed Central

    O'Kelly, Hannah J.; Evans, Tom D.; Stokes, Emma J.; Clements, Tom J.; Dara, An; Gately, Mark; Menghor, Nut; Pollard, Edward H. B.; Soriyun, Men; Walston, Joe

    2012-01-01

    Conservation investment, particularly for charismatic and wide-ranging large mammal species, needs to be evidence-based. Despite the prevalence of this theme within the literature, examples of robust data being generated to guide conservation policy and funding decisions are rare. We present the first published case-study of tiger conservation in Indochina, from a site where an evidence-based approach has been implemented for this iconic predator and its prey. Despite the persistence of extensive areas of habitat, Indochina's tiger and ungulate prey populations are widely supposed to have precipitously declined in recent decades. The Seima Protection Forest (SPF), and broader Eastern Plains Landscape, was identified in 2000 as representing Cambodia's best hope for tiger recovery; reflected in its designation as a Global Priority Tiger Conservation Landscape. Since 2005 distance sampling, camera-trapping and detection-dog surveys have been employed to assess the recovery potential of ungulate and tiger populations in SPF. Our results show that while conservation efforts have ensured that small but regionally significant populations of larger ungulates persist, and density trends in smaller ungulates are stable, overall ungulate populations remain well below theoretical carrying capacity. Extensive field surveys failed to yield any evidence of tiger, and we contend that there is no longer a resident population within the SPF. This local extirpation is believed to be primarily attributable to two decades of intensive hunting; but importantly, prey densities are also currently below the level necessary to support a viable tiger population. Based on these results and similar findings from neighbouring sites, Eastern Cambodia does not currently constitute a Tiger Source Site nor meet the criteria of a Global Priority Tiger Landscape. However, SPF retains global importance for many other elements of biodiversity. It retains high regional importance for ungulate

  9. Identifying conservation successes, failures and future opportunities; assessing recovery potential of wild ungulates and tigers in Eastern Cambodia.

    PubMed

    O'Kelly, Hannah J; Evans, Tom D; Stokes, Emma J; Clements, Tom J; Dara, An; Gately, Mark; Menghor, Nut; Pollard, Edward H B; Soriyun, Men; Walston, Joe

    2012-01-01

    Conservation investment, particularly for charismatic and wide-ranging large mammal species, needs to be evidence-based. Despite the prevalence of this theme within the literature, examples of robust data being generated to guide conservation policy and funding decisions are rare. We present the first published case-study of tiger conservation in Indochina, from a site where an evidence-based approach has been implemented for this iconic predator and its prey. Despite the persistence of extensive areas of habitat, Indochina's tiger and ungulate prey populations are widely supposed to have precipitously declined in recent decades. The Seima Protection Forest (SPF), and broader Eastern Plains Landscape, was identified in 2000 as representing Cambodia's best hope for tiger recovery; reflected in its designation as a Global Priority Tiger Conservation Landscape. Since 2005 distance sampling, camera-trapping and detection-dog surveys have been employed to assess the recovery potential of ungulate and tiger populations in SPF. Our results show that while conservation efforts have ensured that small but regionally significant populations of larger ungulates persist, and density trends in smaller ungulates are stable, overall ungulate populations remain well below theoretical carrying capacity. Extensive field surveys failed to yield any evidence of tiger, and we contend that there is no longer a resident population within the SPF. This local extirpation is believed to be primarily attributable to two decades of intensive hunting; but importantly, prey densities are also currently below the level necessary to support a viable tiger population. Based on these results and similar findings from neighbouring sites, Eastern Cambodia does not currently constitute a Tiger Source Site nor meet the criteria of a Global Priority Tiger Landscape. However, SPF retains global importance for many other elements of biodiversity. It retains high regional importance for ungulate

  10. Biodiversity conservation in local planning.

    PubMed

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

    2009-02-01

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

  11. Detection of hyper-conserved regions in hepatitis B virus X gene potentially useful for gene therapy.

    PubMed

    González, Carolina; Tabernero, David; Cortese, Maria Francesca; Gregori, Josep; Casillas, Rosario; Riveiro-Barciela, Mar; Godoy, Cristina; Sopena, Sara; Rando, Ariadna; Yll, Marçal; Lopez-Martinez, Rosa; Quer, Josep; Esteban, Rafael; Buti, Maria; Rodríguez-Frías, Francisco

    2018-05-21

    To detect hyper-conserved regions in the hepatitis B virus (HBV) X gene ( HBX ) 5' region that could be candidates for gene therapy. The study included 27 chronic hepatitis B treatment-naive patients in various clinical stages (from chronic infection to cirrhosis and hepatocellular carcinoma, both HBeAg-negative and HBeAg-positive), and infected with HBV genotypes A-F and H. In a serum sample from each patient with viremia > 3.5 log IU/mL, the HBX 5' end region [nucleotide (nt) 1255-1611] was PCR-amplified and submitted to next-generation sequencing (NGS). We assessed genotype variants by phylogenetic analysis, and evaluated conservation of this region by calculating the information content of each nucleotide position in a multiple alignment of all unique sequences (haplotypes) obtained by NGS. Conservation at the HBx protein amino acid (aa) level was also analyzed. NGS yielded 1333069 sequences from the 27 samples, with a median of 4578 sequences/sample (2487-9279, IQR 2817). In 14/27 patients (51.8%), phylogenetic analysis of viral nucleotide haplotypes showed a complex mixture of genotypic variants. Analysis of the information content in the haplotype multiple alignments detected 2 hyper-conserved nucleotide regions, one in the HBX upstream non-coding region (nt 1255-1286) and the other in the 5' end coding region (nt 1519-1603). This last region coded for a conserved amino acid region (aa 63-76) that partially overlaps a Kunitz-like domain. Two hyper-conserved regions detected in the HBX 5' end may be of value for targeted gene therapy, regardless of the patients' clinical stage or HBV genotype.

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

    USGS Publications Warehouse

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

    1996-01-01

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

  13. Multivariate ordination identifies vegetation types associated with spider conservation in brassica crops

    PubMed Central

    Saqib, Hafiz Sohaib Ahmed; You, Minsheng

    2017-01-01

    Conservation biological control emphasizes natural and other non-crop vegetation as a source of natural enemies to focal crops. There is an unmet need for better methods to identify the types of vegetation that are optimal to support specific natural enemies that may colonize the crops. Here we explore the commonality of the spider assemblage—considering abundance and diversity (H)—in brassica crops with that of adjacent non-crop and non-brassica crop vegetation. We employ spatial-based multivariate ordination approaches, hierarchical clustering and spatial eigenvector analysis. The small-scale mixed cropping and high disturbance frequency of southern Chinese vegetation farming offered a setting to test the role of alternate vegetation for spider conservation. Our findings indicate that spider families differ markedly in occurrence with respect to vegetation type. Grassy field margins, non-crop vegetation, taro and sweetpotato harbour spider morphospecies and functional groups that are also present in brassica crops. In contrast, pumpkin and litchi contain spiders not found in brassicas, and so may have little benefit for conservation biological control services for brassicas. Our findings also illustrate the utility of advanced statistical approaches for identifying spatial relationships between natural enemies and the land uses most likely to offer alternative habitats for conservation biological control efforts that generates testable hypotheses for future studies. PMID:29085741

  14. The Conservation Effects Assessment Project (CEAP): The U.S. experience in determining a national scale natural resource and conservation needs assessment

    USDA-ARS?s Scientific Manuscript database

    The Conservation Effects Assessment Project (CEAP) was initiated to establish a scientific understanding of the impacts of agricultural conservation practices at the watershed scale, to quantify agricultural conservation practice benefits at the national and regional scales, and to identify outstand...

  15. A trans-national monarch butterfly population model and implications for regional conservation priorities

    USGS Publications Warehouse

    Oberhauser, Karen; Wiederholt, Ruscena; Diffendorfer, James E.; Semmens, Darius J.; Ries, Leslie; Thogmartin, Wayne E.; Lopez-Hoffman, Laura; Semmens, Brice

    2017-01-01

    1. The monarch has undergone considerable population declines over the past decade, and the governments of Mexico, Canada, and the United States have agreed to work together to conserve the species.2. Given limited resources, understanding where to focus conservation action is key for widespread species like monarchs. To support planning for continental-scale monarch habitat restoration, we address the question of where restoration efforts are likely to have the largest impacts on monarch butterfly (Danaus plexippus Linn.) population growth rates.3. We present a spatially explicit demographic model simulating the multi-generational annual cycle of the eastern monarch population, and use the model to examine management scenarios, some of which focus on particular regions of North America.4. Improving the monarch habitat in the north central or southern parts of the monarch range yields a slightly greater increase in the population growth rate than restoration in other regions. However, combining restoration efforts across multiple regions yields population growth rates above 1 with smaller simulated improvements in habitat per region than single-region strategies.5. Synthesis and applications: These findings suggest that conservation investment in projects across the full monarch range will be more effective than focusing on one or a few regions, and will require international cooperation across many land use categories.

  16. A statistically rigorous sampling design to integrate avian monitoring and management within Bird Conservation Regions.

    PubMed

    Pavlacky, David C; Lukacs, Paul M; Blakesley, Jennifer A; Skorkowsky, Robert C; Klute, David S; Hahn, Beth A; Dreitz, Victoria J; George, T Luke; Hanni, David J

    2017-01-01

    Monitoring is an essential component of wildlife management and conservation. However, the usefulness of monitoring data is often undermined by the lack of 1) coordination across organizations and regions, 2) meaningful management and conservation objectives, and 3) rigorous sampling designs. Although many improvements to avian monitoring have been discussed, the recommendations have been slow to emerge in large-scale programs. We introduce the Integrated Monitoring in Bird Conservation Regions (IMBCR) program designed to overcome the above limitations. Our objectives are to outline the development of a statistically defensible sampling design to increase the value of large-scale monitoring data and provide example applications to demonstrate the ability of the design to meet multiple conservation and management objectives. We outline the sampling process for the IMBCR program with a focus on the Badlands and Prairies Bird Conservation Region (BCR 17). We provide two examples for the Brewer's sparrow (Spizella breweri) in BCR 17 demonstrating the ability of the design to 1) determine hierarchical population responses to landscape change and 2) estimate hierarchical habitat relationships to predict the response of the Brewer's sparrow to conservation efforts at multiple spatial scales. The collaboration across organizations and regions provided economy of scale by leveraging a common data platform over large spatial scales to promote the efficient use of monitoring resources. We designed the IMBCR program to address the information needs and core conservation and management objectives of the participating partner organizations. Although it has been argued that probabilistic sampling designs are not practical for large-scale monitoring, the IMBCR program provides a precedent for implementing a statistically defensible sampling design from local to bioregional scales. We demonstrate that integrating conservation and management objectives with rigorous statistical

  17. A statistically rigorous sampling design to integrate avian monitoring and management within Bird Conservation Regions

    PubMed Central

    Hahn, Beth A.; Dreitz, Victoria J.; George, T. Luke

    2017-01-01

    Monitoring is an essential component of wildlife management and conservation. However, the usefulness of monitoring data is often undermined by the lack of 1) coordination across organizations and regions, 2) meaningful management and conservation objectives, and 3) rigorous sampling designs. Although many improvements to avian monitoring have been discussed, the recommendations have been slow to emerge in large-scale programs. We introduce the Integrated Monitoring in Bird Conservation Regions (IMBCR) program designed to overcome the above limitations. Our objectives are to outline the development of a statistically defensible sampling design to increase the value of large-scale monitoring data and provide example applications to demonstrate the ability of the design to meet multiple conservation and management objectives. We outline the sampling process for the IMBCR program with a focus on the Badlands and Prairies Bird Conservation Region (BCR 17). We provide two examples for the Brewer’s sparrow (Spizella breweri) in BCR 17 demonstrating the ability of the design to 1) determine hierarchical population responses to landscape change and 2) estimate hierarchical habitat relationships to predict the response of the Brewer’s sparrow to conservation efforts at multiple spatial scales. The collaboration across organizations and regions provided economy of scale by leveraging a common data platform over large spatial scales to promote the efficient use of monitoring resources. We designed the IMBCR program to address the information needs and core conservation and management objectives of the participating partner organizations. Although it has been argued that probabilistic sampling designs are not practical for large-scale monitoring, the IMBCR program provides a precedent for implementing a statistically defensible sampling design from local to bioregional scales. We demonstrate that integrating conservation and management objectives with rigorous statistical

  18. Conservation status of the American horseshoe crab, (Limulus polyphemus): A regional assessment

    USGS Publications Warehouse

    Smith, David R.; Brockmann, H. Jane; Beekey, Mark A.; King, Timothy L.; Millard, Michael J.; Zaldívar-Rae, Jaime

    2017-01-01

    Horseshoe crabs have persisted for more than 200 million years, and fossil forms date to 450 million years ago. The American horseshoe crab (Limulus polyphemus), one of four extant horseshoe crab species, is found along the Atlantic coastline of North America ranging from Alabama to Maine, USA with another distinct population on the coasts of Campeche, Yucatán and Quintana Roo in the Yucatán Peninsula, México. Although the American horseshoe crab tolerates broad environmental conditions, exploitation and habitat loss threaten the species. We assessed the conservation status of the American horseshoe crab by comprehensively reviewing available scientific information on its range, life history, genetic structure, population trends and analyses, major threats, and conservation. We structured the status assessment by six genetically-informed regions and accounted for sub-regional differences in environmental conditions, threats, and management. The transnational regions are Gulf of Maine (USA), Mid-Atlantic (USA), Southeast (USA), Florida Atlantic (USA), Northeast Gulf of México (USA), and Yucatán Peninsula (México). Our conclusion is that the American horseshoe crab species is vulnerable to local extirpation and that the degree and extent of risk vary among and within the regions. The risk is elevated in the Gulf of Maine region due to limited and fragmented habitat. The populations of horseshoe crabs in the Mid-Atlantic region are stable in the Delaware Bay area, and regulatory controls are in place, but the risk is elevated in the New England area as evidenced by continuing declines understood to be caused by over-harvest. The populations of horseshoe crabs in the Southeast region are stable or increasing. The populations of horseshoe crabs in the Florida Atlantic region show mixed trends among areas, and continuing population reductions at the embayment level have poorly understood causes. Within the Northeast Gulf of Mexico, causes of population trends are

  19. Global mapping of ecosystem services and conservation priorities

    PubMed Central

    Naidoo, R.; Balmford, A.; Costanza, R.; Fisher, B.; Green, R. E.; Lehner, B.; Malcolm, T. R.; Ricketts, T. H.

    2008-01-01

    Global efforts to conserve biodiversity have the potential to deliver economic benefits to people (i.e., “ecosystem services”). However, regions for which conservation benefits both biodiversity and ecosystem services cannot be identified unless ecosystem services can be quantified and valued and their areas of production mapped. Here we review the theory, data, and analyses needed to produce such maps and find that data availability allows us to quantify imperfect global proxies for only four ecosystem services. Using this incomplete set as an illustration, we compare ecosystem service maps with the global distributions of conventional targets for biodiversity conservation. Our preliminary results show that regions selected to maximize biodiversity provide no more ecosystem services than regions chosen randomly. Furthermore, spatial concordance among different services, and between ecosystem services and established conservation priorities, varies widely. Despite this lack of general concordance, “win–win” areas—regions important for both ecosystem services and biodiversity—can be usefully identified, both among ecoregions and at finer scales within them. An ambitious interdisciplinary research effort is needed to move beyond these preliminary and illustrative analyses to fully assess synergies and trade-offs in conserving biodiversity and ecosystem services. PMID:18621701

  20. [Preparation and characterization of mouse polyclonal antibody against conserved region of human FOXO3].

    PubMed

    Li, Lei; Lyu, Dan

    2017-06-01

    Objective To purify the recombinant protein specific to conserved region of forkhead box O3 (FOXO3) and prepare mouse anti-human FOXO3 polyclonal antibody. Methods The DNA fragment (aa290-472) encoding conserved domain of FOXO3 was amplified by PCR, and subsequently cloned into pET28a vector. Following transformation into E.coli BL21, the soluble fusion protein His-FOXO3 was induced by IPTG and purified by Ni-NTA affinity chromatography. The purified protein was used to immunize BALB/c mice to generate polyclonal antibody. The characteristics of the polyclonal antibody were assessed by ELISA, Western blotting and immunoprecipitation assays. Results We successfully prepared the expression vector pET28a-FOXO3 (aa290-472) and expressed the purified fusion protein in a soluble form. By immunizing mice with the fusion protein, we obtained anti-human FOXO3 polyclonal antibody. ELISA and Western blotting showed that the mouse antibody could recognize specifically the endogenous FOXO3 protein. Conclusion The polyclonal antibody against conserved domain of FOXO3 can identify the endogenous FOXO3 protein. It can be used to analyze the endogenous FOXO3 expression level.

  1. DoOPSearch: a web-based tool for finding and analysing common conserved motifs in the promoter regions of different chordate and plant genes

    PubMed Central

    Sebestyén, Endre; Nagy, Tibor; Suhai, Sándor; Barta, Endre

    2009-01-01

    Background The comparative genomic analysis of a large number of orthologous promoter regions of the chordate and plant genes from the DoOP databases shows thousands of conserved motifs. Most of these motifs differ from any known transcription factor binding site (TFBS). To identify common conserved motifs, we need a specific tool to be able to search amongst them. Since conserved motifs from the DoOP databases are linked to genes, the result of such a search can give a list of genes that are potentially regulated by the same transcription factor(s). Results We have developed a new tool called DoOPSearch for the analysis of the conserved motifs in the promoter regions of chordate or plant genes. We used the orthologous promoters of the DoOP database to extract thousands of conserved motifs from different taxonomic groups. The advantage of this approach is that different sets of conserved motifs might be found depending on how broad the taxonomic coverage of the underlying orthologous promoter sequence collection is (consider e.g. primates vs. mammals or Brassicaceae vs. Viridiplantae). The DoOPSearch tool allows the users to search these motif collections or the promoter regions of DoOP with user supplied query sequences or any of the conserved motifs from the DoOP database. To find overrepresented gene ontologies, the gene lists obtained can be analysed further using a modified version of the GeneMerge program. Conclusion We present here a comparative genomics based promoter analysis tool. Our system is based on a unique collection of conserved promoter motifs characteristic of different taxonomic groups. We offer both a command line and a web-based tool for searching in these motif collections using user specified queries. These can be either short promoter sequences or consensus sequences of known transcription factor binding sites. The GeneMerge analysis of the search results allows the user to identify statistically overrepresented Gene Ontology terms that

  2. Identifying Important Atlantic Areas for the conservation of Balearic shearwaters: Spatial overlap with conservation areas

    NASA Astrophysics Data System (ADS)

    Pérez-Roda, Amparo; Delord, Karine; Boué, Amélie; Arcos, José Manuel; García, David; Micol, Thierry; Weimerskirch, Henri; Pinaud, David; Louzao, Maite

    2017-07-01

    Marine protected areas (MPAs) are considered one of the main tools in both fisheries and conservation management to protect threatened species and their habitats around the globe. However, MPAs are underrepresented in marine environments compared to terrestrial environments. Within this context, we studied the Atlantic non-breeding distribution of the southern population of Balearic shearwaters (Puffinus mauretanicus) breeding in Eivissa during the 2011-2012 period based on global location sensing (GLS) devices. Our objectives were (1) to identify overall Important Atlantic Areas (IAAs) from a southern population, (2) to describe spatio-temporal patterns of oceanographic habitat use, and (3) to assess whether existing conservation areas (Natura 2000 sites and marine Important Bird Areas (IBAs)) cover the main IAAs of Balearic shearwaters. Our results highlighted that the Atlantic staging (from June to October in 2011) dynamic of the southern population was driven by individual segregation at both spatial and temporal scales. Individuals ranged in the North-East Atlantic over four main IAAs (Bay of Biscay: BoB, Western Iberian shelf: WIS, Gulf of Cadiz: GoC, West of Morocco: WoM). While most individuals spent more time on the WIS or in the GoC, a small number of birds visited IAAs at the extremes of their Atlantic distribution range (i.e., BoB and WoM). The chronology of the arrivals to the IAAs showed a latitudinal gradient with northern areas reached earlier during the Atlantic staging. The IAAs coincided with the most productive areas (higher chlorophyll a values) in the NE Atlantic between July and October. The spatial overlap between IAAs and conservation areas was higher for Natura 2000 sites than marine IBAs (areas with and without legal protection, respectively). Concerning the use of these areas, a slightly higher proportion of estimated positions fell within marine IBAs compared to designated Natura 2000 sites, with Spanish and Portuguese conservation

  3. Cheap and Nasty? The Potential Perils of Using Management Costs to Identify Global Conservation Priorities

    PubMed Central

    McCreless, Erin; Visconti, Piero; Carwardine, Josie; Wilcox, Chris; Smith, Robert J.

    2013-01-01

    The financial cost of biodiversity conservation varies widely around the world and such costs should be considered when identifying countries to best focus conservation investments. Previous global prioritizations have been based on global models for protected area management costs, but this metric may be related to other factors that negatively influence the effectiveness and social impacts of conservation. Here we investigate such relationships and first show that countries with low predicted costs are less politically stable. Local support and capacity can mitigate the impacts of such instability, but we also found that these countries have less civil society involvement in conservation. Therefore, externally funded projects in these countries must rely on government agencies for implementation. This can be problematic, as our analyses show that governments in countries with low predicted costs score poorly on indices of corruption, bureaucratic quality and human rights. Taken together, our results demonstrate that using national-level estimates for protected area management costs to set global conservation priorities is simplistic, as projects in apparently low-cost countries are less likely to succeed and more likely to have negative impacts on people. We identify the need for an improved approach to develop global conservation cost metrics that better capture the true costs of avoiding or overcoming such problems. Critically, conservation scientists must engage with practitioners to better understand and implement context-specific solutions. This approach assumes that measures of conservation costs, like measures of conservation value, are organization specific, and would bring a much-needed focus on reducing the negative impacts of conservation to develop projects that benefit people and biodiversity. PMID:24260502

  4. MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.

    2004-10-28

    We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

  5. Identifying Regional Key Eco-Space to Maintain Ecological Security Using GIS

    PubMed Central

    Xie, Hualin; Yao, Guanrong; Wang, Peng

    2014-01-01

    Ecological security and environmental sustainability are the foundations of sustainable development. With the acceleration of urbanization, increasing human activities have promoted greater impacts on the eco-spaces that maintain ecological security. Regional key eco-space has become the primary need to maintain environmental sustainability and can offer society with continued ecosystem services. In this paper, considering the security of water resources, biodiversity conservation, disaster avoidance and protection and natural recreation, an integrated index of eco-space importance was established and a method for identifying key eco-space was created using GIS, with Lanzhou City, China as a case study. The results show that the area of core eco-space in the Lanzhou City is approximately 50,908.7 hm2, accounting for 40% of the region’s total area. These areas mainly consist of geological hazard protection zones and the core zones of regional river systems, wetlands, nature reserves, forest parks and scenic spots. The results of this study provide some guidance for the management of ecological security, ecological restoration and environmental sustainability. PMID:24590051

  6. Identifying regions vulnerable to habitat degradation under future irrigation scenarios

    NASA Astrophysics Data System (ADS)

    Terrado, Marta; Sabater, Sergi; Acuña, Vicenç

    2016-11-01

    The loss and degradation of natural habitats is a primary cause of biodiversity decline. The increasing impacts of climate and land use change affect water availability, ultimately decreasing agricultural production. Areas devoted to irrigation have been increased to compensate this reduction, causing habitat and biodiversity losses, especially in regions undergoing severe water stress. These effects might intensify under global change, probably contributing to a decrease in habitat quality. We selected four European river basins across a gradient of water scarcity and irrigation agriculture. The habitat quality in the basins was assessed as a function of habitat suitability and threats under current and future global change scenarios of irrigation. Results revealed that the most threatened regions under future scenarios of global change were among those suffering of water scarcity and with bigger areas devoted to irrigation. Loss of habitat quality reached 10% in terrestrial and 25% in aquatic ecosystems under climate change scenarios involving drier conditions. The aquatic habitats were the most degraded in all scenarios, since they were affected by threats from both the terrestrial and the aquatic parts of the basin. By identifying in advance the regions most vulnerable to habitat and biodiversity loss, our approach can assist decision makers in deciding the conservation actions to be prioritized for mitigation and adaptation to the effects of climate change, particularly front the development of irrigation plans.

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

    USGS Publications Warehouse

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

    2006-01-01

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

  8. Designing large-scale conservation corridors for pattern and process.

    PubMed

    Rouget, Mathieu; Cowling, Richard M; Lombard, Amanda T; Knight, Andrew T; Kerley, Graham I H

    2006-04-01

    A major challenge for conservation assessments is to identify priority areas that incorporate biological patterns and processes. Because large-scale processes are mostly oriented along environmental gradients, we propose to accommodate them by designing regional-scale corridors to capture these gradients. Based on systematic conservation planning principles such as representation and persistence, we identified large tracts of untransformed land (i.e., conservation corridors) for conservation that would achieve biodiversity targets for pattern and process in the Subtropical Thicket Biome of South Africa. We combined least-cost path analysis with a target-driven algorithm to identify the best option for capturing key environmental gradients while considering biodiversity targets and conservation opportunities and constraints. We identified seven conservation corridors on the basis of subtropical thicket representation, habitat transformation and degradation, wildlife suitability, irreplaceability of vegetation types, protected area networks, and future land-use pressures. These conservation corridors covered 21.1% of the planning region (ranging from 600 to 5200 km2) and successfully achieved targets for biological processes and to a lesser extent for vegetation types. The corridors we identified are intended to promote the persistence of ecological processes (gradients and fixed processes) and fulfill half of the biodiversity pattern target. We compared the conservation corridors with a simplified corridor design consisting of a fixed-width buffer along major rivers. Conservation corridors outperformed river buffers in seven out of eight criteria. Our corridor design can provide a tool for quantifying trade-offs between various criteria (biodiversity pattern and process, implementation constraints and opportunities). A land-use management model was developed to facilitate implementation of conservation actions within these corridors.

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

    DOEpatents

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

    2013-05-28

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

  10. Structural analysis of the 5{prime} region of mouse and human Huntington disease genes reveals conservation of putative promoter region and Di- and trinucleotide polymorphisms

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Lin, Biaoyang; Nasir, J.; Kalchman, M.A.

    1995-02-10

    We have previously cloned and characterized the murine homologue of the Huntington disease (HD) gene and shown that it maps to mouse chromosome 5 within a region of conserved synteny with human chromosome 4p16.3. Here we present a detailed comparison of the sequence of the putative promoter and the organization of the 5{prime} genomic region of the murine (Hdh) and human HD genes encompassing the first five exons. We show that in this region these two genes share identical exon boundaries, but have different-size introns. Two dinucleotide (CT) and one trinucleotide intronic polymorphism in Hdh and an intronic CA polymorphismmore » in the HD gene were identified. Comparison of 940-bp sequence 5{prime} to the putative translation start site reveals a highly conserved region (78.8% nucleotide identity) between Hdh and the HD gene from nucleotide -56 to -206 (of Hdh). Neither Hdh nor the HD gene have typical TATA or CCAAT elements, but both show one putative AP2 binding site and numerous potential Sp1 binding sites. The high sequence identity between Hdh and the HD gene for approximately 200 bp 5{prime} to the putative translation start site indicates that these sequences may play a role in regulating expression of the Huntington disease gene. 30 refs., 4 figs., 2 tabs.« less

  11. Optimized spatial priorities for biodiversity conservation in China: a systematic conservation planning perspective.

    PubMed

    Wu, Ruidong; Long, Yongcheng; Malanson, George P; Garber, Paul A; Zhang, Shuang; Li, Diqiang; Zhao, Peng; Wang, Longzhu; Duo, Hairui

    2014-01-01

    By addressing several key features overlooked in previous studies, i.e. human disturbance, integration of ecosystem- and species-level conservation features, and principles of complementarity and representativeness, we present the first national-scale systematic conservation planning for China to determine the optimized spatial priorities for biodiversity conservation. We compiled a spatial database on the distributions of ecosystem- and species-level conservation features, and modeled a human disturbance index (HDI) by aggregating information using several socioeconomic proxies. We ran Marxan with two scenarios (HDI-ignored and HDI-considered) to investigate the effects of human disturbance, and explored the geographic patterns of the optimized spatial conservation priorities. Compared to when HDI was ignored, the HDI-considered scenario resulted in (1) a marked reduction (∼9%) in the total HDI score and a slight increase (∼7%) in the total area of the portfolio of priority units, (2) a significant increase (∼43%) in the total irreplaceable area and (3) more irreplaceable units being identified in almost all environmental zones and highly-disturbed provinces. Thus the inclusion of human disturbance is essential for cost-effective priority-setting. Attention should be targeted to the areas that are characterized as moderately-disturbed, <2,000 m in altitude, and/or intermediately- to extremely-rugged in terrain to identify potentially important regions for implementing cost-effective conservation. We delineated 23 primary large-scale priority areas that are significant for conserving China's biodiversity, but those isolated priority units in disturbed regions are in more urgent need of conservation actions so as to prevent immediate and severe biodiversity loss. This study presents a spatially optimized national-scale portfolio of conservation priorities--effectively representing the overall biodiversity of China while minimizing conflicts with economic

  12. Optimized Spatial Priorities for Biodiversity Conservation in China: A Systematic Conservation Planning Perspective

    PubMed Central

    Wu, Ruidong; Long, Yongcheng; Malanson, George P.; Garber, Paul A.; Zhang, Shuang; Li, Diqiang; Zhao, Peng; Wang, Longzhu; Duo, Hairui

    2014-01-01

    By addressing several key features overlooked in previous studies, i.e. human disturbance, integration of ecosystem- and species-level conservation features, and principles of complementarity and representativeness, we present the first national-scale systematic conservation planning for China to determine the optimized spatial priorities for biodiversity conservation. We compiled a spatial database on the distributions of ecosystem- and species-level conservation features, and modeled a human disturbance index (HDI) by aggregating information using several socioeconomic proxies. We ran Marxan with two scenarios (HDI-ignored and HDI-considered) to investigate the effects of human disturbance, and explored the geographic patterns of the optimized spatial conservation priorities. Compared to when HDI was ignored, the HDI-considered scenario resulted in (1) a marked reduction (∼9%) in the total HDI score and a slight increase (∼7%) in the total area of the portfolio of priority units, (2) a significant increase (∼43%) in the total irreplaceable area and (3) more irreplaceable units being identified in almost all environmental zones and highly-disturbed provinces. Thus the inclusion of human disturbance is essential for cost-effective priority-setting. Attention should be targeted to the areas that are characterized as moderately-disturbed, <2,000 m in altitude, and/or intermediately- to extremely-rugged in terrain to identify potentially important regions for implementing cost-effective conservation. We delineated 23 primary large-scale priority areas that are significant for conserving China's biodiversity, but those isolated priority units in disturbed regions are in more urgent need of conservation actions so as to prevent immediate and severe biodiversity loss. This study presents a spatially optimized national-scale portfolio of conservation priorities – effectively representing the overall biodiversity of China while minimizing conflicts with economic

  13. Conserving and managing the subnivium.

    PubMed

    Zuckerberg, Benjamin; Pauli, Jonathan N

    2018-02-08

    In regions where snowfall historically has been a defining seasonal characteristic of the landscape, warming winters have reduced the depth, duration, and extent of snowpack. However, most management and conservation has focused on how aboveground wildlife will be affected by altered snow conditions, even though the majority of species that persist through the winter do so under the snowpack in a thermally stable refugium: the subnivium. Shortened winters, forest management practices, and winter recreation can alter subnivium conditions by increasing snow compaction and compromising thermal stability at the soil-snow interface. To help slow the loss of the subnivium in the face of rapidly changing winter conditions, we suggest managers adopt regional conservation plans for identifying threatened snow-covered environments; measure and predict the effects land cover and habitat management has on local subnivium conditions; and control the timing and distribution of activities that disturb and compact snow cover (e.g., silvicultural practices, snow recreation, and road and trail maintenance). As a case study, we developed a spatially explicit model of subnivium presence in a working landscape of the Chequamegon National Forest, Wisconsin. We identified landscapes where winter recreation and management practices could threaten potentially important areas for subnivium persistence. Similar modeling approaches could inform management decisions related to subnivium conservation. Current climate projections predict that snow seasons will change rapidly in many regions, and as result, we advocate for the immediate recognition, conservation, and management of the subnivium and its dependent species. © 2018 Society for Conservation Biology.

  14. Identifying conserved gene clusters in the presence of homology families.

    PubMed

    He, Xin; Goldwasser, Michael H

    2005-01-01

    The study of conserved gene clusters is important for understanding the forces behind genome organization and evolution, as well as the function of individual genes or gene groups. In this paper, we present a new model and algorithm for identifying conserved gene clusters from pairwise genome comparison. This generalizes a recent model called "gene teams." A gene team is a set of genes that appear homologously in two or more species, possibly in a different order yet with the distance of adjacent genes in the team for each chromosome always no more than a certain threshold. We remove the constraint in the original model that each gene must have a unique occurrence in each chromosome and thus allow the analysis on complex prokaryotic or eukaryotic genomes with extensive paralogs. Our algorithm analyzes a pair of chromosomes in O(mn) time and uses O(m+n) space, where m and n are the number of genes in the respective chromosomes. We demonstrate the utility of our methods by studying two bacterial genomes, E. coli K-12 and B. subtilis. Many of the teams identified by our algorithm correlate with documented E. coli operons, while several others match predicted operons, previously suggested by computational techniques. Our implementation and data are publicly available at euler.slu.edu/ approximately goldwasser/homologyteams/.

  15. Accessing local knowledge to identify where species of conservation concern occur in a tropical forest landscape.

    PubMed

    Padmanaba, Michael; Sheil, Douglas; Basuki, Imam; Liswanti, Nining

    2013-08-01

    Conventional biodiversity surveys play an important role in ensuring good conservation friendly management in tropical forest regions but are demanding in terms of expertise, time, and budget. Can local people help? Here, we illustrate how local knowledge can support low cost conservation surveys. We worked in the Malinau watershed, East Kalimantan, Indonesia, an area currently at risk of extensive forest loss. We selected eight species of regional conservation interest: rafflesia (Rafflesia spp.), black orchid (Coelogyne pandurata), sun bear (Helarctos malayanus), tarsier (Tarsius bancanus), slow loris (Nycticebus coucang), proboscis monkey (Nasalis larvatus), clouded leopard (Neofelis diardi/N. nebulosa), and orang-utan (Pongo pygmaeus). We asked 52 informants in seven villages if, where and when they had observed these species. We used maps, based on both geo-referenced and sketched features, to record these observations. Verification concerns and related issues are discussed. Evaluations suggest our local information is reliable. Our study took 6 weeks and cost about USD 5000. Extensive expert based field surveys across the same region would cost one or two orders of magnitude more. The records extend the known distribution for sun bear, tarsier, slow loris, and clouded leopard. Reports of rafflesia, proboscis monkey, and orang-utan are of immediate conservation significance. While quality concerns should never be abandoned, we conclude that local people can help expand our knowledge of large areas in an effective, reliable, and low cost manner and thus contribute to improved management.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2013-07-01

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

  18. Extinction risks and the conservation of Madagascar's reptiles.

    PubMed

    Jenkins, Richard K B; Tognelli, Marcelo F; Bowles, Philip; Cox, Neil; Brown, Jason L; Chan, Lauren; Andreone, Franco; Andriamazava, Alain; Andriantsimanarilafy, Raphali R; Anjeriniaina, Mirana; Bora, Parfait; Brady, Lee D; Hantalalaina, Elisoa F; Glaw, Frank; Griffiths, Richard A; Hilton-Taylor, Craig; Hoffmann, Michael; Katariya, Vineet; Rabibisoa, Nirhy H; Rafanomezantsoa, Jeannot; Rakotomalala, Domoina; Rakotondravony, Hery; Rakotondrazafy, Ny A; Ralambonirainy, Johans; Ramanamanjato, Jean-Baptiste; Randriamahazo, Herilala; Randrianantoandro, J Christian; Randrianasolo, Harison H; Randrianirina, Jasmin E; Randrianizahana, Hiarinirina; Raselimanana, Achille P; Rasolohery, Andriambolantsoa; Ratsoavina, Fanomezana M; Raxworthy, Christopher J; Robsomanitrandrasana, Eric; Rollande, Finoana; van Dijk, Peter P; Yoder, Anne D; Vences, Miguel

    2014-01-01

    An understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the island's mammals, birds and amphibians. We report here on the first systematic assessment of the extinction risk of endemic and native non-marine Malagasy snakes, lizards, turtles and tortoises. Species range maps from The IUCN Red List of Threatened Species were analysed to determine patterns in the distribution of threatened reptile species. These data, in addition to information on threats, were used to identify priority areas and actions for conservation. Thirty-nine percent of the data-sufficient Malagasy reptiles in our analyses are threatened with extinction. Areas in the north, west and south-east were identified as having more threatened species than expected and are therefore conservation priorities. Habitat degradation caused by wood harvesting and non-timber crops was the most pervasive threat. The direct removal of reptiles for international trade and human consumption threatened relatively few species, but were the primary threats for tortoises. Nine threatened reptile species are endemic to recently created protected areas. With a few alarming exceptions, the threatened endemic reptiles of Madagascar occur within the national network of protected areas, including some taxa that are only found in new protected areas. Threats to these species, however, operate inside and outside protected area boundaries. This analysis has identified priority sites for reptile conservation and completes the conservation assessment of terrestrial vertebrates in Madagascar which will facilitate conservation planning, monitoring and wise-decision making. In sharp contrast with the amphibians, there is significant reptile diversity and regional endemism in the southern and western regions of Madagascar and this study highlights the importance of

  19. Extinction Risks and the Conservation of Madagascar's Reptiles

    PubMed Central

    Jenkins, Richard K. B.; Tognelli, Marcelo F.; Bowles, Philip; Cox, Neil; Brown, Jason L.; Chan, Lauren; Andreone, Franco; Andriamazava, Alain; Andriantsimanarilafy, Raphali R.; Anjeriniaina, Mirana; Bora, Parfait; Brady, Lee D.; Hantalalaina, Elisoa F.; Glaw, Frank; Griffiths, Richard A.; Hilton-Taylor, Craig; Hoffmann, Michael; Katariya, Vineet; Rabibisoa, Nirhy H.; Rafanomezantsoa, Jeannot; Rakotomalala, Domoina; Rakotondravony, Hery; Rakotondrazafy, Ny A.; Ralambonirainy, Johans; Ramanamanjato, Jean-Baptiste; Randriamahazo, Herilala; Randrianantoandro, J. Christian; Randrianasolo, Harison H.; Randrianirina, Jasmin E.; Randrianizahana, Hiarinirina; Raselimanana, Achille P.; Rasolohery, Andriambolantsoa; Ratsoavina, Fanomezana M.; Raxworthy, Christopher J.; Robsomanitrandrasana, Eric; Rollande, Finoana; van Dijk, Peter P.; Yoder, Anne D.; Vences, Miguel

    2014-01-01

    Background An understanding of the conservation status of Madagascar's endemic reptile species is needed to underpin conservation planning and priority setting in this global biodiversity hotspot, and to complement existing information on the island's mammals, birds and amphibians. We report here on the first systematic assessment of the extinction risk of endemic and native non-marine Malagasy snakes, lizards, turtles and tortoises. Methodology/Principal Findings Species range maps from The IUCN Red List of Threatened Species were analysed to determine patterns in the distribution of threatened reptile species. These data, in addition to information on threats, were used to identify priority areas and actions for conservation. Thirty-nine percent of the data-sufficient Malagasy reptiles in our analyses are threatened with extinction. Areas in the north, west and south-east were identified as having more threatened species than expected and are therefore conservation priorities. Habitat degradation caused by wood harvesting and non-timber crops was the most pervasive threat. The direct removal of reptiles for international trade and human consumption threatened relatively few species, but were the primary threats for tortoises. Nine threatened reptile species are endemic to recently created protected areas. Conclusions/Significance With a few alarming exceptions, the threatened endemic reptiles of Madagascar occur within the national network of protected areas, including some taxa that are only found in new protected areas. Threats to these species, however, operate inside and outside protected area boundaries. This analysis has identified priority sites for reptile conservation and completes the conservation assessment of terrestrial vertebrates in Madagascar which will facilitate conservation planning, monitoring and wise-decision making. In sharp contrast with the amphibians, there is significant reptile diversity and regional endemism in the southern and

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

    PubMed

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

    2007-09-01

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

  1. Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities

    PubMed Central

    Gray, Claudia L.; Wearn, Oliver R.; Owen, Nisha R.

    2018-01-01

    The scale of the ongoing biodiversity crisis requires both effective conservation prioritisation and urgent action. As extinction is non-random across the tree of life, it is important to prioritise threatened species which represent large amounts of evolutionary history. The EDGE metric prioritises species based on their Evolutionary Distinctiveness (ED), which measures the relative contribution of a species to the total evolutionary history of their taxonomic group, and Global Endangerment (GE), or extinction risk. EDGE prioritisations rely on adequate phylogenetic and extinction risk data to generate meaningful priorities for conservation. However, comprehensive phylogenetic trees of large taxonomic groups are extremely rare and, even when available, become quickly out-of-date due to the rapid rate of species descriptions and taxonomic revisions. Thus, it is important that conservationists can use the available data to incorporate evolutionary history into conservation prioritisation. We compared published and new methods to estimate missing ED scores for species absent from a phylogenetic tree whilst simultaneously correcting the ED scores of their close taxonomic relatives. We found that following artificial removal of species from a phylogenetic tree, the new method provided the closest estimates of their “true” ED score, differing from the true ED score by an average of less than 1%, compared to the 31% and 38% difference of the previous methods. The previous methods also substantially under- and over-estimated scores as more species were artificially removed from a phylogenetic tree. We therefore used the new method to estimate ED scores for all tetrapods. From these scores we updated EDGE prioritisation rankings for all tetrapod species with IUCN Red List assessments, including the first EDGE prioritisation for reptiles. Further, we identified criteria to identify robust priority species in an effort to further inform conservation action whilst

  2. A state-based national network for effective wildlife conservation

    USGS Publications Warehouse

    Meretsky, Vicky J.; Maguire, Lynn A.; Davis, Frank W.; Stoms, David M.; Scott, J. Michael; Figg, Dennis; Goble, Dale D.; Griffith, Brad; Henke, Scott E.; Vaughn, Jacqueline; Yaffee, Steven L.

    2012-01-01

    State wildlife conservation programs provide a strong foundation for biodiversity conservation in the United States, building on state wildlife action plans. However, states may miss the species that are at the most risk at rangewide scales, and threats such as novel diseases and climate change increasingly act at regional and national levels. Regional collaborations among states and their partners have had impressive successes, and several federal programs now incorporate state priorities. However, regional collaborations are uneven across the country, and no national counterpart exists to support efforts at that scale. A national conservation-support program could fill this gap and could work across the conservation community to identify large-scale conservation needs and support efforts to meet them. By providing important information-sharing and capacity-building services, such a program would advance collaborative conservation among the states and their partners, thus increasing both the effectiveness and the efficiency of conservation in the United States.

  3. Identifiability of conservative linear mechanical systems. [applied to large flexible spacecraft structures

    NASA Technical Reports Server (NTRS)

    Sirlin, S. W.; Longman, R. W.; Juang, J. N.

    1985-01-01

    With a sufficiently great number of sensors and actuators, any finite dimensional dynamic system is identifiable on the basis of input-output data. It is presently indicated that, for conservative nongyroscopic linear mechanical systems, the number of sensors and actuators required for identifiability is very large, where 'identifiability' is understood as a unique determination of the mass and stiffness matrices. The required number of sensors and actuators drops by a factor of two, given a relaxation of the identifiability criterion so that identification can fail only if the system parameters being identified lie in a set of measure zero. When the mass matrix is known a priori, this additional information does not significantly affect the requirements for guaranteed identifiability, though the number of parameters to be determined is reduced by a factor of two.

  4. Residential energy consumption and conservation programs: A systematic approach to identify inefficient households, provide meaningful feedback, and prioritize homes for conservation intervention

    NASA Astrophysics Data System (ADS)

    Macsleyne, Amelia Chadbourne Carus

    There are three main objectives for residential energy conservation policies: to reduce the use of fossil fuels, reduce greenhouse gas emissions, and reduce the energy costs seen by the consumer (U.S. Department of Energy: Strategic Objectives, 2006). A prominent difficulty currently facing conservation policy makers and program managers is how to identify and communicate with households that would be good candidates for conservation intervention, in such a way that affects a change in consumption patterns and is cost-effective. This research addresses this issue by separating the problem into three components: how to identify houses that are significantly more inefficient than comparable households; how to find the maximum financially-feasible investment in energy efficiency for a household in order to reduce annual energy costs and/or improve indoor comfort; and how to prioritize low-income households for a subsidized weatherization program. Each component of the problem is presented as a paper prepared for publication. Household consumption related to physical house efficiency, thermostat settings, and daily appliance usage is studied in the first and second paper by analyzing natural gas utility meter readings associated with over 10,000 households from 2001-2006. A rich description of a house's architectural characteristics and household demographics is attained by integrating publicly available databases based on the house address. This combination of information allows for the largest number of individual households studied at this level of detail to date. The third paper uses conservation program data from two natural gas utilities that administer and sponsor the program; over 1,000 weatherized households are included in this sample. This research focuses on natural gas-related household conservation. However, the same principles and methods could be applied for electricity-related conservation programs. We find positive policy implications from each of

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  6. An evolutionary analysis identifies a conserved pentapeptide stretch containing the two essential lysine residues for rice L-myo-inositol 1-phosphate synthase catalytic activity

    PubMed Central

    Basak, Papri; Maitra-Majee, Susmita; Das, Jayanta Kumar; Mukherjee, Abhishek; Ghosh Dastidar, Shubhra; Pal Choudhury, Pabitra

    2017-01-01

    A molecular evolutionary analysis of a well conserved protein helps to determine the essential amino acids in the core catalytic region. Based on the chemical properties of amino acid residues, phylogenetic analysis of a total of 172 homologous sequences of a highly conserved enzyme, L-myo-inositol 1-phosphate synthase or MIPS from evolutionarily diverse organisms was performed. This study revealed the presence of six phylogenetically conserved blocks, out of which four embrace the catalytic core of the functional protein. Further, specific amino acid modifications targeting the lysine residues, known to be important for MIPS catalysis, were performed at the catalytic site of a MIPS from monocotyledonous model plant, Oryza sativa (OsMIPS1). Following this study, OsMIPS mutants with deletion or replacement of lysine residues in the conserved blocks were made. Based on the enzyme kinetics performed on the deletion/replacement mutants, phylogenetic and structural comparison with the already established crystal structures from non-plant sources, an evolutionarily conserved peptide stretch was identified at the active pocket which contains the two most important lysine residues essential for catalytic activity. PMID:28950028

  7. Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

    PubMed

    Godec, Jernej; Tan, Yan; Liberzon, Arthur; Tamayo, Pablo; Bhattacharya, Sanchita; Butte, Atul J; Mesirov, Jill P; Haining, W Nicholas

    2016-01-19

    Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Interregional sharing of energy conservation targets in China: Efficiency and equity

    NASA Astrophysics Data System (ADS)

    Wei, Dan

    Energy conservation is a long-term strategic policy in China to support its economic and social development. This policy strategy is important for saving resources, protecting the environment, and ensuring the secure supply of energy to all economic activities. However, energy conservation often involves large amounts of investment and may also have dampening impacts on some local and regional economies. Moreover, energy conservation and efficiency improvement have many features of a public good. Therefore, government policy and intervention play a strong role to foster regional efforts and cooperative interregional actions on this issue. This dissertation introduces and analyzes a promising policy instrument---an interregional energy conservation-quota trading system---to help China fulfill its national energy conservation objective in an efficient and equitable way. To analyze the workings of the energy conservation-quota trading system, trading entities are first determined. In this study, statistical analyses (principal component analysis and cluster analysis) are applied to identify regional aggregations of provinces of China to act as the trading units. The marginal energy conservation cost curves of these regions are developed using engineering-economic methods and regression analysis. Simulations of interregional conservation-quota trading are undertaken after China's conservation goals in 2010 are allocated among regions according to several equity criteria. Various equity criteria are applied and analyzed in this study because of the philosophical differences in the appropriate definition of the concept. The trading simulations yield several important findings. First, the introduction of an interregional quota trading system can minimize both regional net compliance costs and national total conservation costs, irrespective of how the conservation tasks are initially allocated among regions according to different equity rules. Second, regional welfare

  9. Comparing spatially explicit ecological and social values for natural areas to identify effective conservation strategies.

    PubMed

    Bryan, Brett Anthony; Raymond, Christopher Mark; Crossman, Neville David; King, Darran

    2011-02-01

    Consideration of the social values people assign to relatively undisturbed native ecosystems is critical for the success of science-based conservation plans. We used an interview process to identify and map social values assigned to 31 ecosystem services provided by natural areas in an agricultural landscape in southern Australia. We then modeled the spatial distribution of 12 components of ecological value commonly used in setting spatial conservation priorities. We used the analytical hierarchy process to weight these components and used multiattribute utility theory to combine them into a single spatial layer of ecological value. Social values assigned to natural areas were negatively correlated with ecological values overall, but were positively correlated with some components of ecological value. In terms of the spatial distribution of values, people valued protected areas, whereas those natural areas underrepresented in the reserve system were of higher ecological value. The habitats of threatened animal species were assigned both high ecological value and high social value. Only small areas were assigned both high ecological value and high social value in the study area, whereas large areas of high ecological value were of low social value, and vice versa. We used the assigned ecological and social values to identify different conservation strategies (e.g., information sharing, community engagement, incentive payments) that may be effective for specific areas. We suggest that consideration of both ecological and social values in selection of conservation strategies can enhance the success of science-based conservation planning. ©2010 Society for Conservation Biology.

  10. Conservation biology in Asia: the major policy challenges.

    PubMed

    McNeely, Jeffrey A; Kapoor-Vijay, Promila; Zhi, Lu; Olsvig-Whittaker, Linda; Sheikh, Kashif M; Smith, Andrew T

    2009-08-01

    With about half the world's human population and booming economies, Asia faces numerous challenges to its biodiversity. The Asia Section of the Society for Conservation Biology has identified some key policy issues in which significant progress can be made. These include developing new sources of funding for forest conservation; identifying potential impacts of energy alternatives on the conservation of biodiversity; curbing the trade in endangered species of plants and animals; a special focus on the conservation of mountain biodiversity; enhancing relevant research; ensuring that conservation biology contributes to major international conventions and funding mechanisms; using conservation biology to build a better understanding of zoonotic diseases; more effectively addressing human-animal conflicts; enhancing community-based conservation; and using conservation biology to help address the pervasive water-deficit problems in much of Asia. These challenges can be met through improved regional cooperation among the relevant stakeholders.

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

    USGS Publications Warehouse

    Mushet, David M.; Neau, Jordan L.

    2014-01-01

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

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

    PubMed

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

    2007-10-01

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

  13. smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni

    PubMed Central

    2012-01-01

    Background MicroRNAs (miRNAs) constitute a family of small RNA (sRNA) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. Extensive studies on miRNAs have been performed in different plants such as Arabidopsis thaliana, Oryza sativa etc. and volume of the miRNA database, mirBASE, has been increasing on day to day basis. Stevia rebaudiana Bertoni is an important perennial herb which accumulates high concentrations of diterpene steviol glycosides which contributes to its high indexed sweetening property with no calorific value. Several studies have been carried out for understanding molecular mechanism involved in biosynthesis of these glycosides, however, information about miRNAs has been lacking in S. rebaudiana. Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs irrespective of availability of genome sequence data. Results To identify miRNAs in S. rebaudiana, sRNA library was constructed and sequenced using Illumina genome analyzer II. A total of 30,472,534 reads representing 2,509,190 distinct sequences were obtained from sRNA library. Based on sequence similarity, we identified 100 miRNAs belonging to 34 highly conserved families. Also, we identified 12 novel miRNAs whose precursors were potentially generated from stevia EST and nucleotide sequences. All novel sequences have not been earlier described in other plant species. Putative target genes were predicted for most conserved and novel miRNAs. The predicted targets are mainly mRNA encoding enzymes regulating essential plant metabolic and signaling pathways. Conclusions This study led to the identification of 34 highly conserved miRNA families and 12 novel potential miRNAs indicating that specific miRNAs exist in stevia species. Our results provided information on stevia miRNAs and their targets building a foundation for future studies to

  14. smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni.

    PubMed

    Mandhan, Vibha; Kaur, Jagdeep; Singh, Kashmir

    2012-11-01

    MicroRNAs (miRNAs) constitute a family of small RNA (sRNA) population that regulates the gene expression and plays an important role in plant development, metabolism, signal transduction and stress response. Extensive studies on miRNAs have been performed in different plants such as Arabidopsis thaliana, Oryza sativa etc. and volume of the miRNA database, mirBASE, has been increasing on day to day basis. Stevia rebaudiana Bertoni is an important perennial herb which accumulates high concentrations of diterpene steviol glycosides which contributes to its high indexed sweetening property with no calorific value. Several studies have been carried out for understanding molecular mechanism involved in biosynthesis of these glycosides, however, information about miRNAs has been lacking in S. rebaudiana. Deep sequencing of small RNAs combined with transcriptomic data is a powerful tool for identifying conserved and novel miRNAs irrespective of availability of genome sequence data. To identify miRNAs in S. rebaudiana, sRNA library was constructed and sequenced using Illumina genome analyzer II. A total of 30,472,534 reads representing 2,509,190 distinct sequences were obtained from sRNA library. Based on sequence similarity, we identified 100 miRNAs belonging to 34 highly conserved families. Also, we identified 12 novel miRNAs whose precursors were potentially generated from stevia EST and nucleotide sequences. All novel sequences have not been earlier described in other plant species. Putative target genes were predicted for most conserved and novel miRNAs. The predicted targets are mainly mRNA encoding enzymes regulating essential plant metabolic and signaling pathways. This study led to the identification of 34 highly conserved miRNA families and 12 novel potential miRNAs indicating that specific miRNAs exist in stevia species. Our results provided information on stevia miRNAs and their targets building a foundation for future studies to understand their roles in key

  15. Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns.

    PubMed

    Gruel, Jérémy; LeBorgne, Michel; LeMeur, Nolwenn; Théret, Nathalie

    2011-09-12

    Regulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed to identify regulatory motifs, mainly based on the recognition of DNA sequences for transcription factor binding sites. Recent integration of additional data from genomic analyses or phylogenetic footprinting has significantly improved these methods. Here, we propose a different approach based on the compilation of Simple Shared Motifs (SSM), groups of sequences defined by their length and similarity and present in conserved sequences of gene promoters. We developed an original algorithm to search and count SSM in pairs of genes. An exceptional number of SSM is considered as a common regulatory pattern. The SSM approach is applied to a sample set of genes and validated using functional gene-set enrichment analyses. We demonstrate that the SSM approach selects genes that are over-represented in specific biological categories (Ontology and Pathways) and are enriched in co-expressed genes. Finally we show that genes co-expressed in the same tissue or involved in the same biological pathway have increased SSM values. Using unbiased clustering of genes, Simple Shared Motifs analysis constitutes an original contribution to provide a clearer definition of expression networks.

  16. Simple Shared Motifs (SSM) in conserved region of promoters: a new approach to identify co-regulation patterns

    PubMed Central

    2011-01-01

    Background Regulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed to identify regulatory motifs, mainly based on the recognition of DNA sequences for transcription factor binding sites. Recent integration of additional data from genomic analyses or phylogenetic footprinting has significantly improved these methods. Results Here, we propose a different approach based on the compilation of Simple Shared Motifs (SSM), groups of sequences defined by their length and similarity and present in conserved sequences of gene promoters. We developed an original algorithm to search and count SSM in pairs of genes. An exceptional number of SSM is considered as a common regulatory pattern. The SSM approach is applied to a sample set of genes and validated using functional gene-set enrichment analyses. We demonstrate that the SSM approach selects genes that are over-represented in specific biological categories (Ontology and Pathways) and are enriched in co-expressed genes. Finally we show that genes co-expressed in the same tissue or involved in the same biological pathway have increased SSM values. Conclusions Using unbiased clustering of genes, Simple Shared Motifs analysis constitutes an original contribution to provide a clearer definition of expression networks. PMID:21910886

  17. The Prp19 WD40 Domain Contains a Conserved Protein Interaction Region Essential for its Function

    PubMed Central

    Vander Kooi, Craig W.; Ren, Liping; Xu, Ping; Ohi, Melanie D.; Gould, Kathleen L.; Chazin, Walter J.

    2010-01-01

    Summary Prp19 is a member of the WD40-repeat family of E3 ubiquitin ligases and a conserved eukaryotic RNA splicing factor essential for activation and stabilization of the spliceosome. To understand the role of the WD40 repeat domain of Prp19 we have determined its structure using X-ray crystallography. The domain has a distorted seven bladed WD40 architecture with significant asymmetry due to irregular packing of blades one and seven into the core of the WD40 domain. Structure-based mutagenesis identified a highly conserved surface centered around blade five that is required for the physical interaction between Prp19 and Cwc2, another essential splicing factor. This region is found to be required for Prp19 function and yeast viability. Experiments in vitro and in vivo demonstrate that two molecules of Cwc2 bind to the Prp19 tetramer. These coupled structural and functional studies provide a model for the functional architecture of Prp19. PMID:20462492

  18. Global priorities for conservation across multiple dimensions of mammalian diversity

    PubMed Central

    Graham, Catherine H.; Costa, Gabriel C.; Hedges, S. Blair; Penone, Caterina; Radeloff, Volker C.; Rondinini, Carlo; Davidson, Ana D.

    2017-01-01

    Conservation priorities that are based on species distribution, endemism, and vulnerability may underrepresent biologically unique species as well as their functional roles and evolutionary histories. To ensure that priorities are biologically comprehensive, multiple dimensions of diversity must be considered. Further, understanding how the different dimensions relate to one another spatially is important for conservation prioritization, but the relationship remains poorly understood. Here, we use spatial conservation planning to (i) identify and compare priority regions for global mammal conservation across three key dimensions of biodiversity—taxonomic, phylogenetic, and traits—and (ii) determine the overlap of these regions with the locations of threatened species and existing protected areas. We show that priority areas for mammal conservation exhibit low overlap across the three dimensions, highlighting the need for an integrative approach for biodiversity conservation. Additionally, currently protected areas poorly represent the three dimensions of mammalian biodiversity. We identify areas of high conservation priority among and across the dimensions that should receive special attention for expanding the global protected area network. These high-priority areas, combined with areas of high priority for other taxonomic groups and with social, economic, and political considerations, provide a biological foundation for future conservation planning efforts. PMID:28674013

  19. Global priorities for conservation across multiple dimensions of mammalian diversity.

    PubMed

    Brum, Fernanda T; Graham, Catherine H; Costa, Gabriel C; Hedges, S Blair; Penone, Caterina; Radeloff, Volker C; Rondinini, Carlo; Loyola, Rafael; Davidson, Ana D

    2017-07-18

    Conservation priorities that are based on species distribution, endemism, and vulnerability may underrepresent biologically unique species as well as their functional roles and evolutionary histories. To ensure that priorities are biologically comprehensive, multiple dimensions of diversity must be considered. Further, understanding how the different dimensions relate to one another spatially is important for conservation prioritization, but the relationship remains poorly understood. Here, we use spatial conservation planning to ( i ) identify and compare priority regions for global mammal conservation across three key dimensions of biodiversity-taxonomic, phylogenetic, and traits-and ( ii ) determine the overlap of these regions with the locations of threatened species and existing protected areas. We show that priority areas for mammal conservation exhibit low overlap across the three dimensions, highlighting the need for an integrative approach for biodiversity conservation. Additionally, currently protected areas poorly represent the three dimensions of mammalian biodiversity. We identify areas of high conservation priority among and across the dimensions that should receive special attention for expanding the global protected area network. These high-priority areas, combined with areas of high priority for other taxonomic groups and with social, economic, and political considerations, provide a biological foundation for future conservation planning efforts.

  20. The research on regional conservation planning of urban historical and cultural areas based on GIS

    NASA Astrophysics Data System (ADS)

    Li, Shangli; Xu, Jian; Li, Qian

    2017-06-01

    With the rapid economic development and the growth of population happening in the urban historical and cultural areas, heritage and historical buildings along with their natural and artificial surrounding environments are suffering constructive destruction. Due to the lack of precise partition of protection region and construction control region in the local cultural relics protection law, traditional regional conservation planning cannot engaged with the urban controllability detailed planning very well. According to the several protection regulations about heritage and historical buildings from latest laws, we choose Baxian Temple area to study on the improvments of traditional regional conservation planning. The technical methods of this study mainly rely on GIS, which can complete the fundamental work of each stage. With the analytic hierarchy process(AHP), the comprehensive architectural value assessments can be calculated according to the investigation results. Based on the calculation results and visual corridor analysis, the precise range of protection region and construction control region can be decided and the specific protection measures can be formulated.

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

    PubMed

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

    2016-01-01

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

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

    PubMed Central

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

    2016-01-01

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

  3. ECASTAR: Energy conservation. An assessment of systems, technologies and requirements

    NASA Technical Reports Server (NTRS)

    1975-01-01

    A methodology was presented for a systems approach to energy conservation actions and their potentials and impacts in the United States. Constraints affecting the approach were ranked, and the most important ones are the present economic and technical conditions. The following unresolved issues were identified: consumptive lifestyles vs. conservation ethic, environmental standards vs. energy conservation, capital availability, decentralization and vertical integration vs. centralization, fuel rich regions vs. fuel poor regions, supply vs. end use conservation, life cycle costing vs. initial cost, mandatory savings vs. voluntary savings, labor intensive vs. capital intensive, price control vs. free market. The following recommendations were made: provide action/impact assessment, establish regional energy centers, improve technology articulation with government, design total energy systems, utilize existing systems approach expertise.

  4. Distinct Contributions of Conserved Modules to Runt Transcription Factor Activity

    PubMed Central

    Walrad, Pegine B.; Hang, Saiyu; Joseph, Genevieve S.; Salas, Julia

    2010-01-01

    Runx proteins play vital roles in regulating transcription in numerous developmental pathways throughout the animal kingdom. Two Runx protein hallmarks are the DNA-binding Runt domain and a C-terminal VWRPY motif that mediates interaction with TLE/Gro corepressor proteins. A phylogenetic analysis of Runt, the founding Runx family member, identifies four distinct regions C-terminal to the Runt domain that are conserved in Drosophila and other insects. We used a series of previously described ectopic expression assays to investigate the functions of these different conserved regions in regulating gene expression during embryogenesis and in controlling axonal projections in the developing eye. The results indicate each conserved region is required for a different subset of activities and identify distinct regions that participate in the transcriptional activation and repression of the segmentation gene sloppy-paired-1 (slp1). Interestingly, the C-terminal VWRPY-containing region is not required for repression but instead plays a role in slp1 activation. Genetic experiments indicating that Groucho (Gro) does not participate in slp1 regulation further suggest that Runt's conserved C-terminus interacts with other factors to promote transcriptional activation. These results provide a foundation for further studies on the molecular interactions that contribute to the context-dependent properties of Runx proteins as developmental regulators. PMID:20462957

  5. A network approach for identifying and delimiting biogeographical regions.

    PubMed

    Vilhena, Daril A; Antonelli, Alexandre

    2015-04-24

    Biogeographical regions (geographically distinct assemblages of species and communities) constitute a cornerstone for ecology, biogeography, evolution and conservation biology. Species turnover measures are often used to quantify spatial biodiversity patterns, but algorithms based on similarity can be sensitive to common sampling biases in species distribution data. Here we apply a community detection approach from network theory that incorporates complex, higher-order presence-absence patterns. We demonstrate the performance of the method by applying it to all amphibian species in the world (c. 6,100 species), all vascular plant species of the USA (c. 17,600) and a hypothetical data set containing a zone of biotic transition. In comparison with current methods, our approach tackles the challenges posed by transition zones and succeeds in retrieving a larger number of commonly recognized biogeographical regions. This method can be applied to generate objective, data-derived identification and delimitation of the world's biogeographical regions.

  6. Temperate non-breeding surveys - a key to shorebird conservation

    Treesearch

    Sue Thomas

    2005-01-01

    Completion of the United States and Canadian shorebird conservation plans recently identified and prioritized shorebird monitoring, management, and conservation needs in the Western Hemisphere. We present an emerging approach to monitor shorebird use of temperate non-breeding areas under the Program for Regional and International Shorebird Monitoring (PRISM). This...

  7. Identifying parameter regions for multistationarity

    PubMed Central

    Conradi, Carsten; Mincheva, Maya; Wiuf, Carsten

    2017-01-01

    Mathematical modelling has become an established tool for studying the dynamics of biological systems. Current applications range from building models that reproduce quantitative data to identifying systems with predefined qualitative features, such as switching behaviour, bistability or oscillations. Mathematically, the latter question amounts to identifying parameter values associated with a given qualitative feature. We introduce a procedure to partition the parameter space of a parameterized system of ordinary differential equations into regions for which the system has a unique or multiple equilibria. The procedure is based on the computation of the Brouwer degree, and it creates a multivariate polynomial with parameter depending coefficients. The signs of the coefficients determine parameter regions with and without multistationarity. A particular strength of the procedure is the avoidance of numerical analysis and parameter sampling. The procedure consists of a number of steps. Each of these steps might be addressed algorithmically using various computer programs and available software, or manually. We demonstrate our procedure on several models of gene transcription and cell signalling, and show that in many cases we obtain a complete partitioning of the parameter space with respect to multistationarity. PMID:28972969

  8. Using a social-ecological framework to inform the implementation of conservation plans.

    PubMed

    Guerrero, Angela M; Wilson, Kerrie A

    2017-04-01

    One of the key determinants of success in biodiversity conservation is how well conservation planning decisions account for the social system in which actions are to be implemented. Understanding elements of how the social and ecological systems interact can help identify opportunities for implementation. Utilizing data from a large-scale conservation initiative in southwestern of Australia, we explored how a social-ecological system framework can be applied to identify how social and ecological factors interact to influence the opportunities for conservation. Using data from semistructured interviews, an online survey, and publicly available data, we developed a conceptual model of the social-ecological system associated with the conservation of the Fitz-Stirling region. We used this model to identify the relevant variables (remnants of vegetation, stakeholder presence, collaboration between stakeholders, and their scale of management) that affect the implementation of conservation actions in the region. We combined measures for these variables to ascertain how areas associated with different levels of ecological importance coincided with areas associated with different levels of stakeholder presence, stakeholder collaboration, and scales of management. We identified areas that could benefit from different implementation strategies, from those suitable for immediate conservation action to areas requiring implementation over the long term to increase on-the-ground capacity and identify mechanisms to incentivize implementation. The application of a social-ecological framework can help conservation planners and practitioners facilitate the integration of ecological and social data to inform the translation of priorities for action into implementation strategies that account for the complexities of conservation problems in a focused way. © 2016 Society for Conservation Biology.

  9. Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells

    PubMed Central

    Camp, J. Gray; Weiser, Matthew; Cocchiaro, Jordan L.; Kingsley, David M.; Furey, Terrence S.; Sheikh, Shehzad Z.; Rawls, John F.

    2017-01-01

    The intestinal epithelium serves critical physiologic functions that are shared among all vertebrates. However, it is unknown how the transcriptional regulatory mechanisms underlying these functions have changed over the course of vertebrate evolution. We generated genome-wide mRNA and accessible chromatin data from adult intestinal epithelial cells (IECs) in zebrafish, stickleback, mouse, and human species to determine if conserved IEC functions are achieved through common transcriptional regulation. We found evidence for substantial common regulation and conservation of gene expression regionally along the length of the intestine from fish to mammals and identified a core set of genes comprising a vertebrate IEC signature. We also identified transcriptional start sites and other putative regulatory regions that are differentially accessible in IECs in all 4 species. Although these sites rarely showed sequence conservation from fish to mammals, surprisingly, they drove highly conserved IEC expression in a zebrafish reporter assay. Common putative transcription factor binding sites (TFBS) found at these sites in multiple species indicate that sequence conservation alone is insufficient to identify much of the functionally conserved IEC regulatory information. Among the rare, highly sequence-conserved, IEC-specific regulatory regions, we discovered an ancient enhancer upstream from her6/HES1 that is active in a distinct population of Notch-positive cells in the intestinal epithelium. Together, these results show how combining accessible chromatin and mRNA datasets with TFBS prediction and in vivo reporter assays can reveal tissue-specific regulatory information conserved across 420 million years of vertebrate evolution. We define an IEC transcriptional regulatory network that is shared between fish and mammals and establish an experimental platform for studying how evolutionarily distilled regulatory information commonly controls IEC development and physiology. PMID

  10. Identifying species from the air: UAVs and the very high resolution challenge for plant conservation

    PubMed Central

    Moat, Justin; Whaley, Oliver; Boyd, Doreen S.

    2017-01-01

    The Pacific Equatorial dry forest of Northern Peru is recognised for its unique endemic biodiversity. Although highly threatened the forest provides livelihoods and ecosystem services to local communities. As agro-industrial expansion and climatic variation transform the region, close ecosystem monitoring is essential for viable adaptation strategies. UAVs offer an affordable alternative to satellites in obtaining both colour and near infrared imagery to meet the specific requirements of spatial and temporal resolution of a monitoring system. Combining this with their capacity to produce three dimensional models of the environment provides an invaluable tool for species level monitoring. Here we demonstrate that object-based image analysis of very high resolution UAV images can identify and quantify keystone tree species and their health across wide heterogeneous landscapes. The analysis exposes the state of the vegetation and serves as a baseline for monitoring and adaptive implementation of community based conservation and restoration in the area. PMID:29176860

  11. Identifying species from the air: UAVs and the very high resolution challenge for plant conservation.

    PubMed

    Baena, Susana; Moat, Justin; Whaley, Oliver; Boyd, Doreen S

    2017-01-01

    The Pacific Equatorial dry forest of Northern Peru is recognised for its unique endemic biodiversity. Although highly threatened the forest provides livelihoods and ecosystem services to local communities. As agro-industrial expansion and climatic variation transform the region, close ecosystem monitoring is essential for viable adaptation strategies. UAVs offer an affordable alternative to satellites in obtaining both colour and near infrared imagery to meet the specific requirements of spatial and temporal resolution of a monitoring system. Combining this with their capacity to produce three dimensional models of the environment provides an invaluable tool for species level monitoring. Here we demonstrate that object-based image analysis of very high resolution UAV images can identify and quantify keystone tree species and their health across wide heterogeneous landscapes. The analysis exposes the state of the vegetation and serves as a baseline for monitoring and adaptive implementation of community based conservation and restoration in the area.

  12. 76 FR 45606 - Desert Renewable Energy Conservation Plan, Habitat Conservation Plan and Possible Land Use Plan...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-07-29

    ... than would a project-by-project, species-by-species review; and Identify and incorporate climate change... environmental justice, outdoor recreation, visual resources, induced growth, climate change and greenhouse gases... biological resource conservation across the Mojave and Colorado Desert regions of southern California. The...

  13. Defining and predicting structurally conserved regions in protein superfamilies

    PubMed Central

    Huang, Ivan K.; Grishin, Nick V.

    2013-01-01

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

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

    PubMed Central

    2016-01-01

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

  15. Evolutionary conservation of regulatory elements in vertebrate HOX gene clusters

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Santini, Simona; Boore, Jeffrey L.; Meyer, Axel

    2003-12-31

    Due to their high degree of conservation, comparisons of DNA sequences among evolutionarily distantly-related genomes permit to identify functional regions in noncoding DNA. Hox genes are optimal candidate sequences for comparative genome analyses, because they are extremely conserved in vertebrates and occur in clusters. We aligned (Pipmaker) the nucleotide sequences of HoxA clusters of tilapia, pufferfish, striped bass, zebrafish, horn shark, human and mouse (over 500 million years of evolutionary distance). We identified several highly conserved intergenic sequences, likely to be important in gene regulation. Only a few of these putative regulatory elements have been previously described as being involvedmore » in the regulation of Hox genes, while several others are new elements that might have regulatory functions. The majority of these newly identified putative regulatory elements contain short fragments that are almost completely conserved and are identical to known binding sites for regulatory proteins (Transfac). The conserved intergenic regions located between the most rostrally expressed genes in the developing embryo are longer and better retained through evolution. We document that presumed regulatory sequences are retained differentially in either A or A clusters resulting from a genome duplication in the fish lineage. This observation supports both the hypothesis that the conserved elements are involved in gene regulation and the Duplication-Deletion-Complementation model.« less

  16. Integrating climate change into the state wildlife action plans: Biological responses to climate impacts with a focus on Regional Species of Greatest Conservation Need (RSGCN)

    USGS Publications Warehouse

    Morelli, Toni Lyn; DeLuca, William; Ellison, Colton; Jane, Stephen F.; Matthews, Stephen

    2015-01-01

    This chapter reviews the responses to climate change on the 367 Regional Species of Greatest Conservation Need (RSGCN) identified by the Northeast Fish and Wildlife Diversity Technical Committee (NEFWDTC), technical experts from states’ natural resource agencies (Appendix 3.1). These species were chosen based on their conservation status, listing in SWAPs, and the percentage of their range that occurs in the Northeast. The objectives of this chapter are to: summarize how regional biodiversity has already responded and is expected to respond to climate change; summarize information on specific RSGCN species responses to climate change to date and anticipated under future scenarios; characterize the greatest uncertainties about how biodiversity and RSGCN species will respond to climate change in the future; and highlight where other factors are expected to exacerbate the effects of climate change. This information was obtained through a systematic review of the peer-reviewed literature, primarily using the ISI Web of Knowledge to search for papers on each species related to “climate”, “temperature”, or “precipitation”. Although we undoubtedly missed some sources, the following allows us to review some of the ways climate change will affect regional species of conservation concern

  17. Genomic Organization of the Murine Miller–Dieker/Lissencephaly Region: Conservation of Linkage with the Human Region

    PubMed Central

    Hirotsune, Shinji; Pack, Svetlana D.; Chong, Samuel S.; Robbins, Christiane M.; Pavan, William J.; Ledbetter, David H.; Wynshaw-Boris, Anthony

    1997-01-01

    Several human syndromes are associated with haploinsufficiency of chromosomal regions secondary to microdeletions. Isolated lissencephaly sequence (ILS), a human developmental disease characterized by a smooth cerebral surface (classical lissencephaly) and microscopic evidence of incomplete neuronal migration, is often associated with small deletions or translocations at chromosome 17p13.3. Miller–Dieker syndrome (MDS) is associated with larger deletions of 17p13.3 and consists of classical lissencephaly with additional phenotypes including facial abnormalities. We have isolated the murine homologs of three genes located inside and outside the MDS region: Lis1, Mnt/Rox, and 14-3-3ε. These genes are all located on mouse chromosome 11B2, as determined by metaphase FISH, and the relative order and approximate gene distance was determined by interphase FISH analysis. The transcriptional orientation and intergenic distance of Lis1 and Mnt/Rox were ascertained by fragmentation analysis of a mouse yeast artificial chromosome containing both genes. To determine the distance and orientation of 14-3-3ε with respect to Lis1 and Mnt/Rox, we introduced a super-rare cutter site (VDE) that is unique in the mouse genome into 14-3-3ε by gene targeting. Using the introduced VDE site, the orientation of this gene was determined by pulsed field gel electrophoresis and Southern blot analysis. Our results demonstrate that the MDS region is conserved between human and mouse. This conservation of linkage suggests that the mouse can be used to model microdeletions that occur in ILS and MDS. PMID:9199935

  18. Strategic conservation planning for the Eastern North Carolina/Southeastern Virginia Strategic Habitat Conservation Team

    USGS Publications Warehouse

    Alexander-Vaughn, Louise B.; Collazo, Jaime A.; Drew, C. Ashton

    2014-01-01

    The Eastern North Carolina/Southeastern Virginia Strategic Habitat Conservation Team (ENCSEVA) is a partnership among local federal agencies and programs with a mission to apply Strategic Habitat Conservation to accomplish priority landscape-level conservation within its geographic region. ENCSEVA seeks to further landscape-scale conservation through collaboration with local partners. To accomplish this mission, ENCSEVA is developing a comprehensive Strategic Habitat Conservation Plan (Plan) to provide guidance for its members, partners, and collaborators by establishing mutual conservation goals, objectives, strategies, and metrics to gauge the success of conservation efforts. Identifying common goals allows the ENCSEVA team to develop strategies that leverage joint resources and are more likely to achieve desired impacts across the landscape. The Plan will also provide an approach for ENCSEVA to meet applied research needs (identify knowledge gaps), foster adaptive management principles, identify conservation priorities, prioritize threats (including potential impacts of climate change), and identify the required capacity to implement strategies to create more resilient landscapes. ENCSEVA seeks to support the overarching goals of the South Atlantic Landscape Conservation Cooperative (SALCC) and to provide scientific and technical support for conservation at landscape scales as well as inform the management of natural resources in response to shifts in climate, habitat fragmentation and loss, and other landscape-level challenges (South Atlantic LCC 2012). The ENCSEVA ecoregion encompasses the northern third of the SALCC geography and offers a unique opportunity to apply landscape conservation at multiple scales through the guidance of local conservation and natural resource management efforts and by reporting metrics that reflect the effectiveness of those efforts (Figure 1). The Environmental Decision Analysis Team, housed within the North Carolina Cooperative

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

    PubMed

    Ando, Amy W; Mallory, Mindy L

    2012-04-24

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

  20. Identification of conserved regions and residues within Hedgehog acyltransferase critical for palmitoylation of Sonic Hedgehog.

    PubMed

    Buglino, John A; Resh, Marilyn D

    2010-06-23

    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. 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 K(m) and V(max) for Shh and/or palmitoyl CoA, changes that likely explain the catalytic defects observed for these mutants. 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.

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

    PubMed

    Ahrens, Collin W; James, Elizabeth A

    2016-05-01

    Continued alterations to the Australian environment compromise the long-term viability of many plant species. We investigate the population genetics of Ptilotus macrocephalus, a perennial herb that occurs in 2 nationally endangered communities on the Victorian Volcanic Plain Bioregion (VVP), Australia, to answer key questions regarding regional differentiation and to guide conservation strategies. We evaluate genetic structure and diversity within and among 17 P. macrocephalus populations from 3 regions of southeastern Australia using 17 microsatellite markers developed de novo. Genetic structure was present in P. macrocephalus between the 3 regions but not at the population level. Environmental factors, namely temperature and precipitation, significantly explained differentiation between the North region and the other 2 regions indicating isolation by environment. Within regions, genetic structure currently shows a high level of gene flow and genetic variation. Our results suggest that within-region gene flow does not reflect current habitat fragmentation in southeastern Australia whereas temperature and precipitation are likely to be responsible for the differentiation detected among regions. Climate change may severely impact P. macrocephalus on the VVP and test its evolutionary resilience. We suggest taking a proactive conservation approach to improve long-term viability by sourcing material for restoration to assist gene flow to the VVP region to promote an increased adaptive capacity. © The American Genetic Association. 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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

    PubMed

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

    2005-05-01

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

  3. Human Variation in Short Regions Predisposed to Deep Evolutionary Conservation

    PubMed Central

    Loots, Gabriela G.; Ovcharenko, Ivan

    2010-01-01

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

  4. Opuntia in México: Identifying Priority Areas for Conserving Biodiversity in a Multi-Use Landscape

    PubMed Central

    Illoldi-Rangel, Patricia; Ciarleglio, Michael; Sheinvar, Leia; Linaje, Miguel; Sánchez-Cordero, Victor; Sarkar, Sahotra

    2012-01-01

    Background México is one of the world's centers of species diversity (richness) for Opuntia cacti. Yet, in spite of their economic and ecological importance, Opuntia species remain poorly studied and protected in México. Many of the species are sparsely but widely distributed across the landscape and are subject to a variety of human uses, so devising implementable conservation plans for them presents formidable difficulties. Multi–criteria analysis can be used to design a spatially coherent conservation area network while permitting sustainable human usage. Methods and Findings Species distribution models were created for 60 Opuntia species using MaxEnt. Targets of representation within conservation area networks were assigned at 100% for the geographically rarest species and 10% for the most common ones. Three different conservation plans were developed to represent the species within these networks using total area, shape, and connectivity as relevant criteria. Multi–criteria analysis and a metaheuristic adaptive tabu search algorithm were used to search for optimal solutions. The plans were built on the existing protected areas of México and prioritized additional areas for management for the persistence of Opuntia species. All plans required around one–third of México's total area to be prioritized for attention for Opuntia conservation, underscoring the implausibility of Opuntia conservation through traditional land reservation. Tabu search turned out to be both computationally tractable and easily implementable for search problems of this kind. Conclusions Opuntia conservation in México require the management of large areas of land for multiple uses. The multi-criteria analyses identified priority areas and organized them in large contiguous blocks that can be effectively managed. A high level of connectivity was established among the prioritized areas resulting in the enhancement of possible modes of plant dispersal as well as only a small number

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

    USGS Publications Warehouse

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

    2011-01-01

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

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

    PubMed Central

    Ando, Amy W.; Mallory, Mindy L.

    2012-01-01

    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

  7. Agricultural conservation practices and wetland ecosystem services in the wetland-rich Piedmont–Coastal Plain region

    Treesearch

    Diane De Steven; Richard Lowrance

    2011-01-01

    In the eastern U.S. Coastal Plain and Piedmont region, diverse inland wetlands (riverine, depressional, wet flats) have been impacted by or converted to agriculture. Farm Bill conservation practices that restore or enhance wetlands can return their ecological functions and services to the agricultural landscape. We review the extent of regional knowledge regarding the...

  8. Identifying regional opportunities for accelerated timber managemnet

    Treesearch

    David A. Gansner; Joseph E. Barnard; Samuel F. Gingrich; Samuel F. Gingrich

    1973-01-01

    Describes a procedure for identifying regional opportunities for accelerated timber management and demonstrates its application. Results provide a basis for rational choices among alternative management strategies and permit meaningful micro- and macro-evaluations of treatment response.

  9. A methodological approach to identify agro-biodiversity hotspots for priority in situ conservation of plant genetic resources

    PubMed Central

    Pacicco, Luca; Bodesmo, Mara; Torricelli, Renzo

    2018-01-01

    Agro-biodiversity is seriously threatened worldwide and strategies to preserve it are dramatically required. We propose here a methodological approach aimed to identify areas with a high level of agro-biodiversity in which to set or enhance in situ conservation of plant genetic resources. These areas are identified using three criteria: Presence of Landrace diversity, Presence of wild species and Agro-ecosystem ecological diversity. A Restrictive and an Additive prioritization strategy has been applied on the entire Italian territory and has resulted in establishing nationwide 53 and 197 agro-biodiversity hotspots respectively. At present the strategies can easily be applied at a European level and can be helpful to develop conservation strategies everywhere. PMID:29856765

  10. A Conserved Region in the F2 Subunit of Paramyxovirus Fusion Proteins Is Involved In Fusion Regulation▿

    PubMed Central

    Gardner, Amanda E.; Dutch, Rebecca E.

    2007-01-01

    Paramyxoviruses utilize both an attachment protein and a fusion (F) protein to drive virus-cell and cell-cell fusion. F exists functionally as a trimer of two disulfide-linked subunits: F1 and F2. Alignment and analysis of a set of paramyxovirus F protein sequences identified three conserved blocks (CB): one in the fusion peptide/heptad repeat A domain, known to play important roles in fusion promotion, one in the region between the heptad repeats of F1 (CBF1) (A. E. Gardner, K. L. Martin, and R. E. Dutch, Biochemistry 46:5094-5105, 2007), and one in the F2 subunit (CBF2). To analyze the functions of CBF2, alanine substitutions at conserved positions were created in both the simian virus 5 (SV5) and Hendra virus F proteins. A number of the CBF2 mutations resulted in folding and expression defects. However, the CBF2 mutants that were properly expressed and trafficked had altered fusion promotion activity. The Hendra virus CBF2 Y79A and P89A mutants showed significantly decreased levels of fusion, whereas the SV5 CBF2 I49A mutant exhibited greatly increased cell-cell fusion relative to that for wild-type F. Additional substitutions at SV5 F I49 suggest that both side chain volume and hydrophobicity at this position are important in the folding of the metastable, prefusion state and the subsequent triggering of membrane fusion. The recently published prefusogenic structure of parainfluenza virus 5/SV5 F (H. S. Yin et al., Nature 439:38-44, 2006) places CBF2 in direct contact with heptad repeat A. Our data therefore indicate that this conserved region plays a critical role in stabilizing the prefusion state, likely through interactions with heptad repeat A, and in triggering membrane fusion. PMID:17507474

  11. 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...

  12. The implications of drought and water conservation on the reuse of municipal wastewater: Recognizing impacts and identifying mitigation possibilities.

    PubMed

    Tran, Quynh K; Jassby, David; Schwabe, Kurt A

    2017-11-01

    As water agencies continue to investigate opportunities to increase resilience and local water supply reliability in the face of drought and rising water scarcity, water conservation strategies and the reuse of treated municipal wastewater are garnering significant attention and adoption. Yet a simple water balance thought experiment illustrates that drought, and the conservation strategies that are often enacted in response to it, both likely limit the role reuse may play in improving local water supply reliability. For instance, as a particular drought progresses and agencies enact water conservation measures to cope with drought, influent flows likely decrease while influent pollution concentrations increase, particularly salinity, which adversely affects wastewater treatment plant (WWTP) costs and effluent quality and flow. Consequently, downstream uses of this effluent, whether to maintain streamflow and quality, groundwater recharge, or irrigation may be impacted. This is unfortunate since reuse is often heralded as a drought-proof mechanism to increase resilience. The objectives of this paper are two-fold. First, we illustrate-using a case study from Southern California during its most recent drought- how drought and water conservation strategies combine to reduce influent flow and quality and, subsequently, effluent flow and quality. Second, we use a recently developed regional water reuse decision support model (RWRM) to highlight cost-effective strategies that can be implemented to mitigate the impacts of drought on effluent water quality. While the solutions we identify cannot increase the flow of influent or effluent coming into or out of a treatment plant, they can improve the value of the remaining effluent in a cost-effective manner that takes into account the characteristics of its demand, whether it be for landscaping, golf courses, agricultural irrigation, or surface water augmentation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Research priorities for conservation and natural resource management in Oceania's small-island developing states.

    PubMed

    Weeks, R; Adams, V M

    2018-02-01

    For conservation science to effectively inform management, research must focus on creating the scientific knowledge required to solve conservation problems. We identified research questions that, if answered, would increase the effectiveness of conservation and natural resource management practice and policy in Oceania's small-island developing states. We asked conservation professionals from academia, governmental, and nongovernmental organizations across the region to propose such questions and then identify which were of high priority in an online survey. We compared the high-priority questions with research questions identified globally and for other regions. Of 270 questions proposed by respondents, 38 were considered high priority, including: What are the highest priority areas for conservation in the face of increasing resource demand and climate change? How should marine protected areas be networked to account for connectivity and climate change? What are the most effective fisheries management policies that contribute to sustainable coral reef fisheries? High-priority questions related to the particular challenges of undertaking conservation on small-island developing states and the need for a research agenda that is responsive to the sociocultural context of Oceania. Research priorities for Oceania relative to elsewhere were broadly similar but differed in specific issues relevant to particular conservation contexts. These differences emphasize the importance of involving local practitioners in the identification of research priorities. Priorities were reasonably well aligned among sectoral groups. Only a few questions were widely considered answered, which may indicate a smaller-than-expected knowledge-action gap. We believe these questions can be used to strengthen research collaborations between scientists and practitioners working to further conservation and natural resource management in this region. © 2017 The Authors. Conservation Biology

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

    USGS Publications Warehouse

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

    2004-01-01

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

  15. Identifying appropriate protected areas for endangered fern species under climate change.

    PubMed

    Wang, Chun-Jing; Wan, Ji-Zhong; Zhang, Zhi-Xiang; Zhang, Gang-Min

    2016-01-01

    The management of protected areas (PAs) is widely used in the conservation of endangered plant species under climate change. However, studies that have identified appropriate PAs for endangered fern species are rare. To address this gap, we must develop a workflow to plan appropriate PAs for endangered fern species that will be further impacted by climate change. Here, we used endangered fern species in China as a case study, and we applied conservation planning software coupled with endangered fern species distribution data and distribution modeling to plan conservation areas with high priority protection needs under climate change. We identified appropriate PAs for endangered fern species under climate change based on the IUCN protected area categories (from Ia to VI) and planned additional PAs for endangered fern species. The high priority regions for protecting the endangered fern species were distributed throughout southern China. With decreasing temperature seasonality, the priority ranking of all endangered fern species is projected to increase in existing PAs. Accordingly, we need to establish conservation areas with low climate vulnerability in existing PAs and expand the conservation areas for endangered fern species in the high priority conservation regions.

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

    PubMed Central

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

    2011-01-01

    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

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

    PubMed Central

    2010-01-01

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

  18. Structural basis for recognition of the central conserved region of RSV G by neutralizing human antibodies.

    PubMed

    Jones, Harrison G; Ritschel, Tina; Pascual, Gabriel; Brakenhoff, Just P J; Keogh, Elissa; Furmanova-Hollenstein, Polina; Lanckacker, Ellen; Wadia, Jehangir S; Gilman, Morgan S A; Williamson, R Anthony; Roymans, Dirk; van 't Wout, Angélique B; Langedijk, Johannes P; McLellan, Jason S

    2018-03-01

    Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infections in infants and the elderly, and yet there remains no effective treatment or vaccine. The surface of the virion is decorated with the fusion glycoprotein (RSV F) and the attachment glycoprotein (RSV G), which binds to CX3CR1 on human airway epithelial cells to mediate viral attachment and subsequent infection. RSV G is a major target of the humoral immune response, and antibodies that target the central conserved region of G have been shown to neutralize both subtypes of RSV and to protect against severe RSV disease in animal models. However, the molecular underpinnings for antibody recognition of this region have remained unknown. Therefore, we isolated two human antibodies directed against the central conserved region of RSV G and demonstrated that they neutralize RSV infection of human bronchial epithelial cell cultures in the absence of complement. Moreover, the antibodies protected cotton rats from severe RSV disease. Both antibodies bound with high affinity to a secreted form of RSV G as well as to a peptide corresponding to the unglycosylated central conserved region. High-resolution crystal structures of each antibody in complex with the G peptide revealed two distinct conformational epitopes that require proper folding of the cystine noose located in the C-terminal part of the central conserved region. Comparison of these structures with the structure of fractalkine (CX3CL1) alone or in complex with a viral homolog of CX3CR1 (US28) suggests that RSV G would bind to CX3CR1 in a mode that is distinct from that of fractalkine. Collectively, these results build on recent studies demonstrating the importance of RSV G in antibody-mediated protection from severe RSV disease, and the structural information presented here should guide the development of new vaccines and antibody-based therapies for RSV.

  19. Structural basis for recognition of the central conserved region of RSV G by neutralizing human antibodies

    PubMed Central

    Jones, Harrison G.; Brakenhoff, Just P. J.; Furmanova-Hollenstein, Polina; Wadia, Jehangir S.; Gilman, Morgan S. A.; Roymans, Dirk

    2018-01-01

    Respiratory syncytial virus (RSV) is a major cause of severe lower respiratory tract infections in infants and the elderly, and yet there remains no effective treatment or vaccine. The surface of the virion is decorated with the fusion glycoprotein (RSV F) and the attachment glycoprotein (RSV G), which binds to CX3CR1 on human airway epithelial cells to mediate viral attachment and subsequent infection. RSV G is a major target of the humoral immune response, and antibodies that target the central conserved region of G have been shown to neutralize both subtypes of RSV and to protect against severe RSV disease in animal models. However, the molecular underpinnings for antibody recognition of this region have remained unknown. Therefore, we isolated two human antibodies directed against the central conserved region of RSV G and demonstrated that they neutralize RSV infection of human bronchial epithelial cell cultures in the absence of complement. Moreover, the antibodies protected cotton rats from severe RSV disease. Both antibodies bound with high affinity to a secreted form of RSV G as well as to a peptide corresponding to the unglycosylated central conserved region. High-resolution crystal structures of each antibody in complex with the G peptide revealed two distinct conformational epitopes that require proper folding of the cystine noose located in the C-terminal part of the central conserved region. Comparison of these structures with the structure of fractalkine (CX3CL1) alone or in complex with a viral homolog of CX3CR1 (US28) suggests that RSV G would bind to CX3CR1 in a mode that is distinct from that of fractalkine. Collectively, these results build on recent studies demonstrating the importance of RSV G in antibody-mediated protection from severe RSV disease, and the structural information presented here should guide the development of new vaccines and antibody-based therapies for RSV. PMID:29509814

  20. Close evolutionary relatedness among functionally distantly related members of the (alpha/beta)8-barrel glycosyl hydrolases suggested by the similarity of their fifth conserved sequence region.

    PubMed

    Janecek, S

    1995-12-11

    A short conserved sequence equivalent to the fifth conserved sequence region of alpha-amylases (173_LPDLD, Aspergillus oryzae alpha-amylase) comprising the calcium-ligand aspartate, Asp-175, was identified in the amino acid sequences of several members of the family of (alpha/beta)8-barrel glycosyl hydrolases. Despite the fact that the aspartate is not invariantly conserved, the stretch can be easily recognised in all sequences to be positioned 26-28 amino acid residues in front of the well-known catalytic aspartate (Asp-206, A. oryzae alpha-amylase) located in the beta 4-strand of the barrel. The identification of this region revealed remarkable similarities between some alpha-amylases (those from Bacillus megaterium, Bacillus subtilis and Dictyoglomus thermophilum) on the one hand and several different enzyme specificities (such as oligo-1,6-glucosidase, amylomaltase and neopullulanase, respectively) on the other hand. The most interesting example was offered by B. subtilis alpha-amylase and potato amylomaltase with the regions LYDWN and LYDWK, respectively. These observations support the idea that all members of the family of glycosyl hydrolases adopting the structure of the alpha-amylase-type (alpha/beta)8-barrel are mutually closely related and the strict evolutionary borders separating the individual enzyme specificities can be hardly defined.

  1. Global conservation model for a mushy region over a moving substrate

    NASA Astrophysics Data System (ADS)

    Kyselica, J.; Šimkanin, J.

    2018-03-01

    We study solidification over a cool substrate moving with a relative velocity with respect to the rest of the fluid. A mathematical model based on global conservation of solute is presented. The explicit solutions of the governing equations are found and analysed via the asymptotic methods. The assessment of how the boundary-layer flow influences the physical characteristics of the mushy region is given, together with the discussion of a possible connection with the solidification at the inner core boundary.

  2. Use of a Drosophila Genome-Wide Conserved Sequence Database to Identify Functionally Related cis-Regulatory Enhancers

    PubMed Central

    Brody, Thomas; Yavatkar, Amarendra S; Kuzin, Alexander; Kundu, Mukta; Tyson, Leonard J; Ross, Jermaine; Lin, Tzu-Yang; Lee, Chi-Hon; Awasaki, Takeshi; Lee, Tzumin; Odenwald, Ward F

    2012-01-01

    Background: Phylogenetic footprinting has revealed that cis-regulatory enhancers consist of conserved DNA sequence clusters (CSCs). Currently, there is no systematic approach for enhancer discovery and analysis that takes full-advantage of the sequence information within enhancer CSCs. Results: We have generated a Drosophila genome-wide database of conserved DNA consisting of >100,000 CSCs derived from EvoPrints spanning over 90% of the genome. cis-Decoder database search and alignment algorithms enable the discovery of functionally related enhancers. The program first identifies conserved repeat elements within an input enhancer and then searches the database for CSCs that score highly against the input CSC. Scoring is based on shared repeats as well as uniquely shared matches, and includes measures of the balance of shared elements, a diagnostic that has proven to be useful in predicting cis-regulatory function. To demonstrate the utility of these tools, a temporally-restricted CNS neuroblast enhancer was used to identify other functionally related enhancers and analyze their structural organization. Conclusions: cis-Decoder reveals that co-regulating enhancers consist of combinations of overlapping shared sequence elements, providing insights into the mode of integration of multiple regulating transcription factors. The database and accompanying algorithms should prove useful in the discovery and analysis of enhancers involved in any developmental process. Developmental Dynamics 241:169–189, 2012. © 2011 Wiley Periodicals, Inc. Key findings A genome-wide catalog of Drosophila conserved DNA sequence clusters. cis-Decoder discovers functionally related enhancers. Functionally related enhancers share balanced sequence element copy numbers. Many enhancers function during multiple phases of development. PMID:22174086

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

    PubMed

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

    2014-09-01

    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.

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

    PubMed Central

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

    2014-01-01

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

  5. 10 CFR 72.98 - Identifying regions around an ISFSI or MRS site.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... WASTE Siting Evaluation Factors § 72.98 Identifying regions around an ISFSI or MRS site. (a) The... ISFSI or MRS must be identified. (b) The potential regional impact due to the construction, operation or decommissioning of the ISFSI or MRS must be identified. The extent of regional impacts must be determined on the...

  6. 10 CFR 72.98 - Identifying regions around an ISFSI or MRS site.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... WASTE Siting Evaluation Factors § 72.98 Identifying regions around an ISFSI or MRS site. (a) The... ISFSI or MRS must be identified. (b) The potential regional impact due to the construction, operation or decommissioning of the ISFSI or MRS must be identified. The extent of regional impacts must be determined on the...

  7. Regional effects of agricultural conservation practices on nutrient transport

    Treesearch

    Anna Maria Garcia; Richard B. Alexander; Jeffrey G. Arnold; Lee Norfleet; Mike White; Dale M. Robertson; Gregory Schwarz

    2016-01-01

    The Conservation Effects Assessment Program (CEAP), initiated by USDA Natural Resources Conservation Service (NRCS), has the goal of quantifying the environmental benefits of agricultural conservation practices. As part of this effort, detailed farmer surveyswere compiled to document the adoption of conservation practices. Survey data showed that up to 38...

  8. In silico identification of functional regions in proteins.

    PubMed

    Nimrod, Guy; Glaser, Fabian; Steinberg, David; Ben-Tal, Nir; Pupko, Tal

    2005-06-01

    In silico prediction of functional regions on protein surfaces, i.e. sites of interaction with DNA, ligands, substrates and other proteins, is of utmost importance in various applications in the emerging fields of proteomics and structural genomics. When a sufficient number of homologs is found, powerful prediction schemes can be based on the observation that evolutionarily conserved regions are often functionally important, typically, only the principal functionally important region of the protein is detected, while secondary functional regions with weaker conservation signals are overlooked. Moreover, it is challenging to unambiguously identify the boundaries of the functional regions. We present a new methodology, called PatchFinder, that automatically identifies patches of conserved residues that are located in close proximity to each other on the protein surface. PatchFinder is based on the following steps: (1) Assignment of conservation scores to each amino acid position on the protein surface. (2) Assignment of a score to each putative patch, based on its likelihood to be functionally important. The patch of maximum likelihood is considered to be the main functionally important region, and the search is continued for non-overlapping patches of secondary importance. We examined the accuracy of the method using the IGPS enzyme, the SH2 domain and a benchmark set of 112 proteins. These examples demonstrated that PatchFinder is capable of identifying both the main and secondary functional patches. The PatchFinder program is available at: http://ashtoret.tau.ac.il/~nimrodg/

  9. Tissue-specific DNA methylation is conserved across human, mouse, and rat, and driven by primary sequence conservation.

    PubMed

    Zhou, Jia; Sears, Renee L; Xing, Xiaoyun; Zhang, Bo; Li, Daofeng; Rockweiler, Nicole B; Jang, Hyo Sik; Choudhary, Mayank N K; Lee, Hyung Joo; Lowdon, Rebecca F; Arand, Jason; Tabers, Brianne; Gu, C Charles; Cicero, Theodore J; Wang, Ting

    2017-09-12

    Uncovering mechanisms of epigenome evolution is an essential step towards understanding the evolution of different cellular phenotypes. While studies have confirmed DNA methylation as a conserved epigenetic mechanism in mammalian development, little is known about the conservation of tissue-specific genome-wide DNA methylation patterns. Using a comparative epigenomics approach, we identified and compared the tissue-specific DNA methylation patterns of rat against those of mouse and human across three shared tissue types. We confirmed that tissue-specific differentially methylated regions are strongly associated with tissue-specific regulatory elements. Comparisons between species revealed that at a minimum 11-37% of tissue-specific DNA methylation patterns are conserved, a phenomenon that we define as epigenetic conservation. Conserved DNA methylation is accompanied by conservation of other epigenetic marks including histone modifications. Although a significant amount of locus-specific methylation is epigenetically conserved, the majority of tissue-specific DNA methylation is not conserved across the species and tissue types that we investigated. Examination of the genetic underpinning of epigenetic conservation suggests that primary sequence conservation is a driving force behind epigenetic conservation. In contrast, evolutionary dynamics of tissue-specific DNA methylation are best explained by the maintenance or turnover of binding sites for important transcription factors. Our study extends the limited literature of comparative epigenomics and suggests a new paradigm for epigenetic conservation without genetic conservation through analysis of transcription factor binding sites.

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

    PubMed

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

    2013-06-01

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

  11. Identifying local-scale wilderness for on-ground conservation actions within a global biodiversity hotspot

    PubMed Central

    Lin, Shiwei; Wu, Ruidong; Hua, Chaolang; Ma, Jianzhong; Wang, Wenli; Yang, Feiling; Wang, Junjun

    2016-01-01

    Protecting wilderness areas (WAs) is a crucial proactive approach to sustain biodiversity. However, studies identifying local-scale WAs for on-ground conservation efforts are still very limited. This paper investigated the spatial patterns of wilderness in a global biodiversity hotspot – Three Parallel Rivers Region (TPRR) in southwest China. Wilderness was classified into levels 1 to 10 based on a cluster analysis of five indicators, namely human population density, naturalness, fragmentation, remoteness, and ruggedness. Only patches characterized by wilderness level 1 and ≥1.0 km2 were considered WAs. The wilderness levels in the northwest were significantly higher than those in the southeast, and clearly increased with the increase in elevation. The WAs covered approximately 25% of TPRR’s land, 89.3% of which was located in the >3,000 m elevation zones. WAs consisted of 20 vegetation types, among which temperate conifer forest, cold temperate shrub and alpine ecosystems covered 79.4% of WAs’ total area. Most WAs were still not protected yet by existing reserves. Topography and human activities are the primary influencing factors on the spatial patterns of wilderness. We suggest establishing strictly protected reserves for most large WAs, while some sustainable management approaches might be more optimal solutions for many highly fragmented small WAs. PMID:27181186

  12. Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5′-phosphate-dependent enzymes

    PubMed Central

    Paiardini, Alessandro; Bossa, Francesco; Pascarella, Stefano

    2004-01-01

    The wealth of biological information provided by structural and genomic projects opens new prospects of understanding life and evolution at the molecular level. In this work, it is shown how computational approaches can be exploited to pinpoint protein structural features that remain invariant upon long evolutionary periods in the fold-type I, PLP-dependent enzymes. A nonredundant set of 23 superposed crystallographic structures belonging to this superfamily was built. Members of this family typically display high-structural conservation despite low-sequence identity. For each structure, a multiple-sequence alignment of orthologous sequences was obtained, and the 23 alignments were merged using the structural information to obtain a comprehensive multiple alignment of 921 sequences of fold-type I enzymes. The structurally conserved regions (SCRs), the evolutionarily conserved residues, and the conserved hydrophobic contacts (CHCs) were extracted from this data set, using both sequence and structural information. The results of this study identified a structural pattern of hydrophobic contacts shared by all of the superfamily members of fold-type I enzymes and involved in native interactions. This profile highlights the presence of a nucleus for this fold, in which residues participating in the most conserved native interactions exhibit preferential evolutionary conservation, that correlates significantly (r = 0.70) with the extent of mean hydrophobic contact value of their apolar fraction. PMID:15498941

  13. Priority Questions and Horizon Scanning for Conservation: A Comparative Study

    PubMed Central

    Kark, Salit; Sutherland, William J.; Shanas, Uri; Klass, Keren; Achisar, Hila; Dayan, Tamar; Gavrieli, Yael; Justo-Hanani, Ronit; Mandelik, Yael; Orion, Nir; Pargament, David; Portman, Michelle; Reisman-Berman, Orna; Safriel, Uriel N.; Schaffer, Gad; Steiner, Noa; Tauber, Israel; Levin, Noam

    2016-01-01

    Several projects aimed at identifying priority issues for conservation with high relevance to policy have recently been completed in several countries. Two major types of projects have been undertaken, aimed at identifying (i) policy-relevant questions most imperative to conservation and (ii) horizon scanning topics, defined as emerging issues that are expected to have substantial implications for biodiversity conservation and policy in the future. Here, we provide the first overview of the outcomes of biodiversity and conservation-oriented projects recently completed around the world using this framework. We also include the results of the first questions and horizon scanning project completed for a Mediterranean country. Overall, the outcomes of the different projects undertaken (at the global scale, in the UK, US, Canada, Switzerland and in Israel) were strongly correlated in terms of the proportion of questions and/or horizon scanning topics selected when comparing different topic areas. However, some major differences were found across regions. There was large variation among regions in the percentage of proactive (i.e. action and response oriented) versus descriptive (non-response oriented) priority questions and in the emphasis given to socio-political issues. Substantial differences were also found when comparing outcomes of priority questions versus horizon scanning projects undertaken for the same region. For example, issues related to climate change, human demography and marine ecosystems received higher priority as horizon scanning topics, while ecosystem services were more emphasized as current priority questions. We suggest that future initiatives aimed at identifying priority conservation questions and horizon scanning topics should allow simultaneous identification of both current and future priority issues, as presented here for the first time. We propose that further emphasis on social-political issues should be explicitly integrated into future

  14. 40 CFR 255.24 - Procedure for identifying interstate regions.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Procedure for identifying interstate regions. 255.24 Section 255.24 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) SOLID... recommendation, the local consensus, or a neighboring Governor's recommendation is that an interstate region be...

  15. Species of conservation concern and environmental stressors: Local, regional and global effects [Chapter 6] (Executive Summary)

    Treesearch

    Steven M. Ostoja; Matthew L. Brooks; Jeanne C. Chambers; Burton K. Pendleton

    2013-01-01

    Southern Nevada’s unique landscapes and landforms provide habitat for a diversity of plant and wildlife species of conservation concern including many locally and regionally endemic species. The high population density and urbanization of the Las Vegas metropolitan area is the source of many local and regional stressors that affect these species and their habitats:...

  16. THE THREATENED AND THE IRREPLACEABLE: IDENTIFYING AREAS FOR THE CONSERVATION OF FAUNAL SPECIES DIVERSITY IN THE MIDDLE-ATLANTIC REGION OF THE UNITED STATES

    EPA Science Inventory

    One fundamental step in conservation planning involves determining where to concentrate efforts to protect conservation targets. Here we demonstrate an approach to prioritizing areas based on both species composition and potential threats facing the species. First, we determine...

  17. Nucleotide sequence determination of guinea-pig casein B mRNA reveals homology with bovine and rat alpha s1 caseins and conservation of the non-coding regions of the mRNA.

    PubMed Central

    Hall, L; Laird, J E; Craig, R K

    1984-01-01

    Nucleotide sequence analysis of cloned guinea-pig casein B cDNA sequences has identified two casein B variants related to the bovine and rat alpha s1 caseins. Amino acid homology was largely confined to the known bovine or predicted rat phosphorylation sites and within the 'signal' precursor sequence. Comparison of the deduced nucleotide sequence of the guinea-pig and rat alpha s1 casein mRNA species showed greater sequence conservation in the non-coding than in the coding regions, suggesting a functional and possibly regulatory role for the non-coding regions of casein mRNA. The results provide insight into the evolution of the casein genes, and raise questions as to the role of conserved nucleotide sequences within the non-coding regions of mRNA species. Images Fig. 1. PMID:6548375

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

    PubMed

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

    2011-08-01

    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. Copyright © 2011 Elsevier Ltd. All rights reserved.

  19. Stakeholder-led science: engaging resource managers to identify science needs for long-term management of floodplain conservation lands

    USGS Publications Warehouse

    Bouska, Kristin L.; Lindner, Garth; Paukert, Craig P.; Jacobson, Robert B.

    2016-01-01

    Floodplains pose challenges to managers of conservation lands because of constantly changing interactions with their rivers. Although scientific knowledge and understanding of the dynamics and drivers of river-floodplain systems can provide guidance to floodplain managers, the scientific process often occurs in isolation from management. Further, communication barriers between scientists and managers can be obstacles to appropriate application of scientific knowledge. With the coproduction of science in mind, our objectives were the following: (1) to document management priorities of floodplain conservation lands, and (2) identify science needs required to better manage the identified management priorities under nonstationary conditions, i.e., climate change, through stakeholder queries and interactions. We conducted an online survey with 80 resource managers of floodplain conservation lands along the Upper and Middle Mississippi River and Lower Missouri River, USA, to evaluate management priority, management intensity, and available scientific information for management objectives and conservation targets. Management objectives with the least information available relative to priority included controlling invasive species, maintaining respectful relationships with neighbors, and managing native, nongame species. Conservation targets with the least information available to manage relative to management priority included pollinators, marsh birds, reptiles, and shore birds. A follow-up workshop and survey focused on clarifying science needs to achieve management objectives under nonstationary conditions. Managers agreed that metrics of inundation, including depth and extent of inundation, and frequency, duration, and timing of inundation would be the most useful metrics for management of floodplain conservation lands with multiple objectives. This assessment provides guidance for developing relevant and accessible science products to inform management of highly

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

    PubMed Central

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

    2015-01-01

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

  1. Bird conservation would complement landslide prevention in the Central Andes of Colombia.

    PubMed

    Ocampo-Peñuela, Natalia; Pimm, Stuart L

    2015-01-01

    Conservation and restoration priorities often focus on separate ecosystem problems. Inspired by the November 11th (2011) landslide event near Manizales, and the current poor results of Colombia's Article 111 of Law 99 of 1993 as a conservation measure in this country, we set out to prioritize conservation and restoration areas where landslide prevention would complement bird conservation in the Central Andes. This area is one of the most biodiverse places on Earth, but also one of the most threatened. Using the case of the Rio Blanco Reserve, near Manizales, we identified areas for conservation where endemic and small-range bird diversity was high, and where landslide risk was also high. We further prioritized restoration areas by overlapping these conservation priorities with a forest cover map. Restoring forests in bare areas of high landslide risk and important bird diversity yields benefits for both biodiversity and people. We developed a simple landslide susceptibility model using slope, forest cover, aspect, and stream proximity. Using publicly available bird range maps, refined by elevation, we mapped concentrations of endemic and small-range bird species. We identified 1.54 km(2) of potential restoration areas in the Rio Blanco Reserve, and 886 km(2) in the Central Andes region. By prioritizing these areas, we facilitate the application of Article 111 which requires local and regional governments to invest in land purchases for the conservation of watersheds.

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

    NASA Astrophysics Data System (ADS)

    Hogue, T. S.

    2015-12-01

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

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

    USGS Publications Warehouse

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

    2016-01-01

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

  4. Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection

    PubMed Central

    Maciag, Joseph J.; Mackenzie, Sarah H.; Tucker, Matthew B.; Schipper, Joshua L.; Swartz, Paul; Clark, A. Clay

    2016-01-01

    The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. The data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection. PMID:27681633

  5. Tunable allosteric library of caspase-3 identifies coupling between conserved water molecules and conformational selection.

    PubMed

    Maciag, Joseph J; Mackenzie, Sarah H; Tucker, Matthew B; Schipper, Joshua L; Swartz, Paul; Clark, A Clay

    2016-10-11

    The native ensemble of caspases is described globally by a complex energy landscape where the binding of substrate selects for the active conformation, whereas targeting an allosteric site in the dimer interface selects an inactive conformation that contains disordered active-site loops. Mutations and posttranslational modifications stabilize high-energy inactive conformations, with mostly formed, but distorted, active sites. To examine the interconversion of active and inactive states in the ensemble, we used detection of related solvent positions to analyze 4,995 waters in 15 high-resolution (<2.0 Å) structures of wild-type caspase-3, resulting in 450 clusters with the most highly conserved set containing 145 water molecules. The data show that regions of the protein that contact the conserved waters also correspond to sites of posttranslational modifications, suggesting that the conserved waters are an integral part of allosteric mechanisms. To test this hypothesis, we created a library of 19 caspase-3 variants through saturation mutagenesis in a single position of the allosteric site of the dimer interface, and we show that the enzyme activity varies by more than four orders of magnitude. Altogether, our database consists of 37 high-resolution structures of caspase-3 variants, and we demonstrate that the decrease in activity correlates with a loss of conserved water molecules. The data show that the activity of caspase-3 can be fine-tuned through globally desolvating the active conformation within the native ensemble, providing a mechanism for cells to repartition the ensemble and thus fine-tune activity through conformational selection.

  6. Bat Accelerated Regions Identify a Bat Forelimb Specific Enhancer in the HoxD Locus

    PubMed Central

    Mason, Mandy K.; VanderMeer, Julia E.; Zhao, Jingjing; Eckalbar, Walter L.; Logan, Malcolm; Illing, Nicola; Pollard, Katherine S.; Ahituv, Nadav

    2016-01-01

    The molecular events leading to the development of the bat wing remain largely unknown, and are thought to be caused, in part, by changes in gene expression during limb development. These expression changes could be instigated by variations in gene regulatory enhancers. Here, we used a comparative genomics approach to identify regions that evolved rapidly in the bat ancestor, but are highly conserved in other vertebrates. We discovered 166 bat accelerated regions (BARs) that overlap H3K27ac and p300 ChIP-seq peaks in developing mouse limbs. Using a mouse enhancer assay, we show that five Myotis lucifugus BARs drive gene expression in the developing mouse limb, with the majority showing differential enhancer activity compared to the mouse orthologous BAR sequences. These include BAR116, which is located telomeric to the HoxD cluster and had robust forelimb expression for the M. lucifugus sequence and no activity for the mouse sequence at embryonic day 12.5. Developing limb expression analysis of Hoxd10-Hoxd13 in Miniopterus natalensis bats showed a high-forelimb weak-hindlimb expression for Hoxd10-Hoxd11, similar to the expression trend observed for M. lucifugus BAR116 in mice, suggesting that it could be involved in the regulation of the bat HoxD complex. Combined, our results highlight novel regulatory regions that could be instrumental for the morphological differences leading to the development of the bat wing. PMID:27019019

  7. ChIP-seq Identification of Weakly Conserved Heart Enhancers

    PubMed Central

    Blow, Matthew J.; McCulley, David J.; Li, Zirong; Zhang, Tao; Akiyama, Jennifer A.; Holt, Amy; Plajzer-Frick, Ingrid; Shoukry, Malak; Wright, Crystal; Chen, Feng; Afzal, Veena; Bristow, James; Ren, Bing; Black, Brian L.; Rubin, Edward M.; Visel, Axel; Pennacchio, Len A.

    2011-01-01

    Accurate control of tissue-specific gene expression plays a pivotal role in heart development, but few cardiac transcriptional enhancers have thus far been identified. Extreme non-coding sequence conservation successfully predicts enhancers active in many tissues, but fails to identify substantial numbers of heart enhancers. Here we used ChIP-seq with the enhancer-associated protein p300 from mouse embryonic day 11.5 heart tissue to identify over three thousand candidate heart enhancers genome-wide. Compared to other tissues studied at this time-point, most candidate heart enhancers are less deeply conserved in vertebrate evolution. Nevertheless, the testing of 130 candidate regions in a transgenic mouse assay revealed that most of them reproducibly function as enhancers active in the heart, irrespective of their degree of evolutionary constraint. These results provide evidence for a large population of poorly conserved heart enhancers and suggest that the evolutionary constraint of embryonic enhancers can vary depending on tissue type. PMID:20729851

  8. Role of Tibetan Buddhist monasteries in snow leopard conservation.

    PubMed

    Li, Juan; Wang, Dajun; Yin, Hang; Zhaxi, Duojie; Jiagong, Zhala; Schaller, George B; Mishra, Charudutt; McCarthy, Thomas M; Wang, Hao; Wu, Lan; Xiao, Lingyun; Basang, Lamao; Zhang, Yuguang; Zhou, Yunyun; Lu, Zhi

    2014-02-01

    The snow leopard (Panthera uncia) inhabits the rugged mountains in 12 countries of Central Asia, including the Tibetan Plateau. Due to poaching, decreased abundance of prey, and habitat degradation, it was listed as endangered by the International Union for Conservation of Nature in 1972. Current conservation strategies, including nature reserves and incentive programs, have limited capacities to protect snow leopards. We investigated the role of Tibetan Buddhist monasteries in snow leopard conservation in the Sanjiangyuan region in China's Qinghai Province on the Tibetan Plateau. From 2009 to 2011, we systematically surveyed snow leopards in the Sanjiangyuan region. We used the MaxEnt model to determine the relation of their presence to environmental variables (e.g., elevation, ruggedness) and to predict snow leopard distribution. Model results showed 89,602 km(2) of snow leopard habitat in the Sanjiangyuan region, of which 7674 km(2) lay within Sanjiangyuan Nature Reserve's core zones. We analyzed the spatial relation between snow leopard habitat and Buddhist monasteries and found that 46% of monasteries were located in snow leopard habitat and 90% were within 5 km of snow leopard habitat. The 336 monasteries in the Sanjiangyuan region could protect more snow leopard habitat (8342 km(2) ) through social norms and active patrols than the nature reserve's core zones. We conducted 144 household interviews to identify local herders' attitudes and behavior toward snow leopards and other wildlife. Most local herders claimed that they did not kill wildlife, and 42% said they did not kill wildlife because it was a sin in Buddhism. Our results indicate monasteries play an important role in snow leopard conservation. Monastery-based snow leopard conservation could be extended to other Tibetan Buddhist regions that in total would encompass about 80% of the global range of snow leopards. © 2013 Society for Conservation Biology.

  9. Comparative sequence analysis of a region on human chromosome 13q14, frequently deleted in B-cell chronic lymphocytic leukemia, and its homologous region on mouse chromosome 14.

    PubMed

    Kapanadze, B; Makeeva, N; Corcoran, M; Jareborg, N; Hammarsund, M; Baranova, A; Zabarovsky, E; Vorontsova, O; Merup, M; Gahrton, G; Jansson, M; Yankovsky, N; Einhorn, S; Oscier, D; Grandér, D; Sangfelt, O

    2000-12-15

    Previous studies have indicated the presence of a putative tumor suppressor gene on human chromosome 13q14, commonly deleted in patients with B-cell chronic lymphocytic leukemia (B-CLL). We have recently identified a minimally deleted region encompassing parts of two adjacent genes, termed LEU1 and LEU2 (leukemia-associated genes 1 and 2), and several additional transcripts. In addition, 50 kb centromeric to this region we have identified another gene, LEU5/RFP2. To elucidate further the complex genomic organization of this region, we have identified, mapped, and sequenced the homologous region in the mouse. Fluorescence in situ hybridization analysis demonstrated that the region maps to mouse chromosome 14. The overall organization and gene order in this region were found to be highly conserved in the mouse. Sequence comparison between the human deletion hotspot region and its homologous mouse region revealed a high degree of sequence conservation with an overall score of 74%. However, our data also show that in terms of transcribed sequences, only two of those, human LEU2 and LEU5/RFP2, are clearly conserved, strengthening the case for these genes as putative candidate B-CLL tumor suppressor genes.

  10. All Conservation Opportunity Areas (ECO.RES.ALL_OP_AREAS)

    EPA Pesticide Factsheets

    The All_OP_Areas GIS layer are all the Conservation Opportunity Areas identified by MoRAP (produced for EPA Region 7). They designate areas with potential for forest, grassland and forest/grassland mosaic conservation. These are areas of natural or semi-natural forest land cover that are at least 75 meters away from roads and away from patch edges. OAs were modeled by creating distance grids using the National Land Cover Database and the Census Bureau's TIGER roads files.

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

    PubMed

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

    2013-04-01

    Fire influences the distribution of fauna in terrestrial biomes throughout the world. Use of fire to achieve a mosaic of vegetation in different stages of succession after burning (i.e., patch-mosaic burning) is a dominant conservation practice in many regions. Despite this, knowledge of how the spatial attributes of vegetation mosaics created by fire affect fauna is extremely scarce, and it is unclear what kind of mosaic land managers should aim to achieve. We selected 28 landscapes (each 12.6 km(2) ) that varied in the spatial extent and diversity of vegetation succession after fire in a 104,000 km(2) area in the semiarid region of southeastern Australia. We surveyed for reptiles at 280 sites nested within the 28 landscapes. The landscape-level occurrence of 9 of the 22 species modeled was associated with the spatial extent of vegetation age classes created by fire. Biogeographic context and the extent of a vegetation type influenced 7 and 4 species, respectively. No species were associated with the diversity of vegetation ages within a landscape. Negative relations between reptile occurrence and both extent of recently burned vegetation (≤10 years postfire, n = 6) and long unburned vegetation (>35 years postfire, n = 4) suggested that a coarse-grained mosaic of areas (e.g. >1000 ha) of midsuccessional vegetation (11-35 years postfire) may support the fire-sensitive reptile species we modeled. This age class coincides with a peak in spinifex cover, a keystone structure for reptiles in semiarid and arid Australia. Maintaining over the long term a coarse-grained mosaic of large areas of midsuccessional vegetation in mallee ecosystems will need to be balanced against the short-term negative effects of large fires on many reptile species and a documented preference by species from other taxonomic groups, particularly birds, for older vegetation. © 2012 Society for Conservation Biology.

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

    USGS Publications Warehouse

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

    1999-01-01

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

  13. Identifying Priority Areas for Conservation: A Global Assessment for Forest-Dependent Birds

    PubMed Central

    Buchanan, Graeme M.; Donald, Paul F.; Butchart, Stuart H. M.

    2011-01-01

    Limited resources are available to address the world's growing environmental problems, requiring conservationists to identify priority sites for action. Using new distribution maps for all of the world's forest-dependent birds (60.6% of all bird species), we quantify the contribution of remaining forest to conserving global avian biodiversity. For each of the world's partly or wholly forested 5-km cells, we estimated an impact score of its contribution to the distribution of all the forest bird species estimated to occur within it, and so is proportional to the impact on the conservation status of the world's forest-dependent birds were the forest it contains lost. The distribution of scores was highly skewed, a very small proportion of cells having scores several orders of magnitude above the global mean. Ecoregions containing the highest values of this score included relatively species-poor islands such as Hawaii and Palau, the relatively species-rich islands of Indonesia and the Philippines, and the megadiverse Atlantic Forests and northern Andes of South America. Ecoregions with high impact scores and high deforestation rates (2000–2005) included montane forests in Cameroon and the Eastern Arc of Tanzania, although deforestation data were not available for all ecoregions. Ecoregions with high impact scores, high rates of recent deforestation and low coverage by the protected area network included Indonesia's Seram rain forests and the moist forests of Trinidad and Tobago. Key sites in these ecoregions represent some of the most urgent priorities for expansion of the global protected areas network to meet Convention on Biological Diversity targets to increase the proportion of land formally protected to 17% by 2020. Areas with high impact scores, rapid deforestation, low protection and high carbon storage values may represent significant opportunities for both biodiversity conservation and climate change mitigation, for example through Reducing Emissions from

  14. Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans.

    PubMed

    Awan, Ali R; Manfredo, Amanda; Pleiss, Jeffrey A

    2013-07-30

    Alternative splicing is a potent regulator of gene expression that vastly increases proteomic diversity in multicellular eukaryotes and is associated with organismal complexity. Although alternative splicing is widespread in vertebrates, little is known about the evolutionary origins of this process, in part because of the absence of phylogenetically conserved events that cross major eukaryotic clades. Here we describe a lariat-sequencing approach, which offers high sensitivity for detecting splicing events, and its application to the unicellular fungus, Schizosaccharomyces pombe, an organism that shares many of the hallmarks of alternative splicing in mammalian systems but for which no previous examples of exon-skipping had been demonstrated. Over 200 previously unannotated splicing events were identified, including examples of regulated alternative splicing. Remarkably, an evolutionary analysis of four of the exons identified here as subject to skipping in S. pombe reveals high sequence conservation and perfect length conservation with their homologs in scores of plants, animals, and fungi. Moreover, alternative splicing of two of these exons have been documented in multiple vertebrate organisms, making these the first demonstrations of identical alternative-splicing patterns in species that are separated by over 1 billion y of evolution.

  15. 10 CFR 72.98 - Identifying regions around an ISFSI or MRS site.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... regional extent of external phenomena, man-made or natural, that are used as a basis for the design of the ISFSI or MRS must be identified. (b) The potential regional impact due to the construction, operation or decommissioning of the ISFSI or MRS must be identified. The extent of regional impacts must be determined on the...

  16. 10 CFR 72.98 - Identifying regions around an ISFSI or MRS site.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... regional extent of external phenomena, man-made or natural, that are used as a basis for the design of the ISFSI or MRS must be identified. (b) The potential regional impact due to the construction, operation or decommissioning of the ISFSI or MRS must be identified. The extent of regional impacts must be determined on the...

  17. 10 CFR 72.98 - Identifying regions around an ISFSI or MRS site.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... regional extent of external phenomena, man-made or natural, that are used as a basis for the design of the ISFSI or MRS must be identified. (b) The potential regional impact due to the construction, operation or decommissioning of the ISFSI or MRS must be identified. The extent of regional impacts must be determined on the...

  18. Arid Green Infrastructure for Water Control and Conservation ...

    EPA Pesticide Factsheets

    Green infrastructure is an approach to managing wet weather flows using systems and practices that mimic natural processes. It is designed to manage stormwater as close to its source as possible and protect the quality of receiving waters. Although most green infrastructure practices were first developed in temperate climates, green infrastructure also can be a cost-effective approach to stormwater management and water conservation in arid and semi-arid regions, such as those found in the western and southwestern United States. Green infrastructure practices can be applied at the site, neighborhood and watershed scales. In addition to water management and conservation, implementing green infrastructure confers many social and economic benefits and can address issues of environmental justice. The U.S. Environmental Protection Agency (EPA) commissioned a literature review to identify the state-of-the science practices dealing with water control and conservation in arid and semi-arid regions, with emphasis on these regions in the United States. The search focused on stormwater control measures or practices that slow, capture, treat, infiltrate and/or store runoff at its source (i.e., green infrastructure). The material in Chapters 1 through 3 provides background to EPA’s current activities related to the application of green infrastructure practices in arid and semi-arid regions. An introduction to the topic of green infrastructure in arid and semi-arid regions i

  19. Bird conservation would complement landslide prevention in the Central Andes of Colombia

    PubMed Central

    Ocampo-Peñuela, Natalia

    2015-01-01

    Conservation and restoration priorities often focus on separate ecosystem problems. Inspired by the November 11th (2011) landslide event near Manizales, and the current poor results of Colombia’s Article 111 of Law 99 of 1993 as a conservation measure in this country, we set out to prioritize conservation and restoration areas where landslide prevention would complement bird conservation in the Central Andes. This area is one of the most biodiverse places on Earth, but also one of the most threatened. Using the case of the Rio Blanco Reserve, near Manizales, we identified areas for conservation where endemic and small-range bird diversity was high, and where landslide risk was also high. We further prioritized restoration areas by overlapping these conservation priorities with a forest cover map. Restoring forests in bare areas of high landslide risk and important bird diversity yields benefits for both biodiversity and people. We developed a simple landslide susceptibility model using slope, forest cover, aspect, and stream proximity. Using publicly available bird range maps, refined by elevation, we mapped concentrations of endemic and small-range bird species. We identified 1.54 km2 of potential restoration areas in the Rio Blanco Reserve, and 886 km2 in the Central Andes region. By prioritizing these areas, we facilitate the application of Article 111 which requires local and regional governments to invest in land purchases for the conservation of watersheds. PMID:25737819

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

    USGS Publications Warehouse

    Cartwright, Jennifer M.; Wolfe, William J.

    2016-08-11

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

  1. Small RNA analysis in Petunia hybrida identifies unusual tissue-specific expression patterns of conserved miRNAs and of a 24mer RNA

    PubMed Central

    Tedder, Philip; Zubko, Elena; Westhead, David R.; Meyer, Peter

    2009-01-01

    Two pools of small RNAs were cloned from inflorescences of Petunia hybrida using a 5′-ligation dependent and a 5′-ligation independent approach. The two libraries were integrated into a public website that allows the screening of individual sequences against 359,769 unique clones. The library contains 15 clones with 100% identity and 53 clones with one mismatch to miRNAs described for other plant species. For two conserved miRNAs, miR159 and miR390, we find clear differences in tissue-specific distribution, compared with other species. This shows that evolutionary conservation of miRNA sequences does not necessarily include a conservation of the miRNA expression profile. Almost 60% of all clones in the database are 24-nucleotide clones. In accordance with the role of 24mers in marking repetitive regions, we find them distributed across retroviral and transposable element sequences but other 24mers map to promoter regions and to different transcript regions. For one target region we observe tissue-specific variation of matching 24mers, which demonstrates that, as for 21mers, 24mer concentrations are not necessarily identical in different tissues. Asymmetric distribution of a putative novel miRNA in the two libraries suggests that the cloning method can be selective for the representation of certain small RNAs in a collection. PMID:19369427

  2. IDENTIFYING IONIZED REGIONS IN NOISY REDSHIFTED 21 cm DATA SETS

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Malloy, Matthew; Lidz, Adam, E-mail: mattma@sas.upenn.edu

    One of the most promising approaches for studying reionization is to use the redshifted 21 cm line. Early generations of redshifted 21 cm surveys will not, however, have the sensitivity to make detailed maps of the reionization process, and will instead focus on statistical measurements. Here, we show that it may nonetheless be possible to directly identify ionized regions in upcoming data sets by applying suitable filters to the noisy data. The locations of prominent minima in the filtered data correspond well with the positions of ionized regions. In particular, we corrupt semi-numeric simulations of the redshifted 21 cm signalmore » during reionization with thermal noise at the level expected for a 500 antenna tile version of the Murchison Widefield Array (MWA), and mimic the degrading effects of foreground cleaning. Using a matched filter technique, we find that the MWA should be able to directly identify ionized regions despite the large thermal noise. In a plausible fiducial model in which {approx}20% of the volume of the universe is neutral at z {approx} 7, we find that a 500-tile MWA may directly identify as many as {approx}150 ionized regions in a 6 MHz portion of its survey volume and roughly determine the size of each of these regions. This may, in turn, allow interesting multi-wavelength follow-up observations, comparing galaxy properties inside and outside of ionized regions. We discuss how the optimal configuration of radio antenna tiles for detecting ionized regions with a matched filter technique differs from the optimal design for measuring power spectra. These considerations have potentially important implications for the design of future redshifted 21 cm surveys.« less

  3. Potent influenza A virus entry inhibitors targeting a conserved region of hemagglutinin.

    PubMed

    Lin, Dongguo; Luo, Yinzhu; Yang, Guang; Li, Fangfang; Xie, Xiangkun; Chen, Daiwei; He, Lifang; Wang, Jingyu; Ye, Chunfeng; Lu, Shengsheng; Lv, Lin; Liu, Shuwen; He, Jian

    2017-11-15

    Influenza A viruses (IAVs) induce acute respiratory disease and cause significant morbidity and mortality throughout the world. With the emergence of drug-resistant viral strains, new and effective anti-IAV drugs with different modes of action are urgently needed. In this study, by conjugating cholesterol to the N-terminus of the short peptide KKWK, a lipopeptide named S-KKWK was created. The anti-IAV test indicated that S-KKWK and its derivatives displayed potent antiviral activities against a broad variety of influenza A viral strains including oseltamivir-resistant strains and clinically relevant isolates with IC 50 values ranging from 0.7 to 3.0µM. An extensive mechanistic study showed that these peptides functioned as viral "entry blockers" by inhibiting the conformational rearrangements of HA2 subunit, thereby interrupting the fusion of virus-host cell membranes. Significantly, a computer-aided docking simulation and protein sequence alignment identified conserved residues in the stem region of HA2 as the possible binding site of S-KKWK, which may be employed as a potential drug target for designing anti-IAVs with a broad-spectrum of activity. By targeting this region, a potent anti-IAV agent was subsequently created. In addition, the anti-IAV activity of S-KKWK was assessed by experiments with influenza A virus-infected mice, in which S-KKWK reduced the mortality of infected animals and extended survival time significantly. Overall, in addition to providing a strategy for designing broad-spectrum anti-IAV agents, these results indicate that S-KKWK and its derivatives are prospective candidates for potent antivirals. Copyright © 2017 Elsevier Inc. All rights reserved.

  4. Systems and Trans-System Level Analysis Identifies Conserved Iron Deficiency Responses in the Plant Lineage[W][OA

    PubMed Central

    Urzica, Eugen I.; Casero, David; Yamasaki, Hiroaki; Hsieh, Scott I.; Adler, Lital N.; Karpowicz, Steven J.; Blaby-Haas, Crysten E.; Clarke, Steven G.; Loo, Joseph A.; Pellegrini, Matteo; Merchant, Sabeeha S.

    2012-01-01

    We surveyed the iron nutrition-responsive transcriptome of Chlamydomonas reinhardtii using RNA-Seq methodology. Presumed primary targets were identified in comparisons between visually asymptomatic iron-deficient versus iron-replete cells. This includes the known components of high-affinity iron uptake as well as candidates for distributive iron transport in C. reinhardtii. Comparison of growth-inhibited iron-limited versus iron-replete cells revealed changes in the expression of genes in chloroplastic oxidative stress response pathways, among hundreds of other genes. The output from the transcriptome was validated at multiple levels: by quantitative RT-PCR for assessing the data analysis pipeline, by quantitative proteomics for assessing the impact of changes in RNA abundance on the proteome, and by cross-species comparison for identifying conserved or universal response pathways. In addition, we assessed the functional importance of three target genes, VITAMIN C 2 (VTC2), MONODEHYDROASCORBATE REDUCTASE 1 (MDAR1), and CONSERVED IN THE GREEN LINEAGE AND DIATOMS 27 (CGLD27), by biochemistry or reverse genetics. VTC2 and MDAR1, which are key enzymes in de novo ascorbate synthesis and ascorbate recycling, respectively, are likely responsible for the 10-fold increase in ascorbate content of iron-limited cells. CGLD27/At5g67370 is a highly conserved, presumed chloroplast-localized pioneer protein and is important for growth of Arabidopsis thaliana in low iron. PMID:23043051

  5. Governance factors in the identification of global conservation priorities for mammals

    PubMed Central

    Eklund, Johanna; Arponen, Anni; Visconti, Piero; Cabeza, Mar

    2011-01-01

    Global conservation priorities have often been identified based on the combination of species richness and threat information. With the development of the field of systematic conservation planning, more attention has been given to conservation costs. This leads to prioritizing developing countries, where costs are generally low and biodiversity is high. But many of these countries have poor governance, which may result in ineffective conservation or in larger costs than initially expected. We explore how the consideration of governance affects the selection of global conservation priorities for the world's mammals in a complementarity-based conservation prioritization. We use data on Control of Corruption (Worldwide Governance Indicators project) as an indicator of governance effectiveness, and gross domestic product per capita as an indicator of cost. We show that, while core areas with high levels of endemism are always selected as important regardless of governance and cost values, there are clear regional differences in selected sites when biodiversity, cost or governance are taken into account separately. Overall, the analysis supports the concentration of conservation efforts in most of the regions generally considered of high priority, but stresses the need for different conservation approaches in different continents owing to spatial patterns of governance and economic development. PMID:21844045

  6. Governance factors in the identification of global conservation priorities for mammals.

    PubMed

    Eklund, Johanna; Arponen, Anni; Visconti, Piero; Cabeza, Mar

    2011-09-27

    Global conservation priorities have often been identified based on the combination of species richness and threat information. With the development of the field of systematic conservation planning, more attention has been given to conservation costs. This leads to prioritizing developing countries, where costs are generally low and biodiversity is high. But many of these countries have poor governance, which may result in ineffective conservation or in larger costs than initially expected. We explore how the consideration of governance affects the selection of global conservation priorities for the world's mammals in a complementarity-based conservation prioritization. We use data on Control of Corruption (Worldwide Governance Indicators project) as an indicator of governance effectiveness, and gross domestic product per capita as an indicator of cost. We show that, while core areas with high levels of endemism are always selected as important regardless of governance and cost values, there are clear regional differences in selected sites when biodiversity, cost or governance are taken into account separately. Overall, the analysis supports the concentration of conservation efforts in most of the regions generally considered of high priority, but stresses the need for different conservation approaches in different continents owing to spatial patterns of governance and economic development.

  7. Genomic perspectives of spider silk genes through target capture sequencing: Conservation of stabilization mechanisms and homology-based structural models of spidroin terminal regions.

    PubMed

    Collin, Matthew A; Clarke, Thomas H; Ayoub, Nadia A; Hayashi, Cheryl Y

    2018-07-01

    A powerful system for studying protein aggregation, particularly rapid self-assembly, is spider silk. Spider silks are proteinaceous and silk proteins are synthesized and stored within silk glands as liquid dope. As needed, liquid dope is near-instantaneously transformed into solid fibers or viscous adhesives. The dominant constituents of silks are spidroins (spider fibroins) and their terminal domains are vital for the tight control of silk self-assembly. To better understand spidroin termini, we used target capture and deep sequencing to identify spidroin gene sequences from six species representing the araneoid families of Araneidae, Nephilidae, and Theridiidae. We obtained 145 terminal regions, of which 103 are newly annotated here, as well as novel variants within nine diverse spidroin types. Our comparative analyses demonstrated the conservation of acidic, basic, and cysteine amino acid residues across spidroin types that had been proposed to be important for monomer stability, dimer formation, and self-assembly from a limited sampling of spidroins. Computational, protein homology modeling revealed areas of spidroin terminal regions that are highly conserved in three-dimensions despite sequence divergence across spidroin types. Analyses of our dense sampling of terminal regions suggest that most spidroins share stabilization mechanisms, dimer formation, and tertiary structure, despite producing functionally distinct materials. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

  8. Correlation approach to identify coding regions in DNA sequences

    NASA Technical Reports Server (NTRS)

    Ossadnik, S. M.; Buldyrev, S. V.; Goldberger, A. L.; Havlin, S.; Mantegna, R. N.; Peng, C. K.; Simons, M.; Stanley, H. E.

    1994-01-01

    Recently, it was observed that noncoding regions of DNA sequences possess long-range power-law correlations, whereas coding regions typically display only short-range correlations. We develop an algorithm based on this finding that enables investigators to perform a statistical analysis on long DNA sequences to locate possible coding regions. The algorithm is particularly successful in predicting the location of lengthy coding regions. For example, for the complete genome of yeast chromosome III (315,344 nucleotides), at least 82% of the predictions correspond to putative coding regions; the algorithm correctly identified all coding regions larger than 3000 nucleotides, 92% of coding regions between 2000 and 3000 nucleotides long, and 79% of coding regions between 1000 and 2000 nucleotides. The predictive ability of this new algorithm supports the claim that there is a fundamental difference in the correlation property between coding and noncoding sequences. This algorithm, which is not species-dependent, can be implemented with other techniques for rapidly and accurately locating relatively long coding regions in genomic sequences.

  9. Regional Seismic Methods of Identifying Explosions

    NASA Astrophysics Data System (ADS)

    Walter, W. R.; Ford, S. R.; Pasyanos, M.; Pyle, M. L.; Hauk, T. F.

    2013-12-01

    A lesson from the 2006, 2009 and 2013 DPRK declared nuclear explosion Ms:mb observations is that our historic collection of data may not be representative of future nuclear test signatures (e.g. Selby et al., 2012). To have confidence in identifying future explosions amongst the background of other seismic signals, we need to put our empirical methods on a firmer physical footing. Here we review the two of the main identification methods: 1) P/S ratios and 2) Moment Tensor techniques, which can be applied at the regional distance (200-1600 km) to very small events, improving nuclear explosion monitoring and confidence in verifying compliance with the Comprehensive Nuclear-Test-Ban Treaty (CTBT). Amplitude ratios of seismic P-to-S waves at sufficiently high frequencies (~>2 Hz) can identify explosions among a background of natural earthquakes (e.g. Walter et al., 1995). However the physical basis for the generation of explosion S-waves, and therefore the predictability of this P/S technique as a function of event properties such as size, depth, geology and path, remains incompletely understood. Calculated intermediate period (10-100s) waveforms from regional 1-D models can match data and provide moment tensor results that separate explosions from earthquakes and cavity collapses (e.g. Ford et al. 2009). However it has long been observed that some nuclear tests produce large Love waves and reversed Rayleigh waves that complicate moment tensor modeling. Again the physical basis for the generation of these effects from explosions remains incompletely understood. We are re-examining regional seismic data from a variety of nuclear test sites including the DPRK and the former Nevada Test Site (now the Nevada National Security Site (NNSS)). Newer relative amplitude techniques can be employed to better quantify differences between explosions and used to understand those differences in term of depth, media and other properties. We are also making use of the Source Physics

  10. Environmental Performance Information Use by Conservation Agency Staff

    NASA Astrophysics Data System (ADS)

    Wardropper, Chloe Bradley

    2018-04-01

    Performance-based conservation has long been recognized as crucial to improving program effectiveness, particularly when environmental conditions are dynamic. Yet few studies have investigated the use of environmental performance information by staff of conservation organizations. This article identifies attitudinal, policy and organizational factors influencing the use of a type of performance information—water quality information—by Soil and Water Conservation District staff in the Upper Mississippi River Basin region. An online survey ( n = 277) revealed a number of important variables associated with greater information use. Variables included employees' prosocial motivation, or the belief that they helped people and natural resources through their job, the perceived trustworthiness of data, the presence of a U.S. Clean Water Act Total Maximum Daily Load standard designation, and staff discretion to prioritize programs locally. Conservation programs that retain motivated staff and provide them the resources and flexibility to plan and evaluate their work with environmental data may increase conservation effectiveness under changing conditions.

  11. The Conservation Effects Assessment Project (CEAP): a national scale natural resources and conservation needs assessment and decision support tool

    NASA Astrophysics Data System (ADS)

    Johnson, M.-V. V.; Norfleet, M. L.; Atwood, J. D.; Behrman, K. D.; Kiniry, J. R.; Arnold, J. G.; White, M. J.; Williams, J.

    2015-07-01

    The Conservation Effects Assessment Project (CEAP) was initiated to quantify the impacts of agricultural conservation practices at the watershed, regional, and national scales across the United States. Representative cropland acres in all major U.S. watersheds were surveyed in 2003-2006 as part of the seminal CEAP Cropland National Assessment. Two process-based models, the Agricultural Policy Environmental eXtender(APEX) and the Soil Water Assessment Tool (SWAT), were applied to the survey data to provide a quantitative assessment of current conservation practice impacts, establish a benchmark against which future conservation trends and efforts could be measured, and identify outstanding conservation concerns. The flexibility of these models and the unprecedented amount of data on current conservation practices across the country enabled Cropland CEAP to meet its Congressional mandate of quantifying the value of current conservation practices. It also enabled scientifically grounded exploration of a variety of conservation scenarios, empowering CEAP to not only inform on past successes and additional needs, but to also provide a decision support tool to help guide future policy development and conservation practice decision making. The CEAP effort will repeat the national survey in 2015-2016, enabling CEAP to provide analyses of emergent conservation trends, outstanding needs, and potential costs and benefits of pursuing various treatment scenarios for all agricultural watersheds across the United States.

  12. Southwest Region: A Report Identifying and Addressing the Educational Needs

    ERIC Educational Resources Information Center

    US Department of Education, 2011

    2011-01-01

    The Educational Technical Assistance Act of 2002, authorized the Southwest Regional Advisory Committee (RAC), whose members represent the states of Arkansas, Louisiana, New Mexico, Oklahoma, and Texas, to identify and prioritize the region's educational needs and recommend how those needs can be met. The Southwest RAC conducted three public…

  13. Identifying Fossil Shell Resources via Geophysical Surveys: Chesapeake Bay Region, Virginia

    DTIC Science & Technology

    2016-05-01

    ER D C/ CH L TR -1 6- 4 Chesapeake Fossil Shell Survey Identifying Fossil Shell Resources via Geophysical Surveys: Chesapeake Bay Region...other technical reports published by ERDC, visit the ERDC online library at http://acwc.sdp.sirsi.net/client/default. Chesapeake Fossil Shell...Survey ERDC/CHL TR-16-4 May 2016 Identifying Fossil Shell Resources via Geophysical Surveys: Chesapeake Bay Region, Virginia Heidi M. Wadman and Jesse

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

    USGS Publications Warehouse

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

    2016-01-01

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

  15. Regions of extreme synonymous codon selection in mammalian genes

    PubMed Central

    Schattner, Peter; Diekhans, Mark

    2006-01-01

    Recently there has been increasing evidence that purifying selection occurs among synonymous codons in mammalian genes. This selection appears to be a consequence of either cis-regulatory motifs, such as exonic splicing enhancers (ESEs), or mRNA secondary structures, being superimposed on the coding sequence of the gene. We have developed a program to identify regions likely to be enriched for such motifs by searching for extended regions of extreme codon conservation between homologous genes of related species. Here we present the results of applying this approach to five mammalian species (human, chimpanzee, mouse, rat and dog). Even with very conservative selection criteria, we find over 200 regions of extreme codon conservation, ranging in length from 60 to 178 codons. The regions are often found within genes involved in DNA-binding, RNA-binding or zinc-ion-binding. They are highly depleted for synonymous single nucleotide polymorphisms (SNPs) but not for non-synonymous SNPs, further indicating that the observed codon conservation is being driven by negative selection. Forty-three percent of the regions overlap conserved alternative transcript isoforms and are enriched for known ESEs. Other regions are enriched for TpA dinucleotides and may contain conserved motifs/structures relating to mRNA stability and/or degradation. We anticipate that this tool will be useful for detecting regions enriched in other classes of coding-sequence motifs and structures as well. PMID:16556911

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

    PubMed

    Brown, Jenna R; Livesay, Dennis R

    2015-01-01

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

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

    PubMed Central

    Brown, Jenna R.; Livesay, Dennis R.

    2015-01-01

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

  18. Stereophysicochemical variability plots highlight conserved antigenic areas in Flaviviruses

    PubMed Central

    Schein, Catherine H; Zhou, Bin; Braun, Werner

    2005-01-01

    Background Flaviviruses, which include Dengue (DV) and West Nile (WN), mutate in response to immune system pressure. Identifying escape mutants, variant progeny that replicate in the presence of neutralizing antibodies, is a common way to identify functionally important residues of viral proteins. However, the mutations typically occur at variable positions on the viral surface that are not essential for viral replication. Methods are needed to determine the true targets of the neutralizing antibodies. Results Stereophysicochemical variability plots (SVPs), 3-D images of protein structures colored according to variability, as determined by our PCPMer program, were used to visualize residues conserved in their physical chemical properties (PCPs) near escape mutant positions. The analysis showed 1) that escape mutations in the flavivirus envelope protein are variable residues by our criteria and 2) two escape mutants found at the same position in many flaviviruses sit above clusters of conserved residues from different regions of the linear sequence. Conservation patterns in T-cell epitopes in the NS3- protease suggest a similar mechanism of immune system evasion. Conclusion The SVPs add another dimension to structurally defining the binding sites of neutralizing antibodies. They provide a useful aid for determining antigenically important regions and designing vaccines. PMID:15845145

  19. Conservation Action Handbook.

    ERIC Educational Resources Information Center

    National Rifle Association, Washington, DC.

    Conservation problems are identified, with some suggestions for action. General areas covered are: Wildlife Conservation, Soil Conservation, Clean Water, Air Pollution Action, and Outdoor Recreation Action. Appendices list private organizations or agencies concerned with natural resource use and/or management, congressional committees considering…

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

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

    2014-11-15

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

  1. Global patterns of terrestrial vertebrate diversity and conservation

    PubMed Central

    Jenkins, Clinton N.; Pimm, Stuart L.; Joppa, Lucas N.

    2013-01-01

    Identifying priority areas for biodiversity is essential for directing conservation resources. Fundamentally, we must know where individual species live, which ones are vulnerable, where human actions threaten them, and their levels of protection. As conservation knowledge and threats change, we must reevaluate priorities. We mapped priority areas for vertebrates using newly updated data on >21,000 species of mammals, amphibians, and birds. For each taxon, we identified centers of richness for all species, small-ranged species, and threatened species listed with the International Union for the Conservation of Nature. Importantly, all analyses were at a spatial grain of 10 × 10 km, 100 times finer than previous assessments. This fine scale is a significant methodological improvement, because it brings mapping to scales comparable with regional decisions on where to place protected areas. We also mapped recent species discoveries, because they suggest where as-yet-unknown species might be living. To assess the protection of the priority areas, we calculated the percentage of priority areas within protected areas using the latest data from the World Database of Protected Areas, providing a snapshot of how well the planet’s protected area system encompasses vertebrate biodiversity. Although the priority areas do have more protection than the global average, the level of protection still is insufficient given the importance of these areas for preventing vertebrate extinctions. We also found substantial differences between our identified vertebrate priorities and the leading map of global conservation priorities, the biodiversity hotspots. Our findings suggest a need to reassess the global allocation of conservation resources to reflect today’s improved knowledge of biodiversity and conservation. PMID:23803854

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

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

    PubMed

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

    2016-08-24

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

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed Central

    2011-01-01

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

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

    PubMed Central

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

    2013-01-01

    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

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

    PubMed

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

    2013-08-01

    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.

  8. Combining Natural History Collections with Fisher Knowledge for Community-Based Conservation in Fiji

    PubMed Central

    Golden, Abigail S.; Naisilsisili, Waisea; Ligairi, Isikele; Drew, Joshua A.

    2014-01-01

    Harnessing the traditional ecological knowledge (TEK) of local communities has the potential to enhance conservation planning in developing regions. Marine protected areas (MPAs) that incorporate traditional beliefs about reef tenure are generally more successful in reaching conservation goals and ensuring the participation of local fishermen on vulnerable tropical reef systems. Fiji possesses a unique system of traditional reef management in which local clans or villages, called mataqali, control individual units of a reef, known as qoliqoli, and make independent management decisions based on traditional beliefs and conservation concerns. This is an example of a system, known as customary marine tenure, which has attracted interest from conservation scientists hoping to set up MPAs in vulnerable regions. As one example of this grassroots participation, Nagigi village on the Fijian island of Vanua Levu has expressed interest in setting up an MPA in part of its qoliqoli because of concerns about overfishing. In response to this interest, we took a two-pronged approach to assessing Nagigi's fishery status and conservation needs, first conducting a fishery-independent species survey using destructive sampling and then focusing on fisheries targets identified through fisher interviews. These interviews allowed us to identify heavily targeted species, assess villagers' understanding of reef dynamics over 30 or 40 years of fisheries expansion, and evaluate village support and expectations for a proposed conservation program. Based on our findings we recommend a temporary closure to be in effect for at least three years, allowing one of the more important fishery targets, Lethrinus harak (Forsskål, 1775; Lethrinidae), to complete at least one generation within the reserve. The methodology of matching the proposed marine protected area with the life histories and ecologies of heavily targeted species identified through fisherman and -woman interviews can offer a template

  9. Combining natural history collections with fisher knowledge for community-based conservation in Fiji.

    PubMed

    Golden, Abigail S; Naisilsisili, Waisea; Ligairi, Isikele; Drew, Joshua A

    2014-01-01

    Harnessing the traditional ecological knowledge (TEK) of local communities has the potential to enhance conservation planning in developing regions. Marine protected areas (MPAs) that incorporate traditional beliefs about reef tenure are generally more successful in reaching conservation goals and ensuring the participation of local fishermen on vulnerable tropical reef systems. Fiji possesses a unique system of traditional reef management in which local clans or villages, called mataqali, control individual units of a reef, known as qoliqoli, and make independent management decisions based on traditional beliefs and conservation concerns. This is an example of a system, known as customary marine tenure, which has attracted interest from conservation scientists hoping to set up MPAs in vulnerable regions. As one example of this grassroots participation, Nagigi village on the Fijian island of Vanua Levu has expressed interest in setting up an MPA in part of its qoliqoli because of concerns about overfishing. In response to this interest, we took a two-pronged approach to assessing Nagigi's fishery status and conservation needs, first conducting a fishery-independent species survey using destructive sampling and then focusing on fisheries targets identified through fisher interviews. These interviews allowed us to identify heavily targeted species, assess villagers' understanding of reef dynamics over 30 or 40 years of fisheries expansion, and evaluate village support and expectations for a proposed conservation program. Based on our findings we recommend a temporary closure to be in effect for at least three years, allowing one of the more important fishery targets, Lethrinus harak (Forsskål, 1775; Lethrinidae), to complete at least one generation within the reserve. The methodology of matching the proposed marine protected area with the life histories and ecologies of heavily targeted species identified through fisherman and -woman interviews can offer a template

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

    NASA Astrophysics Data System (ADS)

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

    2014-12-01

    High soil-conservation herbs are very important for slope vegetation restoration of a highway in serious sandstorm regions. In this study, nine common herbs in northeast China were selected and compared to study soil-conservation effects by using an undisturbed-soil trough scouring method for soil anti-scourability enhancement and hydrostatic collapse method for soil anti-erodibility. Further, principal components analysis was used to identify significant root features that affected soil erosion resistance. Results indicated that different herbs had distinct enhancement effects on soil erosion resistance. Soil anti-scourability enhancement index decreased with increases of soil depth, slope gradient and rainfall amount. Relationship between soil anti-erodibility enhancement index ( S) and immersion time ( t) is a cubic spline in each different herb type ( R 2 ≥ 0.88). Herb root features such as micro-aggregates, organic matter, net leaf weight, thick root length, fine root length and biomass contributed a leading role in soil erosion resistance enhancement effect, and all their common factor variances were more than 0.81. Descending order of soil erosion resistance enhancement effect in soil anti-scourability for nine herbs is Poa pratensis, Medicago sativa, Viola philippica, Rudbeckia hirta, Clematis heracleifolia, Kalimeris indica, Cosmos bipinnata, Hemerocallis fulva and Sedum elatinoides, while the sequence of soil anti-erodibility is M. sativa, S. elatinoides, P. pratensis, R. hirta, H. fulva, V. philippica, C. heracleifolia, C. bipinnata and K. indica. Therefore, we concluded that P. pratensis and M. sativa were the most suitable herbs for resisting soil erosion and recommended to be widely planted for road vegetation recovery in this region.

  11. A Conserved Region between the Heptad Repeats of Paramyxovirus Fusion Proteins is Critical for Proper F Protein Folding†

    PubMed Central

    Gardner, Amanda E.; Martin, Kimberly L.; Dutch, Rebecca E.

    2008-01-01

    Paramyxoviruses are a diverse family which utilizes a fusion (F) protein to enter cells via fusion of the viral lipid bilayer with a target cell membrane. Although certain regions of F are known to play critical roles in membrane fusion, the function of much of the protein remains unclear. Sequence alignment of a set of paramyxovirus F proteins and analysis utilizing Block Maker identified a region of conserved amino acid sequence in a large domain between the heptad repeats of F1, designated CBF1. We employed site-directed mutagenesis to analyze the function of completely conserved residues of CBF1 in both the simian virus 5 (SV5) and Hendra virus F proteins. The majority of CBF1 point mutants were deficient in homotrimer formation, proteolytic processing, and transport to the cell surface. For some SV5 F mutants, proteolytic cleavage and surface expression could be restored by expression at 30°C, and varying levels of fusion promotion were observed at this temperature. In addition, the mutant SV5 F V402A displayed a hyperfusogenic phenotype at both 30°C and 37°C, indicating this mutation allows for efficient fusion with only an extremely small amount of cleaved, active protein. The recently published prefusogenic structure of PIV5/SV5 F [Yin, H.S., et al. (2006) Nature 439, 38–44] indicates that residues within and flanking CBF1 interact with the fusion peptide domain. Together, these data suggest that CBF1-fusion peptide interactions are critical for the initial folding of paramyxovirus F proteins from across this important viral family, and can also modulate subsequent membrane fusion promotion. PMID:17417875

  12. Conservation Planning for Ecosystem Services

    PubMed Central

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

    2006-01-01

    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

  13. Conservation Action Planning: Lessons learned from the St. Marys River watershed biodiversity conservation planning process

    USGS Publications Warehouse

    Patterson, Tamatha A.; Grundel, Ralph

    2014-01-01

    Conservation Action Planning (CAP) is an adaptive management planning process refined by The Nature Conservancy (TNC) and embraced worldwide as the Open Standards for the Practice of Conservation. The CAP process facilitates open, multi-institutional collaboration on a common conservation agenda through organized actions and quantified results. While specifically designed for conservation efforts, the framework is adaptable and flexible to multiple scales and can be used for any collaborative planning effort. The CAP framework addresses inception; design and development of goals, measures, and strategies; and plan implementation and evaluation. The specific components of the CAP include defining the project scope and conservation targets; assessing the ecological viability; ascertaining threats and surrounding situation; identifying opportunities and designing strategies for action; and implementing actions and monitoring results. In 2007, TNC and a multidisciplinary graduate student team from the University of Michigan's School of Natural Resources and Environment initiated a CAP for the St. Marys River, the connecting channel between Lake Superior and Lake Huron, and its local watershed. The students not only gained experience in conservation planning, but also learned lessons that notably benefited the CAP process and were valuable for any successful collaborative effort—a dedicated core team improved product quality, accelerated the timeline, and provided necessary support for ongoing efforts; an academic approach in preparation for engagement in the planning process brought applicable scientific research to the forefront, enhanced workshop facilitation, and improved stakeholder participation; and early and continuous interactions with regional stakeholders improved cooperation and built a supportive network for collaboration.

  14. List identifies threatened ecosystems

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2012-09-01

    The International Union for Conservation of Nature (IUCN) announced on 9 September that it will develop a new Red List of Ecosystems that will identify which ecosystems are vulnerable or endangered. The list, which is modeled on the group's Red List of Threatened Species™, could help to guide conservation activities and influence policy processes such as the Convention on Biological Diversity, according to the group. “We will assess the status of marine, terrestrial, freshwater, and subterranean ecosystems at local, regional, and global levels,” stated Jon Paul Rodriguez, leader of IUCN's Ecosystems Red List Thematic Group. “The assessment can then form the basis for concerted implementation action so that we can manage them sustainably if their risk of collapse is low or restore them if they are threatened and then monitor their recovery.”

  15. Identifying care actions to conserve dignity in end-of-life care.

    PubMed

    Brown, Hilary; Johnston, Bridget; Ostlund, Ulrika

    2011-05-01

    Community nurses have a central role in the provision of palliative and end-of-life care; helping people to die with dignity is an important component of this care. To conserve dignity, care should comprise a broad range of actions addressing the distress that might impact on the patient's sense of dignity. These care actions need to be defined. This study aims to suggest care actions that conserve dignity at the end of life based on evidence from local experience and community nursing practice. Data were collected by focus group interviews and analysed by framework analysis using the Chochinov model of dignity as a predefined framework. Suggestions on care actions were given in relation to all themes. As part of a multi-phase project developing and testing a dignity care pathway, this study might help community nurses to conserve dying patients' dignity.

  16. Conserved intergenic sequences revealed by CTAG-profiling in Salmonella: thermodynamic modeling for function prediction

    NASA Astrophysics Data System (ADS)

    Tang, Le; Zhu, Songling; Mastriani, Emilio; Fang, Xin; Zhou, Yu-Jie; Li, Yong-Guo; Johnston, Randal N.; Guo, Zheng; Liu, Gui-Rong; Liu, Shu-Lin

    2017-03-01

    Highly conserved short sequences help identify functional genomic regions and facilitate genomic annotation. We used Salmonella as the model to search the genome for evolutionarily conserved regions and focused on the tetranucleotide sequence CTAG for its potentially important functions. In Salmonella, CTAG is highly conserved across the lineages and large numbers of CTAG-containing short sequences fall in intergenic regions, strongly indicating their biological importance. Computer modeling demonstrated stable stem-loop structures in some of the CTAG-containing intergenic regions, and substitution of a nucleotide of the CTAG sequence would radically rearrange the free energy and disrupt the structure. The postulated degeneration of CTAG takes distinct patterns among Salmonella lineages and provides novel information about genomic divergence and evolution of these bacterial pathogens. Comparison of the vertically and horizontally transmitted genomic segments showed different CTAG distribution landscapes, with the genome amelioration process to remove CTAG taking place inward from both terminals of the horizontally acquired segment.

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

    USDA-ARS?s Scientific Manuscript database

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

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

    PubMed Central

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

    2014-01-01

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

  19. Fish diversity and its conservation in major wetlands of Mysore.

    PubMed

    Prasad, A G Devi; Venkataramana, G V; Thomas, Mathew

    2009-09-01

    The paper highlights the fish diversity in major wetlands of Mysore district, Karnataka, India and its conservation status. Forty-five species of fishes belonging to 15 families, 31 genera have been identified. Fish species belonging to genus Puntius were more common in many of these lakes. However it was observed that the fish diversity was decreasing since last two years unprecedently mainly due to manifold human activities. Fish diversity in the lakes is becoming rare and about seven species were identified as endangered. Out of the 45 identified fishes, six fish species were identified as threatened species. Tork hudree, also known as Deccan mahseer and seven other species were identified as vulnerable fish species. Though there were 40 species of fish endemic to this region, their number decreased with introduction of more exotic species. Conservation of endemic fishes, propagation of endangered and threatened fishes should be therefore, undertaken to preserve and protect fish diversity in the wetlands of Mysore district.

  20. Bird Conservation Planning and Implementation in Canada's Intermountain Region

    Treesearch

    Ilia Hartasanchez; Krista De Groot; Andre Breault; Rob W. Butler

    2005-01-01

    Bird conservation planning in British Columbia and Yukon has been carried out by each of the major bird initiatives. The purpose of this paper is to provide a status report of planning activities and to discuss how integration of the initiatives is being accomplished for efficient and effective implementation of bird conservation actions.

  1. Large expansion of oil industry in the Ecuadorian Amazon: biodiversity vulnerability and conservation alternatives.

    PubMed

    Lessmann, Janeth; Fajardo, Javier; Muñoz, Jesús; Bonaccorso, Elisa

    2016-07-01

    Ecuador will experience a significant expansion of the oil industry in its Amazonian region, one of the most biodiverse areas of the world. In view of the changes that are about to come, we explore the conflicts between oil extraction interests and biodiversity protection and apply systematic conservation planning to identify priority areas that should be protected in different oil exploitation scenarios. First, we quantified the current extent of oil blocks and protected zones and their overlap with two biodiversity indicators: 25 ecosystems and 745 species (whose distributions were estimated via species distribution models). With the new scheme of oil exploitation, oil blocks cover 68% (68,196 km(2)) of the Ecuadorian Amazon; half of it occupied by new blocks open for bids in the southern Amazon. This region is especially vulnerable to biodiversity losses, because peaks of species diversity, 19 ecosystems, and a third of its protected zones coincide spatially with oil blocks. Under these circumstances, we used Marxan software to identify priority areas for conservation outside oil blocks, but their coverage was insufficient to completely represent biodiversity. Instead, priority areas that include southern oil blocks provide a higher representation of biodiversity indicators. Therefore, preserving the southern Amazon becomes essential to improve the protection of Amazonian biodiversity in Ecuador, and avoiding oil exploitation in these areas (33% of the extent of southern oil blocks) should be considered a conservation alternative. Also, it is highly recommended to improve current oil exploitation technology to reduce environmental impacts in the region, especially within five oil blocks that we identified as most valuable for the conservation of biodiversity. The application of these and other recommendations depends heavily on the Ecuadorian government, which needs to find a better balance between the use of the Amazon resources and biodiversity conservation.

  2. Conservation status and regional habitat priorities for the Orinoco crocodile: Past, present, and future.

    PubMed

    Balaguera-Reina, Sergio A; Espinosa-Blanco, Ariel S; Morales-Betancourt, Mónica A; Seijas, Andrés E; Lasso, Carlos A; Antelo, Rafael; Densmore, Llewellyn D

    2017-01-01

    Conservation of large predator species has historically been a challenge because they often overlap in resource utilization with humans; furthermore, there is a general lack of in-depth knowledge of their ecology and natural history. We assessed the conservation status of the Orinoco crocodile (Crocodylus intermedius), defining regional habitat priorities/crocodile conservation units (RHP/CCU) and regional research priorities (RRP) for this species. We also estimated a species distribution model (SDM) to define current suitable areas where the species might inhabit and/or that might be successfully colonized. The SDM area obtained with a suitable habitat probability ≥ 0.5 was 23,621 km2. Out of 2,562 km2 are included within protected areas in both Colombia (1,643 km2) and Venezuela (919 km2), which represents only 10.8% of C. intermedius' potential range. Areas such as Laguna de Chigüichigüe (flood plain lagoon) exhibited an increase in population abundance. In contrast, localities such as the Cojedes and Manapire Rivers reported a significant reduction in relative abundance values. In Colombia, disparity in previous survey methods prevented accurate estimation of population trends. Only one study in this country described an increase over a 13 years span in the Ele, Lipa, and Cravo Norte River populations based on nest surveys. We defined 34 critical areas (16 in Colombia, 17 in Venezuela, and one covering both countries) where we need to preserve/research/monitor and/or generate management actions, 10 RHP/CCU (six from Venezuela and four from Colombia) and 24 RRP (11 from Venezuela, 12 from Colombia, and one in both countries). Caño Guaritico (Creek) and the Capanaparo River in Venezuela and the Ele, Lipa, Cravo Norte River System and the Guayabero River in Colombia were defined as areas with the most optimal conditions for long-term preservation and maintenance of C. intermedius populations. We conclude that the conservation status of this species is still

  3. Conservation status and regional habitat priorities for the Orinoco crocodile: Past, present, and future

    PubMed Central

    Espinosa-Blanco, Ariel S.; Morales-Betancourt, Mónica A.; Seijas, Andrés E.; Lasso, Carlos A.; Antelo, Rafael; Densmore, Llewellyn D.

    2017-01-01

    Conservation of large predator species has historically been a challenge because they often overlap in resource utilization with humans; furthermore, there is a general lack of in-depth knowledge of their ecology and natural history. We assessed the conservation status of the Orinoco crocodile (Crocodylus intermedius), defining regional habitat priorities/crocodile conservation units (RHP/CCU) and regional research priorities (RRP) for this species. We also estimated a species distribution model (SDM) to define current suitable areas where the species might inhabit and/or that might be successfully colonized. The SDM area obtained with a suitable habitat probability ≥ 0.5 was 23,621 km2. Out of 2,562 km2 are included within protected areas in both Colombia (1,643 km2) and Venezuela (919 km2), which represents only 10.8% of C. intermedius’ potential range. Areas such as Laguna de Chigüichigüe (flood plain lagoon) exhibited an increase in population abundance. In contrast, localities such as the Cojedes and Manapire Rivers reported a significant reduction in relative abundance values. In Colombia, disparity in previous survey methods prevented accurate estimation of population trends. Only one study in this country described an increase over a 13 years span in the Ele, Lipa, and Cravo Norte River populations based on nest surveys. We defined 34 critical areas (16 in Colombia, 17 in Venezuela, and one covering both countries) where we need to preserve/research/monitor and/or generate management actions, 10 RHP/CCU (six from Venezuela and four from Colombia) and 24 RRP (11 from Venezuela, 12 from Colombia, and one in both countries). Caño Guaritico (Creek) and the Capanaparo River in Venezuela and the Ele, Lipa, Cravo Norte River System and the Guayabero River in Colombia were defined as areas with the most optimal conditions for long-term preservation and maintenance of C. intermedius populations. We conclude that the conservation status of this species is

  4. The non-conserved region of MRP is involved in the virulence of Streptococcus suis serotype 2

    PubMed Central

    Li, Quan; Fu, Yang; Ma, Caifeng; He, Yanan; Yu, Yanfei; Du, Dechao; Yao, Huochun; Lu, Chengping; Zhang, Wei

    2017-01-01

    ABSTRACT Muramidase-released protein (MRP) of Streptococcus suis serotype 2 (SS2) is an important epidemic virulence marker with an unclear role in bacterial infection. To investigate the biologic functions of MRP, 3 mutants named Δmrp, Δmrp domain 1 (Δmrp-d1), and Δmrp domain 2 (Δmrp-d2) were constructed to assess the phenotypic changes between the parental strain and the mutant strains. The results indicated that MRP domain 1 (MRP-D1, the non-conserved region of MRP from a virulent strain, a.a. 242–596) played a critical role in adherence of SS2 to host cells, compared with MRP domain 1* (MRP-D1*, the non-conserved region of MRP from a low virulent strain, a.a. 239–598) or MRP domain 2 (MRP-D2, the conserved region of MRP, a.a. 848–1222). We found that MRP-D1 but not MRP-D2, could bind specifically to fibronectin (FN), factor H (FH), fibrinogen (FG), and immunoglobulin G (IgG). Additionally, we confirmed that mrp-d1 mutation significantly inhibited bacteremia and brain invasion in a mouse infection model. The mrp-d1 mutation also attenuated the intracellular survival of SS2 in RAW246.7 macrophages, shortened the growth ability in pig blood and decreased the virulence of SS2 in BALB/c mice. Furthermore, antiserum against MRP-D1 was found to dramatically impede SS2 survival in pig blood. Finally, immunization with recombinant MRP-D1 efficiently enhanced murine viability after SS2 challenge, indicating its potential use in vaccination strategies. Collectively, these results indicated that MRP-D1 is involved in SS2 virulence and eloquently demonstrate the function of MRP in pathogenesis of infection. PMID:28362221

  5. The non-conserved region of MRP is involved in the virulence of Streptococcus suis serotype 2.

    PubMed

    Li, Quan; Fu, Yang; Ma, Caifeng; He, Yanan; Yu, Yanfei; Du, Dechao; Yao, Huochun; Lu, Chengping; Zhang, Wei

    2017-10-03

    Muramidase-released protein (MRP) of Streptococcus suis serotype 2 (SS2) is an important epidemic virulence marker with an unclear role in bacterial infection. To investigate the biologic functions of MRP, 3 mutants named Δmrp, Δmrp domain 1 (Δmrp-d1), and Δmrp domain 2 (Δmrp-d2) were constructed to assess the phenotypic changes between the parental strain and the mutant strains. The results indicated that MRP domain 1 (MRP-D1, the non-conserved region of MRP from a virulent strain, a.a. 242-596) played a critical role in adherence of SS2 to host cells, compared with MRP domain 1* (MRP-D1*, the non-conserved region of MRP from a low virulent strain, a.a. 239-598) or MRP domain 2 (MRP-D2, the conserved region of MRP, a.a. 848-1222). We found that MRP-D1 but not MRP-D2, could bind specifically to fibronectin (FN), factor H (FH), fibrinogen (FG), and immunoglobulin G (IgG). Additionally, we confirmed that mrp-d1 mutation significantly inhibited bacteremia and brain invasion in a mouse infection model. The mrp-d1 mutation also attenuated the intracellular survival of SS2 in RAW246.7 macrophages, shortened the growth ability in pig blood and decreased the virulence of SS2 in BALB/c mice. Furthermore, antiserum against MRP-D1 was found to dramatically impede SS2 survival in pig blood. Finally, immunization with recombinant MRP-D1 efficiently enhanced murine viability after SS2 challenge, indicating its potential use in vaccination strategies. Collectively, these results indicated that MRP-D1 is involved in SS2 virulence and eloquently demonstrate the function of MRP in pathogenesis of infection.

  6. Improving genetic conservation of tree species

    Treesearch

    Pam Allenstein; Jennifer DeWoody; David Gwaze; Valerie Hipkins; Gary Man; Anna Schoettle; Kirsty Shaw; Murphy Westwood

    2017-01-01

    The aim of this workshop breakout group session was to review significant gaps within each of three major themes (In-situ Conservation, Ex-situ Conservation, and Restoration of Species and Ecosystems) and to identify actionable solutions to move genetic conservation efforts forward. In order to identify solutions and action items for the tree conservation community,...

  7. One hundred questions of importance to the conservation of global biological diversity.

    PubMed

    Sutherland, W J; Adams, W M; Aronson, R B; Aveling, R; Blackburn, T M; Broad, S; Ceballos, G; Côté, I M; Cowling, R M; Da Fonseca, G A B; Dinerstein, E; Ferraro, P J; Fleishman, E; Gascon, C; Hunter, M; Hutton, J; Kareiva, P; Kuria, A; Macdonald, D W; Mackinnon, K; Madgwick, F J; Mascia, M B; McNeely, J; Milner-Gulland, E J; Moon, S; Morley, C G; Nelson, S; Osborn, D; Pai, M; Parsons, E C M; Peck, L S; Possingham, H; Prior, S V; Pullin, A S; Rands, M R W; Ranganathan, J; Redford, K H; Rodriguez, J P; Seymour, F; Sobel, J; Sodhi, N S; Stott, A; Vance-Borland, K; Watkinson, A R

    2009-06-01

    We identified 100 scientific questions that, if answered, would have the greatest impact on conservation practice and policy. Representatives from 21 international organizations, regional sections and working groups of the Society for Conservation Biology, and 12 academics, from all continents except Antarctica, compiled 2291 questions of relevance to conservation of biological diversity worldwide. The questions were gathered from 761 individuals through workshops, email requests, and discussions. Voting by email to short-list questions, followed by a 2-day workshop, was used to derive the final list of 100 questions. Most of the final questions were derived through a process of modification and combination as the workshop progressed. The questions are divided into 12 sections: ecosystem functions and services, climate change, technological change, protected areas, ecosystem management and restoration, terrestrial ecosystems, marine ecosystems, freshwater ecosystems, species management, organizational systems and processes, societal context and change, and impacts of conservation interventions. We anticipate that these questions will help identify new directions for researchers and assist funders in directing funds. ©2009 Society for Conservation Biology.

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

    NASA Astrophysics Data System (ADS)

    Mote, P.; Bisbal, G.

    2012-12-01

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

  9. Mutations in the conserved carboxy-terminal hydrophobic region of glycoprotein gB affect infectivity of herpes simplex virus.

    PubMed

    Wanas, E; Efler, S; Ghosh, K; Ghosh, H P

    1999-12-01

    Glycoprotein gB is the most highly conserved glycoprotein in the herpesvirus family and plays a critical role in virus entry and fusion. Glycoprotein gB of herpes simplex virus type 1 contains a hydrophobic stretch of 69 aa near the carboxy terminus that is essential for its biological activity. To determine the role(s) of specific amino acids in the carboxy-terminal hydrophobic region, a number of amino acids were mutagenized that are highly conserved in this region within the gB homologues of the family HERPESVIRIDAE: Three conserved residues in the membrane anchor domain, namely A786, A790 and A791, as well as amino acids G743, G746, G766, G770 and P774, that are non-variant in Herpesviridae, were mutagenized. The ability of the mutant proteins to rescue the infectivity of the gB-null virus, K082, in trans was measured by a complementation assay. All of the mutant proteins formed dimers and were incorporated in virion particles produced in the complementation assay. Mutants G746N, G766N, F770S and P774L showed negligible complementation of K082, whereas mutant G743R showed a reduced activity. Virion particles containing these four mutant glycoproteins also showed a markedly reduced rate of entry compared to the wild-type. The results suggest that non-variant residues in the carboxy-terminal hydrophobic region of the gB protein may be important in virus infectivity.

  10. Molecular genetic aetiology of general cognitive function is enriched in evolutionarily conserved regions.

    PubMed

    Hill, W D; Davies, G; Harris, S E; Hagenaars, S P; Liewald, D C; Penke, L; Gale, C R; Deary, I J

    2016-12-13

    Differences in general cognitive function have been shown to be partly heritable and to show genetic correlations with several psychiatric and physical disease states. However, to date, few single-nucleotide polymorphisms (SNPs) have demonstrated genome-wide significance, hampering efforts aimed at determining which genetic variants are most important for cognitive function and which regions drive the genetic associations between cognitive function and disease states. Here, we combine multiple large genome-wide association study (GWAS) data sets, from the CHARGE cognitive consortium (n=53 949) and UK Biobank (n=36 035), to partition the genome into 52 functional annotations and an additional 10 annotations describing tissue-specific histone marks. Using stratified linkage disequilibrium score regression we show that, in two measures of cognitive function, SNPs associated with cognitive function cluster in regions of the genome that are under evolutionary negative selective pressure. These conserved regions contained ~2.6% of the SNPs from each GWAS but accounted for ~40% of the SNP-based heritability. The results suggest that the search for causal variants associated with cognitive function, and those variants that exert a pleiotropic effect between cognitive function and health, will be facilitated by examining these enriched regions.

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

    USDA-ARS?s Scientific Manuscript database

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

  12. Spatio-temporal variations of conservation hotspots based on ecosystem services in Xishuangbanna, Southwest China.

    PubMed

    Liu, Shiliang; Yin, Yijie; Cheng, Fangyan; Hou, Xiaoyun; Dong, Shikui; Wu, Xue

    2017-01-01

    Integrating biodiversity and ecosystem services (BES) has been viewed as an appropriate approach to identifying conservation priorities. Taking Xishuangbanna tropical region in Southwest China, different BESs (habitat quality [used as a proxy for biodiversity], carbon storage, and water yield) were quantified using the InVEST model and conservation hotspots from 1976, 1990, and 2010 were identified by overlapping and ranking the service layers. Results showed that BESs areas were unevenly distributed. High habitat quality and carbon storage areas located in the eastern part of the region were mainly occupied by broad-leaved forest, while high water yield areas were covered by grassland and tropical forests. Recognized hotspots were primarily composed of the broad-leaved forest and shrub grassland. However, these habitat types declined by nearly 50% from 1.25×105 ha to 0.63×105 ha and became more fragmented during the study period. We also found that the sub-watersheds which decreased in BES had fewer hotspots distributed and suffered greater landscape fragmentation. Our study further explored the impacts of land-use conversion on BES, and illustrated the necessity and feasibility of BESs in identifying potential conservation areas.

  13. Spatio-temporal variations of conservation hotspots based on ecosystem services in Xishuangbanna, Southwest China

    PubMed Central

    Liu, Shiliang; Yin, Yijie; Cheng, Fangyan; Hou, Xiaoyun; Dong, Shikui; Wu, Xue

    2017-01-01

    Integrating biodiversity and ecosystem services (BES) has been viewed as an appropriate approach to identifying conservation priorities. Taking Xishuangbanna tropical region in Southwest China, different BESs (habitat quality [used as a proxy for biodiversity], carbon storage, and water yield) were quantified using the InVEST model and conservation hotspots from 1976, 1990, and 2010 were identified by overlapping and ranking the service layers. Results showed that BESs areas were unevenly distributed. High habitat quality and carbon storage areas located in the eastern part of the region were mainly occupied by broad-leaved forest, while high water yield areas were covered by grassland and tropical forests. Recognized hotspots were primarily composed of the broad-leaved forest and shrub grassland. However, these habitat types declined by nearly 50% from 1.25×105 ha to 0.63×105 ha and became more fragmented during the study period. We also found that the sub-watersheds which decreased in BES had fewer hotspots distributed and suffered greater landscape fragmentation. Our study further explored the impacts of land-use conversion on BES, and illustrated the necessity and feasibility of BESs in identifying potential conservation areas. PMID:29232370

  14. Camcore: Thirty-five years of Mesoamerican pine gene conservation

    Treesearch

    J.L. Lopez; W.S. Dvorak; G.R. Hodge

    2017-01-01

    Camcore is an international tree breeding and conservation program with headquarters at North Carolina State University. Camcore was founded in 1980 as a cooperative, non-profit organization to identify and save the dwindling natural populations of pines in the highland regions of Guatemala in Central America. Funded by the private sector, the program has played an...

  15. Identifying potential recommendation domains for conservation agriculture in Ethiopia, Kenya, and Malawi.

    PubMed

    Tesfaye, Kindie; Jaleta, Moti; Jena, Pradyot; Mutenje, Munyaradzi

    2015-02-01

    Conservation agriculture (CA) is being promoted as an option for reducing soil degradation, conserving water, enhancing crop productivity, and maintaining yield stability. However, CA is a knowledge- and technology-intensive practice, and may not be feasible or may not perform better than conventional agriculture under all conditions and farming systems. Using high resolution (≈1 km(2)) biophysical and socioeconomic geospatial data, this study identified potential recommendation domains (RDs) for CA in Ethiopia, Kenya, and Malawi. The biophysical variables used were soil texture, surface slope, and rainfall while the socioeconomic variables were market access and human and livestock population densities. Based on feasibility and comparative performance of CA over conventional agriculture, the biophysical and socioeconomic factors were first used to classify cultivated areas into three biophysical and three socioeconomic potential domains, respectively. Combinations of biophysical and socioeconomic domains were then used to develop potential RDs for CA based on adoption potential within the cultivated areas. About 39, 12, and 5% of the cultivated areas showed high biophysical and socioeconomic potential while 50, 39, and 21% of the cultivated areas showed high biophysical and medium socioeconomic potential for CA in Malawi, Kenya, and Ethiopia, respectively. The results indicate considerable acreages of land with high CA adoption potential in the mixed crop-livestock systems of the studied countries. However, there are large differences among countries depending on biophysical and socio-economic conditions. The information generated in this study could be used for targeting CA and prioritizing CA-related agricultural research and investment priorities in the three countries.

  16. Identifying Potential Recommendation Domains for Conservation Agriculture in Ethiopia, Kenya, and Malawi

    NASA Astrophysics Data System (ADS)

    Tesfaye, Kindie; Jaleta, Moti; Jena, Pradyot; Mutenje, Munyaradzi

    2015-02-01

    Conservation agriculture (CA) is being promoted as an option for reducing soil degradation, conserving water, enhancing crop productivity, and maintaining yield stability. However, CA is a knowledge- and technology-intensive practice, and may not be feasible or may not perform better than conventional agriculture under all conditions and farming systems. Using high resolution (≈1 km2) biophysical and socioeconomic geospatial data, this study identified potential recommendation domains (RDs) for CA in Ethiopia, Kenya, and Malawi. The biophysical variables used were soil texture, surface slope, and rainfall while the socioeconomic variables were market access and human and livestock population densities. Based on feasibility and comparative performance of CA over conventional agriculture, the biophysical and socioeconomic factors were first used to classify cultivated areas into three biophysical and three socioeconomic potential domains, respectively. Combinations of biophysical and socioeconomic domains were then used to develop potential RDs for CA based on adoption potential within the cultivated areas. About 39, 12, and 5 % of the cultivated areas showed high biophysical and socioeconomic potential while 50, 39, and 21 % of the cultivated areas showed high biophysical and medium socioeconomic potential for CA in Malawi, Kenya, and Ethiopia, respectively. The results indicate considerable acreages of land with high CA adoption potential in the mixed crop-livestock systems of the studied countries. However, there are large differences among countries depending on biophysical and socio-economic conditions. The information generated in this study could be used for targeting CA and prioritizing CA-related agricultural research and investment priorities in the three countries.

  17. CORE_TF: a user-friendly interface to identify evolutionary conserved transcription factor binding sites in sets of co-regulated genes

    PubMed Central

    Hestand, Matthew S; van Galen, Michiel; Villerius, Michel P; van Ommen, Gert-Jan B; den Dunnen, Johan T; 't Hoen, Peter AC

    2008-01-01

    Background The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current approaches. Computational methods to reduce false positives are to look for over-representation of transcription factor binding sites in a set of similarly regulated promoters or to look for conservation in orthologous promoter alignments. Results We have developed a novel tool, "CORE_TF" (Conserved and Over-REpresented Transcription Factor binding sites) that identifies common transcription factor binding sites in promoters of co-regulated genes. To improve upon existing binding site predictions, the tool searches for position weight matrices from the TRANSFACR database that are over-represented in an experimental set compared to a random set of promoters and identifies cross-species conservation of the predicted transcription factor binding sites. The algorithm has been evaluated with expression and chromatin-immunoprecipitation on microarray data. We also implement and demonstrate the importance of matching the random set of promoters to the experimental promoters by GC content, which is a unique feature of our tool. Conclusion The program CORE_TF is accessible in a user friendly web interface at . It provides a table of over-represented transcription factor binding sites in the users input genes' promoters and a graphical view of evolutionary conserved transcription factor binding sites. In our test data sets it successfully predicts target transcription factors and their binding sites. PMID:19036135

  18. Identifying the role of conservation biology for solving the environmental crisis.

    PubMed

    Dalerum, Fredrik

    2014-11-01

    Humans are altering their living environment to an extent that could cause environmental collapse. Promoting change into environmental sustainability is therefore urgent. Despite a rapid expansion in conservation biology, appreciation of underlying causes and identification of long-term solutions have largely been lacking. I summarized knowledge regarding the environmental crisis, and argue that the most important contributions toward solutions come from economy, political sciences, and psychology. Roles of conservation biology include providing environmental protection until sustainable solutions have been found, evaluating the effectiveness of implemented solutions, and providing societies with information necessary to align effectively with environmental values. Because of the potential disciplinary discrepancy between finding long-term solutions and short-term protection, we may face critical trade-offs between allocations of resources toward achieving sustainability. Since biological knowledge is required for such trade-offs, an additional role for conservation biologists may be to provide guidance toward finding optimal strategies in such trade-offs.

  19. 75 FR 12144 - Energy Conservation Program for Consumer Products: Energy Conservation Standards for Residential...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-03-15

    ...-2009-BT-STD-0022] RIN 1904-AC06 Energy Conservation Program for Consumer Products: Energy Conservation... that DOE plans to analyze for purposes of amending energy conservation standards for certain... persons may submit comments, identified by the notice title, the NOPM for Energy Conservation Standards...

  20. Conservation businesses and conservation planning in a biological diversity hotspot.

    PubMed

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

    2013-08-01

    The allocation of land to biological diversity conservation competes with other land uses and the needs of society for development, food, and extraction of natural resources. Trade-offs between biological diversity conservation and alternative land uses are unavoidable, given the realities of limited conservation resources and the competing demands of society. We developed a conservation-planning assessment for the South African province of KwaZulu-Natal, which forms the central component of the Maputaland-Pondoland-Albany biological diversity hotspot. Our objective was to enhance biological diversity protection while promoting sustainable development and providing spatial guidance in the resolution of potential policy conflicts over priority areas for conservation at risk of transformation. The conservation-planning assessment combined spatial-distribution models for 646 conservation features, spatial economic-return models for 28 alternative land uses, and spatial maps for 4 threats. Nature-based tourism businesses were competitive with other land uses and could provide revenues of >US$60 million/year to local stakeholders and simultaneously help meeting conservation goals for almost half the conservation features in the planning region. Accounting for opportunity costs substantially decreased conflicts between biological diversity, agricultural use, commercial forestry, and mining. Accounting for economic benefits arising from conservation and reducing potential policy conflicts with alternative plans for development can provide opportunities for successful strategies that combine conservation and sustainable development and facilitate conservation action. © 2013 Society for Conservation Biology.

  1. LAKE PONTCHARTRAIN ESTUARY CONSERVATION PLAN

    EPA Science Inventory

    The Nature Conservancy will conduct a series of a least four science expert workshops to develop a Site Conservation Plan for the Lake Pontchartrain Estuary and adjacent wetlands. The objective of the Site Conservation Plan is to identify conservation targets, threats or stresse...

  2. Environmental Gap Analysis to Prioritize Conservation Efforts in Eastern Africa

    PubMed Central

    van Breugel, Paulo; Kindt, Roeland; Lillesø, Jens-Peter Barnekow; van Breugel, Michiel

    2015-01-01

    Countries in eastern Africa have set aside significant proportions of their land for protection. But are these areas representative of the diverse range of species and habitats found in the region? And do conservation efforts include areas where the state of biodiversity is likely to deteriorate without further interventions? Various studies have addressed these questions at global and continental scales. However, meaningful conservation decisions are required at finer geographical scales. To operate more effectively at the national level, finer scale baseline data on species and on higher levels of biological organization such as the eco-regions are required, among other factors. Here we adopted a recently developed high-resolution potential natural vegetation (PNV) map for eastern Africa as a baseline to more effectively identify conservation priorities. We examined how well different potential natural vegetations (PNVs) are represented in the protected area (PA) network of eastern Africa and used a multivariate environmental similarity index to evaluate biases in PA versus PNV coverage. We additionally overlaid data of anthropogenic factors that potentially influence the natural vegetation to assess the level of threat to different PNVs. Our results indicate substantial differences in the conservation status of PNVs. In addition, particular PNVs in which biodiversity protection and ecological functions are at risk due to human influences are revealed. The data and approach presented here provide a step forward in developing more transparent and better informed translation from global priorities to regional or national implementation in eastern Africa, and are valid for other geographic regions. PMID:25855968

  3. Decentralizing conservation and diversifying livelihoods within Kanchenjunga Conservation Area, Nepal.

    PubMed

    Parker, Pete; Thapa, Brijesh; Jacob, Aerin

    2015-12-01

    To alleviate poverty and enhance conservation in resource dependent communities, managers must identify existing livelihood strategies and the associated factors that impede household access to livelihood assets. Researchers increasingly advocate reallocating management power from exclusionary central institutions to a decentralized system of management based on local and inclusive participation. However, it is yet to be shown if decentralizing conservation leads to diversified livelihoods within a protected area. The purpose of this study was to identify and assess factors affecting household livelihood diversification within Nepal's Kanchenjunga Conservation Area Project, the first protected area in Asia to decentralize conservation. We randomly surveyed 25% of Kanchenjunga households to assess household socioeconomic and demographic characteristics and access to livelihood assets. We used a cluster analysis with the ten most common income generating activities (both on- and off-farm) to group the strategies households use to diversify livelihoods, and a multinomial logistic regression to identify predictors of livelihood diversification. We found four distinct groups of household livelihood strategies with a range of diversification that directly corresponded to household income. The predictors of livelihood diversification were more related to pre-existing socioeconomic and demographic factors (e.g., more landholdings and livestock, fewer dependents, receiving remittances) than activities sponsored by decentralizing conservation (e.g., microcredit, training, education, interaction with project staff). Taken together, our findings indicate that without direct policies to target marginalized groups, decentralized conservation in Kanchenjunga will continue to exclude marginalized groups, limiting a household's ability to diversify their livelihood and perpetuating their dependence on natural resources. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Conservation of tubulin-binding sequences in TRPV1 throughout evolution.

    PubMed

    Sardar, Puspendu; Kumar, Abhishek; Bhandari, Anita; Goswami, Chandan

    2012-01-01

    Transient Receptor Potential Vanilloid sub type 1 (TRPV1), commonly known as capsaicin receptor can detect multiple stimuli ranging from noxious compounds, low pH, temperature as well as electromagnetic wave at different ranges. In addition, this receptor is involved in multiple physiological and sensory processes. Therefore, functions of TRPV1 have direct influences on adaptation and further evolution also. Availability of various eukaryotic genomic sequences in public domain facilitates us in studying the molecular evolution of TRPV1 protein and the respective conservation of certain domains, motifs and interacting regions that are functionally important. Using statistical and bioinformatics tools, our analysis reveals that TRPV1 has evolved about ∼420 million years ago (MYA). Our analysis reveals that specific regions, domains and motifs of TRPV1 has gone through different selection pressure and thus have different levels of conservation. We found that among all, TRP box is the most conserved and thus have functional significance. Our results also indicate that the tubulin binding sequences (TBS) have evolutionary significance as these stretch sequences are more conserved than many other essential regions of TRPV1. The overall distribution of positively charged residues within the TBS motifs is conserved throughout evolution. In silico analysis reveals that the TBS-1 and TBS-2 of TRPV1 can form helical structures and may play important role in TRPV1 function. Our analysis identifies the regions of TRPV1, which are important for structure-function relationship. This analysis indicates that tubulin binding sequence-1 (TBS-1) near the TRP-box forms a potential helix and the tubulin interactions with TRPV1 via TBS-1 have evolutionary significance. This interaction may be required for the proper channel function and regulation and may also have significance in the context of Taxol®-induced neuropathy.

  5. A framework for identifying carbon hotspots and forest management drivers

    Treesearch

    Nilesh Timilsina; Francisco J. Escobedo; Wendell P. Cropper; Amr Abd-Elrahman; Thomas Brandeis; Sonia Delphin; Samuel Lambert

    2013-01-01

    Spatial analyses of ecosystem system services that are directly relevant to both forest management decision making and conservation in the subtropics are rare. Also, frameworks that identify and map carbon stocks and corresponding forest management drivers using available regional, national, and international-level forest inventory datasets could provide insights into...

  6. Molecular genetic aetiology of general cognitive function is enriched in evolutionarily conserved regions

    PubMed Central

    Hill, W D; Davies, G; Harris, S E; Hagenaars, S P; Davies, Gail; Deary, Ian J; Debette, Stephanie; Verbaas, Carla I; Bressler, Jan; Schuur, Maaike; Smith, Albert V; Bis, Joshua C; Bennett, David A; Ikram, M Arfan; Launer, Lenore J; Fitzpatrick, Annette L; Seshadri, Sudha; van Duijn, Cornelia M; Mosley Jr, Thomas H; Liewald, D C; Penke, L; Gale, C R; Deary, I J

    2016-01-01

    Differences in general cognitive function have been shown to be partly heritable and to show genetic correlations with several psychiatric and physical disease states. However, to date, few single-nucleotide polymorphisms (SNPs) have demonstrated genome-wide significance, hampering efforts aimed at determining which genetic variants are most important for cognitive function and which regions drive the genetic associations between cognitive function and disease states. Here, we combine multiple large genome-wide association study (GWAS) data sets, from the CHARGE cognitive consortium (n=53 949) and UK Biobank (n=36 035), to partition the genome into 52 functional annotations and an additional 10 annotations describing tissue-specific histone marks. Using stratified linkage disequilibrium score regression we show that, in two measures of cognitive function, SNPs associated with cognitive function cluster in regions of the genome that are under evolutionary negative selective pressure. These conserved regions contained ~2.6% of the SNPs from each GWAS but accounted for ~40% of the SNP-based heritability. The results suggest that the search for causal variants associated with cognitive function, and those variants that exert a pleiotropic effect between cognitive function and health, will be facilitated by examining these enriched regions. PMID:27959336

  7. Passive seismic experiment in the Olduvai Gorge and Laetoli region (Ngorongoro Conservation Area), Northern Tanzania.

    NASA Astrophysics Data System (ADS)

    Parisi, Laura; Lombardo, Luigi; Tang, Zheng; Mai, P. Martin

    2017-04-01

    The Olduvai Gorge and Laetoli basins, located within the Ngorogoro Conservation Area (NCA), are a cornerstone for understanding the evolution of early humans and are two paleo-antropological excavation sites of global importance. NCA is located at the boundary between the Tanzanian Craton and East African Rift (EAR), in the vicinity of Ngorongoro Crater and other major volcanic edifices. Thus, understanding the geology and tectonics of the NCA may shed light onto the question why early Hominins settled in this region. Environmental and geological conditions in the Olduvai and Laetoli region that promoted human settlement and development are still debated by geologists and paleo-anthropologists. Paleo-geographical reconstructions of the study area of the last 2 million years may take advantage of modern passive seismology. Therefore, we installed a dense seismic network covering a surface of approximately 30 x 40 km within the NCA to map the depth extent of known faults, and to identify seismically active faults that have no surface expression. Our ten seismic stations, equipped with Trillium Compact 120 s sensors, started to operate in June 2016 and will continue for a total of 2 years. At the end of the first year, other 5 stations will densify our network. Here we analyse data quality of the first four months of continuous recordings. Our network provides good quality 3-C waveforms in the frequency range of 0.7-50 Hz. Vertical component seismograms record frequencies reliably down to 8 mHz. Preliminary results of the seismicity obtained with standard location procedures show that NCA is characterised by frequent tectonic seismicity (not volcano-related) with Ml between 0.5 and 2.0. Seismic activity is more frequent in the South (Laetoli region) where major fault systems have not been recognised at the surface yet.

  8. Use of demand for and spatial flow of ecosystem services to identify priority areas.

    PubMed

    Verhagen, Willem; Kukkala, Aija S; Moilanen, Atte; van Teeffelen, Astrid J A; Verburg, Peter H

    2017-08-01

    Policies and research increasingly focus on the protection of ecosystem services (ESs) through priority-area conservation. Priority areas for ESs should be identified based on ES capacity and ES demand and account for the connections between areas of ES capacity and demand (flow) resulting in areas of unique demand-supply connections (flow zones). We tested ways to account for ES demand and flow zones to identify priority areas in the European Union. We mapped the capacity and demand of a global (carbon sequestration), a regional (flood regulation), and 3 local ESs (air quality, pollination, and urban leisure). We used Zonation software to identify priority areas for ESs based on 6 tests: with and without accounting for ES demand and 4 tests that accounted for the effect of ES flow zone. There was only 37.1% overlap between the 25% of priority areas that encompassed the most ESs with and without accounting for ES demand. The level of ESs maintained in the priority areas increased from 23.2% to 57.9% after accounting for ES demand, especially for ESs with a small flow zone. Accounting for flow zone had a small effect on the location of priority areas and level of ESs maintained but resulted in fewer flow zones without ES maintained relative to ignoring flow zones. Accounting for demand and flow zones enhanced representation and distribution of ESs with local to regional flow zones without large trade-offs relative to the global ES. We found that ignoring ES demand led to the identification of priority areas in remote regions where benefits from ES capacity to society were small. Incorporating ESs in conservation planning should therefore always account for ES demand to identify an effective priority network for ESs. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

  9. American Bird conservancy's approach to the U.S. Important Bird Area Program - identifying the top 500 global sites

    Treesearch

    Robert M. Chipley

    2005-01-01

    The idea for the Important Bird Area Program originated in a series of studies in the early 1980s conducted by BirdLife International. Recognizing that these studies could become a powerful tool for conservation, BirdLife International began an effort to identify and gather data regarding the most important areas for birds in Europe and to make this information...

  10. Global Conservation Priorities for Marine Turtles

    PubMed Central

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

    2011-01-01

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

  11. Benefits of coastal recreation in Europe: identifying trade-offs and priority regions for sustainable management.

    PubMed

    Ghermandi, Andrea

    2015-04-01

    This paper examines the welfare dimension of the recreational services of coastal ecosystems through the application of a meta-analytical value transfer framework, which integrates Geographic Information Systems (GIS) for the characterization of climate, biodiversity, accessibility, and anthropogenic pressure in each of 368 regions of the European coastal zone. The relative contribution of international, domestic, and local recreationists to aggregated regional values is examined. The implications of the analysis for prioritization of conservation areas and identification of good management practices are highlighted through the comparative assessment of estimated recreation values, current environmental pressures, and existing network of protected sites. Copyright © 2015 Elsevier Ltd. All rights reserved.

  12. Conserved DNA motifs in the type II-A CRISPR leader region.

    PubMed

    Van Orden, Mason J; Klein, Peter; Babu, Kesavan; Najar, Fares Z; Rajan, Rakhi

    2017-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3' end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3' leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710) and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3' leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci.

  13. Conserved DNA motifs in the type II-A CRISPR leader region

    PubMed Central

    Babu, Kesavan; Najar, Fares Z.

    2017-01-01

    The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3′ end of the leader, are indispensable for adaptation. However, a comprehensive analysis of leader ends remains absent. Here, we have analyzed the leader, repeat, and Cas proteins from 167 type II-A CRISPR loci. Our results indicate two distinct conserved DNA motifs at the 3′ leader end: ATTTGAG (noted previously in the CRISPR1 locus of Streptococcus thermophilus DGCC7710) and a newly defined CTRCGAG, associated with the CRISPR3 locus of S. thermophilus DGCC7710. A third group with a very short CG DNA conservation at the 3′ leader end is observed mostly in lactobacilli. Analysis of the repeats and Cas proteins revealed clustering of these CRISPR components that mirrors the leader motif clustering, in agreement with the coevolution of CRISPR-Cas components. Based on our analysis of the type II-A CRISPR loci, we implicate leader end sequences that could confer site-specificity for the adaptation-machinery in the different subsets of type II-A CRISPR loci. PMID:28392985

  14. SILAC proteomics of planarians identifies Ncoa5 as a conserved component of pluripotent stem cells.

    PubMed

    Böser, Alexander; Drexler, Hannes C A; Reuter, Hanna; Schmitz, Henning; Wu, Guangming; Schöler, Hans R; Gentile, Luca; Bartscherer, Kerstin

    2013-11-27

    Planarian regeneration depends on the presence of pluripotent stem cells in the adult. We developed an in vivo stable isotope labeling by amino acids in cell culture (SILAC) protocol in planarians to identify proteins that are enriched in planarian stem cells. Through a comparison of SILAC proteomes of normal and stem cell-depleted planarians and of a stem cell-enriched population of sorted cells, we identified hundreds of stem cell proteins. One of these is an ortholog of nuclear receptor coactivator-5 (Ncoa5/CIA), which is known to regulate estrogen-receptor-mediated transcription in human cells. We show that Ncoa5 is essential for the maintenance of the pluripotent stem cell population in planarians and that a putative mouse ortholog is expressed in pluripotent cells of the embryo. Our study thus identifies a conserved component of pluripotent stem cells, demonstrating that planarians, in particular, when combined with in vivo SILAC, are a powerful model in stem cell research. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates

    PubMed Central

    McEwen, Gayle K.; Goode, Debbie K.; Parker, Hugo J.; Woolfe, Adam; Callaway, Heather; Elgar, Greg

    2009-01-01

    Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences, an increasing number of which have been shown to function as enhancers during early development. Despite their extreme conservation over 500 million years from humans to cartilaginous fish, these elements appear to be largely absent in invertebrates, and, to date, there has been little understanding of their mode of action or the evolutionary processes that have modelled them. We have now exploited emerging genomic sequence data for the sea lamprey, Petromyzon marinus, to explore the depth of conservation of this type of element in the earliest diverging extant vertebrate lineage, the jawless fish (agnathans). We searched for conserved non-coding elements (CNEs) at 13 human gene loci and identified lamprey elements associated with all but two of these gene regions. Although markedly shorter and less well conserved than within jawed vertebrates, identified lamprey CNEs are able to drive specific patterns of expression in zebrafish embryos, which are almost identical to those driven by the equivalent human elements. These CNEs are therefore a unique and defining characteristic of all vertebrates. Furthermore, alignment of lamprey and other vertebrate CNEs should permit the identification of persistent sequence signatures that are responsible for common patterns of expression and contribute to the elucidation of the regulatory language in CNEs. Identifying the core regulatory code for development, common to all vertebrates, provides a foundation upon which regulatory networks can be constructed and might also illuminate how large conserved regulatory sequence blocks evolve and become fixed in genomic DNA. PMID:20011110

  16. Global sea turtle conservation successes

    PubMed Central

    Mazaris, Antonios D.; Schofield, Gail; Gkazinou, Chrysoula; Almpanidou, Vasiliki; Hays, Graeme C.

    2017-01-01

    We document a tendency for published estimates of population size in sea turtles to be increasing rather than decreasing across the globe. To examine the population status of the seven species of sea turtle globally, we obtained 299 time series of annual nesting abundance with a total of 4417 annual estimates. The time series ranged in length from 6 to 47 years (mean, 16.2 years). When levels of abundance were summed within regional management units (RMUs) for each species, there were upward trends in 12 RMUs versus downward trends in 5 RMUs. This prevalence of more upward than downward trends was also evident in the individual time series, where we found 95 significant increases in abundance and 35 significant decreases. Adding to this encouraging news for sea turtle conservation, we show that even small sea turtle populations have the capacity to recover, that is, Allee effects appear unimportant. Positive trends in abundance are likely linked to the effective protection of eggs and nesting females, as well as reduced bycatch. However, conservation concerns remain, such as the decline in leatherback turtles in the Eastern and Western Pacific. Furthermore, we also show that, often, time series are too short to identify trends in abundance. Our findings highlight the importance of continued conservation and monitoring efforts that underpin this global conservation success story. PMID:28948215

  17. Conservation of wading birds

    USGS Publications Warehouse

    Kushlan, J.A.

    1996-01-01

    The conservation and management of wading birds has received considerable attention over the past twenty years, through research, population monitoring, habitat protection, and through activities of specialist groups devoted to all three groups, the herons, ibises and allies, and flamingos. While populations are best known in North America, greatest advances in knowledge may have come in Australasia. The status of most species and many populations is now sufficiently known to allow assessment of risk. Conservation and management techniques allow creation of global and regional action plans for conservation of many species. Global action plans are being developed, but few regional plans have been undertaken. Management of nesting sites is now particularly well appreciated. Although known in broad stroke, much remains to be learned about managing feeding habitat. Problems related to disturbance, conflict with humans, habitat loss, contaminants and other environmental stresses remain for some species and many populations. New challenges lie in creating conservation action that account for genetic stocks.

  18. Combined Use of Systematic Conservation Planning, Species Distribution Modelling, and Connectivity Analysis Reveals Severe Conservation Gaps in a Megadiverse Country (Peru)

    PubMed Central

    Fajardo, Javier; Lessmann, Janeth; Bonaccorso, Elisa; Devenish, Christian; Muñoz, Jesús

    2014-01-01

    Conservation planning is crucial for megadiverse countries where biodiversity is coupled with incomplete reserve systems and limited resources to invest in conservation. Using Peru as an example of a megadiverse country, we asked whether the national system of protected areas satisfies biodiversity conservation needs. Further, to complement the existing reserve system, we identified and prioritized potential conservation areas using a combination of species distribution modeling, conservation planning and connectivity analysis. Based on a set of 2,869 species, including mammals, birds, amphibians, reptiles, butterflies, and plants, we used species distribution models to represent species' geographic ranges to reduce the effect of biased sampling and partial knowledge about species' distributions. A site-selection algorithm then searched for efficient and complementary proposals, based on the above distributions, for a more representative system of protection. Finally, we incorporated connectivity among areas in an innovative post-hoc analysis to prioritize those areas maximizing connectivity within the system. Our results highlight severe conservation gaps in the Coastal and Andean regions, and we propose several areas, which are not currently covered by the existing network of protected areas. Our approach helps to find areas that contribute to creating a more representative, connected and efficient network. PMID:25479411

  19. Parameter identifiability and regional calibration for reservoir inflow prediction

    NASA Astrophysics Data System (ADS)

    Kolberg, Sjur; Engeland, Kolbjørn; Tøfte, Lena S.; Bruland, Oddbjørn

    2013-04-01

    The large hydropower producer Statkraft is currently testing regional, distributed models for operational reservoir inflow prediction. The need for simultaneous forecasts and consistent updating in a large number of catchments supports the shift from catchment-oriented to regional models. Low-quality naturalized inflow series in the reservoir catchments further encourages the use of donor catchments and regional simulation for calibration purposes. MCMC based parameter estimation (the Dream algorithm; Vrugt et al, 2009) is adapted to regional parameter estimation, and implemented within the open source ENKI framework. The likelihood is based on the concept of effectively independent number of observations, spatially as well as in time. Marginal and conditional (around an optimum) parameter distributions for each catchment may be extracted, even though the MCMC algorithm itself is guided only by the regional likelihood surface. Early results indicate that the average performance loss associated with regional calibration (difference in Nash-Sutcliffe R2 between regionally and locally optimal parameters) is in the range of 0.06. The importance of the seasonal snow storage and melt in Norwegian mountain catchments probably contributes to the high degree of similarity among catchments. The evaluation continues for several regions, focusing on posterior parameter uncertainty and identifiability. Vrugt, J. A., C. J. F. ter Braak, C. G. H. Diks, B. A. Robinson, J. M. Hyman and D. Higdon: Accelerating Markov Chain Monte Carlo Simulation by Differential Evolution with Self-Adaptive Randomized Subspace Sampling. Int. J. of nonlinear sciences and numerical simulation 10, 3, 273-290, 2009.

  20. Conservation and diversification of the miR166 family in soybean and potential roles of newly identified miR166s.

    PubMed

    Li, Xuyan; Xie, Xin; Li, Ji; Cui, Yuhai; Hou, Yanming; Zhai, Lulu; Wang, Xiao; Fu, Yanli; Liu, Ranran; Bian, Shaomin

    2017-02-01

    microRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, which might exhibit functional redundancy and specificity. The soybean miR166 family consists of 21 members according to the miRBase database. However, the evolutionary conservation and functional diversification of miR166 family members in soybean remain poorly understood. We identified five novel miR166s in soybean by data mining approach, thus enlarging the size of miR166 family from 21 to 26 members. Phylogenetic analyses of the 26 miR166s and their precursors indicated that soybean miR166 family exhibited both evolutionary conservation and diversification, and ten pairs of miR166 precursors with high sequence identity were individually grouped into a discrete clade in the phylogenetic tree. The analysis of genomic organization and evolution of MIR166 gene family revealed that eight segmental duplications and four tandem duplications might occur during evolution of the miR166 family in soybean. The cis-elements in promoters of MIR166 family genes and their putative targets pointed to their possible contributions to the functional conservation and diversification. The targets of soybean miR166s were predicted, and the cleavage of ATHB14-LIKE transcript was experimentally validated by RACE PCR. Further, the expression patterns of the five newly identified MIR166s and 12 target genes were examined during seed development and in response to abiotic stresses, which provided important clues for dissecting their functions and isoform specificity. This study enlarged the size of soybean miR166 family from 21 to 26 members, and the 26 soybean miR166s exhibited evolutionary conservation and diversification. These findings have laid a foundation for elucidating functional conservation and diversification of miR166 family members, especially during seed development or

  1. Incorporating climate change into systematic conservation planning

    USGS Publications Warehouse

    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

    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.

  2. Preferential Targeting of Conserved Gag Regions after Vaccination with a Heterologous DNA Prime-Modified Vaccinia Virus Ankara Boost HIV-1 Vaccine Regimen.

    PubMed

    Bauer, Asli; Podola, Lilli; Mann, Philipp; Missanga, Marco; Haule, Antelmo; Sudi, Lwitiho; Nilsson, Charlotta; Kaluwa, Bahati; Lueer, Cornelia; Mwakatima, Maria; Munseri, Patricia J; Maboko, Leonard; Robb, Merlin L; Tovanabutra, Sodsai; Kijak, Gustavo; Marovich, Mary; McCormack, Sheena; Joseph, Sarah; Lyamuya, Eligius; Wahren, Britta; Sandström, Eric; Biberfeld, Gunnel; Hoelscher, Michael; Bakari, Muhammad; Kroidl, Arne; Geldmacher, Christof

    2017-09-15

    Prime-boost vaccination strategies against HIV-1 often include multiple variants for a given immunogen for better coverage of the extensive viral diversity. To study the immunologic effects of this approach, we characterized breadth, phenotype, function, and specificity of Gag-specific T cells induced by a DNA-prime modified vaccinia virus Ankara (MVA)-boost vaccination strategy, which uses mismatched Gag immunogens in the TamoVac 01 phase IIa trial. Healthy Tanzanian volunteers received three injections of the DNA-SMI vaccine encoding a subtype B and AB-recombinant Gag p37 and two vaccinations with MVA-CMDR encoding subtype A Gag p55 Gag-specific T-cell responses were studied in 42 vaccinees using fresh peripheral blood mononuclear cells. After the first MVA-CMDR boost, vaccine-induced gamma interferon-positive (IFN-γ + ) Gag-specific T-cell responses were dominated by CD4 + T cells ( P < 0.001 compared to CD8 + T cells) that coexpressed interleukin-2 (IL-2) (66.4%) and/or tumor necrosis factor alpha (TNF-α) (63.7%). A median of 3 antigenic regions were targeted with a higher-magnitude median response to Gag p24 regions, more conserved between prime and boost, compared to those of regions within Gag p15 (not primed) and Gag p17 (less conserved; P < 0.0001 for both). Four regions within Gag p24 each were targeted by 45% to 74% of vaccinees upon restimulation with DNA-SMI-Gag matched peptides. The response rate to individual antigenic regions correlated with the sequence homology between the MVA- and DNA Gag-encoded immunogens ( P = 0.04, r 2 = 0.47). In summary, after the first MVA-CMDR boost, the sequence-mismatched DNA-prime MVA-boost vaccine strategy induced a Gag-specific T-cell response that was dominated by polyfunctional CD4 + T cells and that targeted multiple antigenic regions within the conserved Gag p24 protein. IMPORTANCE Genetic diversity is a major challenge for the design of vaccines against variable viruses. While including multiple variants for a

  3. NLEAP/GIS approach for identifying and mitigating regional nitrate-nitrogen leaching

    USGS Publications Warehouse

    Shaffer, M.J.; Hall, M.D.; Wylie, B.K.; Wagner, D.G.; Corwin, D.L.; Loague, K.

    1996-01-01

    Improved simulation-based methodology is needed to help identify broad geographical areas where potential NO3-N leaching may be occurring from agriculture and suggest management alternatives that minimize the problem. The Nitrate Leaching and Economic Analysis Package (NLEAP) model was applied to estimate regional NO3-N leaching in eastern Colorado. Results show that a combined NLEAP/GIS technology can be used to identify potential NO3-N hot spots in shallow alluvial aquifers under irrigated agriculture. The NLEAP NO3-N Leached (NL) index provided the most promising single index followed by NO3-N Available for Leaching (NAL). The same combined technology also shows promise in identifying Best Management Practice (BMP) methods that help minimize NO3-N leaching in vulnerable areas. Future plans call for linkage of the NLEAP/GIS procedures with groundwater modeling to establish a mechanistic analysis of agriculture-aquifer interactions at a regional scale.

  4. Identifying regions of interest in medical images using self-organizing maps.

    PubMed

    Teng, Wei-Guang; Chang, Ping-Lin

    2012-10-01

    Advances in data acquisition, processing and visualization techniques have had a tremendous impact on medical imaging in recent years. However, the interpretation of medical images is still almost always performed by radiologists. Developments in artificial intelligence and image processing have shown the increasingly great potential of computer-aided diagnosis (CAD). Nevertheless, it has remained challenging to develop a general approach to process various commonly used types of medical images (e.g., X-ray, MRI, and ultrasound images). To facilitate diagnosis, we recommend the use of image segmentation to discover regions of interest (ROI) using self-organizing maps (SOM). We devise a two-stage SOM approach that can be used to precisely identify the dominant colors of a medical image and then segment it into several small regions. In addition, by appropriately conducting the recursive merging steps to merge smaller regions into larger ones, radiologists can usually identify one or more ROIs within a medical image.

  5. From Connectivity Models to Region Labels: Identifying Foci of a Neurological Disorder

    PubMed Central

    Venkataraman, Archana; Kubicki, Marek; Golland, Polina

    2014-01-01

    We propose a novel approach to identify the foci of a neurological disorder based on anatomical and functional connectivity information. Specifically, we formulate a generative model that characterizes the network of abnormal functional connectivity emanating from the affected foci. This allows us to aggregate pairwise connectivity changes into a region-based representation of the disease. We employ the variational expectation-maximization algorithm to fit the model and subsequently identify both the afflicted regions and the differences in connectivity induced by the disorder. We demonstrate our method on a population study of schizophrenia. PMID:23864168

  6. Prioritizing sites for conservation based on similarity to historical baselines and feasibility of protection.

    PubMed

    Popejoy, Traci; Randklev, Charles R; Neeson, Thomas M; Vaughn, Caryn C

    2018-05-08

    The shifting baseline syndrome concept advocates for the use of historical knowledge to inform conservation baselines, but does not address the feasibility of restoring sites to those baselines. In many regions, conservation feasibility varies among sites due to differences in resource availability, statutory power, and land-owner participation. We use zooarchaeological records to identify a historical baseline of the freshwater mussel community's composition before Euro-American influence at a river-reach scale. We evaluate how the community reference position and the feasibility of conservation might enable identification of sites where conservation actions would preserve historically representative communities and be likely to succeed. We first present a conceptual model that incorporates community information and landscape factors to link the best conservation areas to potential cost and conservation benefits. Using fuzzy ordination, we identify modern mussel beds that are most like the historical baseline. We then quantify the housing density and land use near each reach to estimate feasibility of habitat restoration. Using our conceptual framework, we identify reaches that have high conservation value (i.e., reaches that contain the best mussel beds) and where restoration actions would be most likely to succeed. Reaches above Lake Belton in central Texas, U.S.A. were most similar in species composition and relative abundance to zooarchaeological sites. A subset of these mussel beds occurred in locations where conservation actions appear to be most feasible. This study demonstrates how to use zooarchaeological data (biodiversity data often readily available) and estimates of conservation feasibility to inform conservation priorities at a local spatial scale. This article is protected by copyright. All rights reserved.

  7. Applications of Rapid Evaluation of Metapopulation Persistence (REMP) in Conservation Planning for Vulnerable Fauna Species.

    PubMed

    Taylor, Subhashni; Drielsma, Michael; Taylor, Robert; Kumar, Lalit

    2016-06-01

    In many regions species are declining due to fragmentation and loss of habitat. If species persistence is to be achieved, ecologically informed, effective conservation action is required. Yet it remains a challenge to identify optimal places in a landscape to direct habitat reconstruction and management. Rather than relying on individual landscape metrics, process-based regional scale assessment methodology is needed that focuses primarily on species persistence. This means integrating, according to species' ecology, habitat extent, suitability, quality and spatial configuration. The rapid evaluation of metapopulation persistence (REMP) methodology has been developed for this purpose. However, till now no practical conservation planning application of REMP has been described. By integration of expert ecological knowledge, we extended REMP's capabilities to prioritize conservation action for a highly modified agricultural region of central NSW, Australia based on the metapopulation ecology of 34 fauna species. The region's current capacity to support the species was evaluated in relation to the pre-European state for which there was known viability. Six of the species were found to currently have insufficient habitat to support viable populations. Seeking locations to maximize overall improvement in viability for these species, we prioritized conservation action to locations near the threshold of metapopulation persistence.

  8. Unravelling biodiversity, evolution and threats to conservation in the Sahara-Sahel.

    PubMed

    Brito, José C; Godinho, Raquel; Martínez-Freiría, Fernando; Pleguezuelos, Juan M; Rebelo, Hugo; Santos, Xavier; Vale, Cândida G; Velo-Antón, Guillermo; Boratyński, Zbyszek; Carvalho, Sílvia B; Ferreira, Sónia; Gonçalves, Duarte V; Silva, Teresa L; Tarroso, Pedro; Campos, João C; Leite, João V; Nogueira, Joana; Alvares, Francisco; Sillero, Neftalí; Sow, Andack S; Fahd, Soumia; Crochet, Pierre-André; Carranza, Salvador

    2014-02-01

    Deserts and arid regions are generally perceived as bare and rather homogeneous areas of low diversity. The Sahara is the largest warm desert in the world and together with the arid Sahel displays high topographical and climatic heterogeneity, and has experienced recent and strong climatic oscillations that have greatly shifted biodiversity distribution and community composition. The large size, remoteness and long-term political instability of the Sahara-Sahel, have limited knowledge on its biodiversity. However, over the last decade, there have been an increasing number of published scientific studies based on modern geomatic and molecular tools, and broad sampling of taxa of these regions. This review tracks trends in knowledge about biodiversity patterns, processes and threats across the Sahara-Sahel, and anticipates needs for biodiversity research and conservation. Recent studies are changing completely the perception of regional biodiversity patterns. Instead of relatively low species diversity with distribution covering most of the region, studies now suggest a high rate of endemism and larger number of species, with much narrower and fragmented ranges, frequently limited to micro-hotspots of biodiversity. Molecular-based studies are also unravelling cryptic diversity associated with mountains, which together with recent distribution atlases, allows identifying integrative biogeographic patterns in biodiversity distribution. Mapping of multivariate environmental variation (at 1 km × 1 km resolution) of the region illustrates main biogeographical features of the Sahara-Sahel and supports recently hypothesised dispersal corridors and refugia. Micro-scale water-features present mostly in mountains have been associated with local biodiversity hotspots. However, the distribution of available data on vertebrates highlights current knowledge gaps that still apply to a large proportion of the Sahara-Sahel. Current research is providing insights into key

  9. Persistent leatherback turtle migrations present opportunities for conservation.

    PubMed

    Shillinger, George L; Palacios, Daniel M; Bailey, Helen; Bograd, Steven J; Swithenbank, Alan M; Gaspar, Philippe; Wallace, Bryan P; Spotila, James R; Paladino, Frank V; Piedra, Rotney; Eckert, Scott A; Block, Barbara A

    2008-07-15

    Effective transboundary conservation of highly migratory marine animals requires international management cooperation as well as clear scientific information about habitat use by these species. Populations of leatherback turtles (Dermochelys coriacea) in the eastern Pacific have declined by >90% during the past two decades, primarily due to unsustainable egg harvest and fisheries bycatch mortality. While research and conservation efforts on nesting beaches are ongoing, relatively little is known about this population of leatherbacks' oceanic habitat use and migration pathways. We present the largest multi-year (2004-2005, 2005-2006, and 2007) satellite tracking dataset (12,095 cumulative satellite tracking days) collected for leatherback turtles. Forty-six females were electronically tagged during three field seasons at Playa Grande, Costa Rica, the largest extant nesting colony in the eastern Pacific. After completing nesting, the turtles headed southward, traversing the dynamic equatorial currents with rapid, directed movements. In contrast to the highly varied dispersal patterns seen in many other sea turtle populations, leatherbacks from Playa Grande traveled within a persistent migration corridor from Costa Rica, past the equator, and into the South Pacific Gyre, a vast, low-energy, low-productivity region. We describe the predictable effects of ocean currents on a leatherback migration corridor and characterize long-distance movements by the turtles in the eastern South Pacific. These data from high seas habitats will also elucidate potential areas for mitigating fisheries bycatch interactions. These findings directly inform existing multinational conservation frameworks and provide immediate regions in the migration corridor where conservation can be implemented. We identify high seas locations for focusing future conservation efforts within the leatherback dispersal zone in the South Pacific Gyre.

  10. Persistent Leatherback Turtle Migrations Present Opportunities for Conservation

    PubMed Central

    Shillinger, George L; Palacios, Daniel M; Bailey, Helen; Bograd, Steven J; Swithenbank, Alan M; Gaspar, Philippe; Wallace, Bryan P; Spotila, James R; Paladino, Frank V; Piedra, Rotney; Eckert, Scott A; Block, Barbara A

    2008-01-01

    Effective transboundary conservation of highly migratory marine animals requires international management cooperation as well as clear scientific information about habitat use by these species. Populations of leatherback turtles (Dermochelys coriacea) in the eastern Pacific have declined by >90% during the past two decades, primarily due to unsustainable egg harvest and fisheries bycatch mortality. While research and conservation efforts on nesting beaches are ongoing, relatively little is known about this population of leatherbacks' oceanic habitat use and migration pathways. We present the largest multi-year (2004–2005, 2005–2006, and 2007) satellite tracking dataset (12,095 cumulative satellite tracking days) collected for leatherback turtles. Forty-six females were electronically tagged during three field seasons at Playa Grande, Costa Rica, the largest extant nesting colony in the eastern Pacific. After completing nesting, the turtles headed southward, traversing the dynamic equatorial currents with rapid, directed movements. In contrast to the highly varied dispersal patterns seen in many other sea turtle populations, leatherbacks from Playa Grande traveled within a persistent migration corridor from Costa Rica, past the equator, and into the South Pacific Gyre, a vast, low-energy, low-productivity region. We describe the predictable effects of ocean currents on a leatherback migration corridor and characterize long-distance movements by the turtles in the eastern South Pacific. These data from high seas habitats will also elucidate potential areas for mitigating fisheries bycatch interactions. These findings directly inform existing multinational conservation frameworks and provide immediate regions in the migration corridor where conservation can be implemented. We identify high seas locations for focusing future conservation efforts within the leatherback dispersal zone in the South Pacific Gyre. PMID:18630987

  11. Conservation genetics and genomics of amphibians and reptiles.

    PubMed

    Shaffer, H Bradley; Gidiş, Müge; McCartney-Melstad, Evan; Neal, Kevin M; Oyamaguchi, Hilton M; Tellez, Marisa; Toffelmier, Erin M

    2015-01-01

    Amphibians and reptiles as a group are often secretive, reach their greatest diversity often in remote tropical regions, and contain some of the most endangered groups of organisms on earth. Particularly in the past decade, genetics and genomics have been instrumental in the conservation biology of these cryptic vertebrates, enabling work ranging from the identification of populations subject to trade and exploitation, to the identification of cryptic lineages harboring critical genetic variation, to the analysis of genes controlling key life history traits. In this review, we highlight some of the most important ways that genetic analyses have brought new insights to the conservation of amphibians and reptiles. Although genomics has only recently emerged as part of this conservation tool kit, several large-scale data sources, including full genomes, expressed sequence tags, and transcriptomes, are providing new opportunities to identify key genes, quantify landscape effects, and manage captive breeding stocks of at-risk species.

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

    PubMed

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

    2014-01-01

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

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

    PubMed Central

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

    2014-01-01

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

  14. 50 CFR 665.208 - Protected species conservation.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 13 2013-10-01 2013-10-01 false Protected species conservation. 665.208... Fisheries § 665.208 Protected species conservation. The Regional Administrator may change the size of the protected species study zones defined in § 665.201 of this subpart: (a) If the Regional Administrator...

  15. 50 CFR 665.208 - Protected species conservation.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 50 Wildlife and Fisheries 11 2011-10-01 2011-10-01 false Protected species conservation. 665.208... Fisheries § 665.208 Protected species conservation. The Regional Administrator may change the size of the protected species study zones defined in § 665.201 of this subpart: (a) If the Regional Administrator...

  16. 50 CFR 665.208 - Protected species conservation.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 50 Wildlife and Fisheries 9 2010-10-01 2010-10-01 false Protected species conservation. 665.208... Fisheries § 665.208 Protected species conservation. The Regional Administrator may change the size of the protected species study zones defined in § 665.201 of this subpart: (a) If the Regional Administrator...

  17. 50 CFR 665.208 - Protected species conservation.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 50 Wildlife and Fisheries 13 2012-10-01 2012-10-01 false Protected species conservation. 665.208... Fisheries § 665.208 Protected species conservation. The Regional Administrator may change the size of the protected species study zones defined in § 665.201 of this subpart: (a) If the Regional Administrator...

  18. 50 CFR 665.208 - Protected species conservation.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 13 2014-10-01 2014-10-01 false Protected species conservation. 665.208... Fisheries § 665.208 Protected species conservation. The Regional Administrator may change the size of the protected species study zones defined in § 665.201 of this subpart: (a) If the Regional Administrator...

  19. Conservation buffer distance estimates for Greater Sage-Grouse: a review

    USGS Publications Warehouse

    Manier, Daniel J.; Bowen, Zachary H.; Brooks, Matthew L.; Casazza, Michael L.; Coates, Peter S.; Deibert, Patricia A.; Hanser, Steven E.; Johnson, Douglas H.

    2014-01-01

    Distances in this report reflect radii around lek locations because these locations are typically (although not universally) known, and management plans often refer to these locations. Lek sites are most representative of breeding habitats, but their locations are focal points within populations, and as such, protective buffers around lek sites can offer a useful solution for identifying and conserving seasonal habitats required by sage-grouse throughout their life cycle. However, knowledge of local and regional patterns of seasonal habitat use may improve conservation of those important areas, especially regarding the distribution and utilization of nonbreeding season habitats (which may be underrepresented in lek-based designations).

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

    PubMed

    Chakravorty, S; Sarkar, S; Gachhui, R

    2015-01-01

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

  1. Designing systematic conservation assessments that promote effective implementation: best practice from South Africa.

    PubMed

    Knight, Andrew T; Driver, Amanda; Cowling, Richard M; Maze, Kristal; Desmet, Philip G; Lombard, Amanda T; Rouget, Mathieu; Botha, Mark A; Boshoff, Andre F; Castley, J Guy; Goodman, Peter S; Mackinnon, Kathy; Pierce, Shirley M; Sims-Castley, Rebecca; Stewart, Warrick I; von Hase, Amrei

    2006-06-01

    Systematic conservation assessment and conservation planning are two distinct fields of conservation science often confused as one and the same. Systematic conservation assessment is the technical, often computer-based, identification of priority areas for conservation. Conservation planning is composed of a systematic conservation assessment coupled with processes for development of an implementation strategy and stakeholder collaboration. The peer-reviewed conservation biology literature abounds with studies analyzing the performance of assessments (e.g., area-selection techniques). This information alone, however can never deliver effective conservation action; it informs conservation planning. Examples of how to translate systematic assessment outputs into knowledge and then use them for "doing" conservation are rare. South Africa has received generous international and domestic funding for regional conservation planning since the mid-1990s. We reviewed eight South African conservation planning processes and identified key ingredients of best practice for undertaking systematic conservation assessments in a way that facilitates implementing conservation action. These key ingredients include the design of conservation planning processes, skills for conservation assessment teams, collaboration with stakeholders, and interpretation and mainstreaming of products (e.g., maps) for stakeholders. Social learning institutions are critical to the successful operationalization of assessments within broader conservation planning processes and should include not only conservation planners but also diverse interest groups, including rural landowners, politicians, and government employees.

  2. Incorporating seascape connectivity in conservation prioritisation.

    PubMed

    Weeks, Rebecca

    2017-01-01

    In conservation prioritisation, it is often implicit that representation targets for individual habitat types act as surrogates for the species that inhabit them. Yet for many commercially and ecologically important coral reef fish species, connectivity among different habitats in a seascape may be more important than any single habitat alone. Approaches to conservation prioritisation that consider seascape connectivity are thus warranted. I demonstrate an approach that can be implemented within a relatively data-poor context, using widely available conservation planning software. Based on clearly stated assumptions regarding species' habitat usage and movement ability, this approach can be adapted to different focal species and contexts, or refined as further data become available. I first derive a seascape connectivity metric based on area-weighted proximity between juvenile and adult habitat patches, and then apply this during spatial prioritisation using the decision-support software Marxan. Using a case study from Micronesia, I present two applications: first, to inform prioritisation for a network of marine protected areas to achieve regional objectives for habitat representation; and second, to identify nursery habitat patches that are most likely to supply juveniles to adult populations on reefs within existing protected areas. Incorporating seascape connectivity in conservation prioritisation highlights areas where small marine protected areas placed on coral reefs might benefit from proximity to other habitats in the seascape, and thus be more effective. Within the context of community tenure over resources, identification of critical nursery habitats to improve the effectiveness of existing marine protected areas indicates where collaboration across community boundaries might be required. Outputs from these analyses are likely to be most useful in regions where management is highly decentralised, imposing spatial constraints on the size of individual

  3. Incorporating seascape connectivity in conservation prioritisation

    PubMed Central

    2017-01-01

    In conservation prioritisation, it is often implicit that representation targets for individual habitat types act as surrogates for the species that inhabit them. Yet for many commercially and ecologically important coral reef fish species, connectivity among different habitats in a seascape may be more important than any single habitat alone. Approaches to conservation prioritisation that consider seascape connectivity are thus warranted. I demonstrate an approach that can be implemented within a relatively data-poor context, using widely available conservation planning software. Based on clearly stated assumptions regarding species’ habitat usage and movement ability, this approach can be adapted to different focal species and contexts, or refined as further data become available. I first derive a seascape connectivity metric based on area-weighted proximity between juvenile and adult habitat patches, and then apply this during spatial prioritisation using the decision-support software Marxan. Using a case study from Micronesia, I present two applications: first, to inform prioritisation for a network of marine protected areas to achieve regional objectives for habitat representation; and second, to identify nursery habitat patches that are most likely to supply juveniles to adult populations on reefs within existing protected areas. Incorporating seascape connectivity in conservation prioritisation highlights areas where small marine protected areas placed on coral reefs might benefit from proximity to other habitats in the seascape, and thus be more effective. Within the context of community tenure over resources, identification of critical nursery habitats to improve the effectiveness of existing marine protected areas indicates where collaboration across community boundaries might be required. Outputs from these analyses are likely to be most useful in regions where management is highly decentralised, imposing spatial constraints on the size of individual

  4. Object-based forest classification to facilitate landscape-scale conservation in the Mississippi Alluvial Valley

    USGS Publications Warehouse

    Mitchell, Michael; Wilson, R. Randy; Twedt, Daniel J.; Mini, Anne E.; James, J. Dale

    2016-01-01

    The Mississippi Alluvial Valley is a floodplain along the southern extent of the Mississippi River extending from southern Missouri to the Gulf of Mexico. This area once encompassed nearly 10 million ha of floodplain forests, most of which has been converted to agriculture over the past two centuries. Conservation programs in this region revolve around protection of existing forest and reforestation of converted lands. Therefore, an accurate and up to date classification of forest cover is essential for conservation planning, including efforts that prioritize areas for conservation activities. We used object-based image analysis with Random Forest classification to quickly and accurately classify forest cover. We used Landsat band, band ratio, and band index statistics to identify and define similar objects as our training sets instead of selecting individual training points. This provided a single rule-set that was used to classify each of the 11 Landsat 5 Thematic Mapper scenes that encompassed the Mississippi Alluvial Valley. We classified 3,307,910±85,344 ha (32% of this region) as forest. Our overall classification accuracy was 96.9% with Kappa statistic of 0.96. Because this method of forest classification is rapid and accurate, assessment of forest cover can be regularly updated and progress toward forest habitat goals identified in conservation plans can be periodically evaluated.

  5. Geographic variation in species richness, rarity, and the selection of areas for conservation: An integrative approach with Brazilian estuarine fishes

    NASA Astrophysics Data System (ADS)

    Vilar, Ciro C.; Joyeux, Jean-Christophe; Spach, Henry L.

    2017-09-01

    While the number of species is a key indicator of ecological assemblages, spatial conservation priorities solely identified from species richness are not necessarily efficient to protect other important biological assets. Hence, the results of spatial prioritization analysis would be greatly enhanced if richness were used in association to complementary biodiversity measures. In this study, geographic patterns in estuarine fish species rarity (i.e. the average range size in the study area), endemism and richness, were mapped and integrated to identify regions important for biodiversity conservation along the Brazilian coast. Furthermore, we analyzed the effectiveness of the national system of protected areas to represent these regions. Analyses were performed on presence/absence data of 412 fish species in 0.25° latitudinal bands covering the entire Brazilian biogeographical province. Species richness, rarity and endemism patterns differed and strongly reflected biogeographical limits and regions. However, among the existing 154 latitudinal bands, 48 were recognized as conservation priorities by concomitantly harboring high estuarine fish species richness and assemblages of geographically rare species. Priority areas identified for all estuarine fish species largely differed from those identified for Brazilian endemics. Moreover, there was no significant correlation between the different aspects of the fish assemblages considered (i.e. species richness, endemism or rarity), suggesting that designating reserves based on a single variable may lead to large gaps in the overall protection of biodiversity. Our results further revealed that the existing system of protected areas is insufficient for representing the priority bands we identified. This highlights the urgent need for expanding the national network of protected areas to maintain estuarine ecosystems with high conservation value.

  6. Application of selection mapping to identify genomic regions associated with dairy production in sheep.

    PubMed

    Gutiérrez-Gil, Beatriz; Arranz, Juan Jose; Pong-Wong, Ricardo; García-Gámez, Elsa; Kijas, James; Wiener, Pamela

    2014-01-01

    In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of "dairy breeds." This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep.

  7. Application of Selection Mapping to Identify Genomic Regions Associated with Dairy Production in Sheep

    PubMed Central

    Gutiérrez-Gil, Beatriz; Arranz, Juan Jose; Pong-Wong, Ricardo; García-Gámez, Elsa; Kijas, James; Wiener, Pamela

    2014-01-01

    In Europe, especially in Mediterranean areas, the sheep has been traditionally exploited as a dual purpose species, with income from both meat and milk. Modernization of husbandry methods and the establishment of breeding schemes focused on milk production have led to the development of “dairy breeds.” This study investigated selective sweeps specifically related to dairy production in sheep by searching for regions commonly identified in different European dairy breeds. With this aim, genotypes from 44,545 SNP markers covering the sheep autosomes were analysed in both European dairy and non-dairy sheep breeds using two approaches: (i) identification of genomic regions showing extreme genetic differentiation between each dairy breed and a closely related non-dairy breed, and (ii) identification of regions with reduced variation (heterozygosity) in the dairy breeds using two methods. Regions detected in at least two breeds (breed pairs) by the two approaches (genetic differentiation and at least one of the heterozygosity-based analyses) were labeled as core candidate convergence regions and further investigated for candidate genes. Following this approach six regions were detected. For some of them, strong candidate genes have been proposed (e.g. ABCG2, SPP1), whereas some other genes designated as candidates based on their association with sheep and cattle dairy traits (e.g. LALBA, DGAT1A) were not associated with a detectable sweep signal. Few of the identified regions were coincident with QTL previously reported in sheep, although many of them corresponded to orthologous regions in cattle where QTL for dairy traits have been identified. Due to the limited number of QTL studies reported in sheep compared with cattle, the results illustrate the potential value of selection mapping to identify genomic regions associated with dairy traits in sheep. PMID:24788864

  8. Long-range comparison of human and mouse Sprr loci to identify conserved noncoding sequences involved in coordinate regulation

    PubMed Central

    Martin, Natalia; Patel, Satyakam; Segre, Julia A.

    2004-01-01

    Mammalian epidermis provides a permeability barrier between an organism and its environment. Under homeostatic conditions, epidermal cells produce structural proteins, which are cross-linked in an orderly fashion to form a cornified envelope (CE). However, under genetic or environmental stress, specific genes are induced to rapidly build a temporary barrier. Small proline-rich (SPRR) proteins are the primary constituents of the CE. Under stress the entire family of 14 Sprr genes is upregulated. The Sprr genes are clustered within the larger epidermal differentiation complex on mouse chromosome 3, human chromosome 1q21. The clustering of the Sprr genes and their upregulation under stress suggest that these genes may be coordinately regulated. To identify enhancer elements that regulate this stress response activation of the Sprr locus, we utilized bioinformatic tools and classical biochemical dissection. Long-range comparative sequence analysis identified conserved noncoding sequences (CNSs). Clusters of epidermal-specific DNaseI-hypersensitive sites (HSs) mapped to specific CNSs. Increased prevalence of these HSs in barrier-deficient epidermis provides in vivo evidence of the regulation of the Sprr locus by these conserved sequences. Individual components of these HSs were cloned, and one was shown to have strong enhancer activity specific to conditions when the Sprr genes are coordinately upregulated. PMID:15574822

  9. Future battlegrounds for conservation under global change

    PubMed Central

    Lee, Tien Ming; Jetz, Walter

    2008-01-01

    Global biodiversity is under significant threat from the combined effects of human-induced climate and land-use change. Covering 12% of the Earth's terrestrial surface, protected areas are crucial for conserving biodiversity and supporting ecological processes beneficial to human well-being, but their selection and design are usually uninformed about future global change. Here, we quantify the exposure of the global reserve network to projected climate and land-use change according to the Millennium Ecosystem Assessment and set these threats in relation to the conservation value and capacity of biogeographic and geopolitical regions. We find that geographical patterns of past human impact on the land cover only poorly predict those of forecasted change, thus revealing the inadequacy of existing global conservation prioritization templates. Projected conservation risk, measured as regional levels of land-cover change in relation to area protected, is the greatest at high latitudes (due to climate change) and tropics/subtropics (due to land-use change). Only some high-latitude nations prone to high conservation risk are also of high conservation value, but their high relative wealth may facilitate additional conservation efforts. In contrast, most low-latitude nations tend to be of high conservation value, but they often have limited capacity for conservation which may exacerbate the global biodiversity extinction crisis. While our approach will clearly benefit from improved land-cover projections and a thorough understanding of how species range will shift under climate change, our results provide a first global quantitative demonstration of the urgent need to consider future environmental change in reserve-based conservation planning. They further highlight the pressing need for new reserves in target regions and support a much extended ‘north–south’ transfer of conservation resources that maximizes biodiversity conservation while mitigating global climate

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

    PubMed

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

    2013-11-01

    Documenting and preserving the genetic diversity of populations, which conditions their long-term survival, have become a major issue in conservation biology. The loss of diversity often documented in declining populations is usually assumed to result from human disturbances; however, historical biogeographic events, otherwise known to strongly impact diversity, are rarely considered in this context. We apply a multilocus phylogeographic study to investigate the late-Quaternary history of a tree frog (Hyla arborea) with declining populations in the northern and western part of its distribution range. Mitochondrial and nuclear polymorphisms reveal high genetic diversity in the Balkan Peninsula, with a spatial structure moulded by the last glaciations. While two of the main refugial lineages remained limited to the Balkans (Adriatic coast, southern Balkans), a third one expanded to recolonize Northern and Western Europe, loosing much of its diversity in the process. Our findings show that mobile and a priori homogeneous taxa may also display substructure within glacial refugia ('refugia within refugia') and emphasize the importance of the Balkans as a major European biodiversity centre. Moreover, the distribution of diversity roughly coincides with regional conservation situations, consistent with the idea that historically impoverished genetic diversity may interact with anthropogenic disturbances, and increase the vulnerability of populations. Phylogeographic models seem important to fully appreciate the risks of local declines and inform conservation strategies. © 2013 John Wiley & Sons Ltd.

  11. No Reef Is an Island: Integrating Coral Reef Connectivity Data into the Design of Regional-Scale Marine Protected Area Networks.

    PubMed

    Schill, Steven R; Raber, George T; Roberts, Jason J; Treml, Eric A; Brenner, Jorge; Halpin, Patrick N

    2015-01-01

    We integrated coral reef connectivity data for the Caribbean and Gulf of Mexico into a conservation decision-making framework for designing a regional scale marine protected area (MPA) network that provides insight into ecological and political contexts. We used an ocean circulation model and regional coral reef data to simulate eight spawning events from 2008-2011, applying a maximum 30-day pelagic larval duration and 20% mortality rate. Coral larval dispersal patterns were analyzed between coral reefs across jurisdictional marine zones to identify spatial relationships between larval sources and destinations within countries and territories across the region. We applied our results in Marxan, a conservation planning software tool, to identify a regional coral reef MPA network design that meets conservation goals, minimizes underlying threats, and maintains coral reef connectivity. Our results suggest that approximately 77% of coral reefs identified as having a high regional connectivity value are not included in the existing MPA network. This research is unique because we quantify and report coral larval connectivity data by marine ecoregions and Exclusive Economic Zones (EZZ) and use this information to identify gaps in the current Caribbean-wide MPA network by integrating asymmetric connectivity information in Marxan to design a regional MPA network that includes important reef network connections. The identification of important reef connectivity metrics guides the selection of priority conservation areas and supports resilience at the whole system level into the future.

  12. No Reef Is an Island: Integrating Coral Reef Connectivity Data into the Design of Regional-Scale Marine Protected Area Networks

    PubMed Central

    Schill, Steven R.; Raber, George T.; Roberts, Jason J.; Treml, Eric A.; Brenner, Jorge; Halpin, Patrick N.

    2015-01-01

    We integrated coral reef connectivity data for the Caribbean and Gulf of Mexico into a conservation decision-making framework for designing a regional scale marine protected area (MPA) network that provides insight into ecological and political contexts. We used an ocean circulation model and regional coral reef data to simulate eight spawning events from 2008–2011, applying a maximum 30-day pelagic larval duration and 20% mortality rate. Coral larval dispersal patterns were analyzed between coral reefs across jurisdictional marine zones to identify spatial relationships between larval sources and destinations within countries and territories across the region. We applied our results in Marxan, a conservation planning software tool, to identify a regional coral reef MPA network design that meets conservation goals, minimizes underlying threats, and maintains coral reef connectivity. Our results suggest that approximately 77% of coral reefs identified as having a high regional connectivity value are not included in the existing MPA network. This research is unique because we quantify and report coral larval connectivity data by marine ecoregions and Exclusive Economic Zones (EZZ) and use this information to identify gaps in the current Caribbean-wide MPA network by integrating asymmetric connectivity information in Marxan to design a regional MPA network that includes important reef network connections. The identification of important reef connectivity metrics guides the selection of priority conservation areas and supports resilience at the whole system level into the future. PMID:26641083

  13. Designing coastal conservation to deliver ecosystem and human well-being benefits.

    PubMed

    Annis, Gust M; Pearsall, Douglas R; Kahl, Katherine J; Washburn, Erika L; May, Christopher A; Franks Taylor, Rachael; Cole, James B; Ewert, David N; Game, Edward T; Doran, Patrick J

    2017-01-01

    Conservation scientists increasingly recognize that incorporating human values into conservation planning increases the chances for success by garnering broader project acceptance. However, methods for defining quantitative targets for the spatial representation of human well-being priorities are less developed. In this study we employ an approach for identifying regionally important human values and establishing specific spatial targets for their representation based on stakeholder outreach. Our primary objective was to develop a spatially-explicit conservation plan that identifies the most efficient locations for conservation actions to meet ecological goals while sustaining or enhancing human well-being values within the coastal and nearshore areas of the western Lake Erie basin (WLEB). We conducted an optimization analysis using 26 features representing ecological and human well-being priorities (13 of each), and included seven cost layers. The influence that including human well-being had on project results was tested by running five scenarios and setting targets for human well-being at different levels in each scenario. The most important areas for conservation to achieve multiple goals are clustered along the coast, reflecting a concentration of existing or potentially restorable coastal wetlands, coastal landbird stopover habitat and terrestrial biodiversity, as well as important recreational activities. Inland important areas tended to cluster around trails and high quality inland landbird stopover habitat. Most concentrated areas of importance also are centered on lands that are already conserved, reflecting the lower costs and higher benefits of enlarging these conserved areas rather than conserving isolated, dispersed areas. Including human well-being features in the analysis only influenced the solution at the highest target levels.

  14. Designing coastal conservation to deliver ecosystem and human well-being benefits

    PubMed Central

    Pearsall, Douglas R.; Kahl, Katherine J.; Washburn, Erika L.; May, Christopher A.; Franks Taylor, Rachael; Cole, James B.; Ewert, David N.; Game, Edward T.; Doran, Patrick J.

    2017-01-01

    Conservation scientists increasingly recognize that incorporating human values into conservation planning increases the chances for success by garnering broader project acceptance. However, methods for defining quantitative targets for the spatial representation of human well-being priorities are less developed. In this study we employ an approach for identifying regionally important human values and establishing specific spatial targets for their representation based on stakeholder outreach. Our primary objective was to develop a spatially-explicit conservation plan that identifies the most efficient locations for conservation actions to meet ecological goals while sustaining or enhancing human well-being values within the coastal and nearshore areas of the western Lake Erie basin (WLEB). We conducted an optimization analysis using 26 features representing ecological and human well-being priorities (13 of each), and included seven cost layers. The influence that including human well-being had on project results was tested by running five scenarios and setting targets for human well-being at different levels in each scenario. The most important areas for conservation to achieve multiple goals are clustered along the coast, reflecting a concentration of existing or potentially restorable coastal wetlands, coastal landbird stopover habitat and terrestrial biodiversity, as well as important recreational activities. Inland important areas tended to cluster around trails and high quality inland landbird stopover habitat. Most concentrated areas of importance also are centered on lands that are already conserved, reflecting the lower costs and higher benefits of enlarging these conserved areas rather than conserving isolated, dispersed areas. Including human well-being features in the analysis only influenced the solution at the highest target levels. PMID:28241018

  15. Geographic bias in citation rates of conservation research.

    PubMed

    Meijaard, Erik; Cardillo, Marcel; Meijaard, Emily M; Possingham, Hugh P

    2015-06-01

    We investigated whether the impact of conservation science is greater for research conducted in countries with more pressing conservation problems. We quantified research impact for 231 countries based on 2 citation metrics (mean cites per paper and h index) and fitted models predicting research impact based on number of threatened bird and mammal species (as a measure of conservation importance of a country) and a range of demographic variables. Citation rates of conservation research increased as a country's conservation need increased and as human population, quality of governance, and wealth increased. Even after accounting for these factors, citation rates among regions and countries within regions varied significantly. The conservation research community needs to consider ways to begin addressing the entrenched disadvantages some countries have when it comes to initiating projects and producing high-quality research. © 2015 Society for Conservation Biology.

  16. 75 FR 5544 - Energy Conservation Program: Energy Conservation Standards for Metal Halide Lamp Fixtures: Public...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-02-03

    ...-2009-BT-STD-0018] RIN 1904-AC00 Energy Conservation Program: Energy Conservation Standards for Metal... certain metal halide lamp fixtures. This document announces that the period for submitting comments on the... identify the Framework Document for energy conservation standards for metal halide lamp fixtures and...

  17. Application of models to conservation planning for terrestrial birds in North America

    USGS Publications Warehouse

    Fitzgerald, Jane A.; Thogmartin, Wayne E.; Dettmers, Randy; Jones, Tim; Rustay, Christopher; Ruth, Janet M.; Thompson, Frank R.; Will, Tom; Millspaugh, Joshua J.; Thompson, Frank R.

    2009-01-01

    Partners in Flight (PIF), a public–private coalition for the conservation of land birds, has developed one of four international bird conservation plans recognized under the auspices of the North American Bird Conservation Initiative (NABCI). Partners in Flight prioritized species most in need of conservation attention and set range-wide population goals for 448 species of terrestrial birds. Partnerships are now tasked with developing spatially explicit estimates of the distribution, and abundance of priority species across large ecoregions and identifying habitat acreages needed to support populations at prescribed levels. The PIF Five Elements process of conservation design identifies five steps needed to implement all bird conservation at the ecoregional scale. Habitat assessment and landscape characterization describe the current amounts of different habitat types and summarize patch characteristics, and landscape configurations that define the ability of a landscape to sustain healthy bird populations and are a valuable first step to describing the planning area before pursuing more complex species-specific models. Spatially linked database models, landscape-scale habitat suitability models, and statistical models are viable alternatives for predicting habitat suitability or bird abundance across large planning areas to help assess conservation opportunities, design landscapes to meet population objectives, and monitor change in habitat suitability or bird numbers over time.Bird conservation in the United States is a good example of the use of models in large-scale wildlife conservation planning because of its geographic extent, focus on multiple species, involvement of multiple partners, and use of simple to complex models. We provide some background on the recent development of bird conservation initiatives in the United States and the approaches used for regional conservation assessment and planning. We focus on approaches being used for landscape

  18. The Conserved Foot Domain of RNA Pol II Associates with Proteins Involved in Transcriptional Initiation and/or Early Elongation

    PubMed Central

    García-López, M. Carmen; Pelechano, Vicent; Mirón-García, M. Carmen; Garrido-Godino, Ana I.; García, Alicia; Calvo, Olga; Werner, Michel; Pérez-Ortín, José E.; Navarro, Francisco

    2011-01-01

    RNA polymerase (pol) II establishes many protein–protein interactions with transcriptional regulators to coordinate different steps of transcription. Although some of these interactions have been well described, little is known about the existence of RNA pol II regions involved in contact with transcriptional regulators. We hypothesize that conserved regions on the surface of RNA pol II contact transcriptional regulators. We identified such an RNA pol II conserved region that includes the majority of the “foot” domain and identified interactions of this region with Mvp1, a protein required for sorting proteins to the vacuole, and Spo14, a phospholipase D. Deletion of MVP1 and SPO14 affects the transcription of their target genes and increases phosphorylation of Ser5 in the carboxy-terminal domain (CTD). Genetic, phenotypic, and functional analyses point to a role for these proteins in transcriptional initiation and/or early elongation, consistent with their genetic interactions with CEG1, a guanylyltransferase subunit of the Saccharomyces cerevisiae capping enzyme. PMID:21954159

  19. Using Personal Water Footprints to Identify Consumer Food Choices that Influence the Conservation of Local Water Resources

    NASA Astrophysics Data System (ADS)

    Marrin, D. L.

    2015-12-01

    As the global demand for water and food escalates, the emphasis is on supply side factors rather than demand side factors such as consumers, whose personal water footprints are dominated (>90%) by food. Personal footprints include the water embedded in foods that are produced locally as well as those imported, raising the question of whether local shifts in people's food choices and habits could assist in addressing local water shortages. The current situation in California is interesting in that drought has affected an agriculturally productive region where a substantial portion of its food products are consumed by the state's large population. Unlike most agricultural regions where green water is the primary source of water for crops, California's arid climate demands an enormous volume of blue water as irrigation from its dwindling surface and ground water resources. Although California exports many of its food products, enough is consumed in-state so that residents making relatively minor shifts their food choices could save as much local blue water as their implementing more drastic reductions in household water use (comprising <5% of their personal footprint). One of those shifts is reducing the intake of meat and dairy products that account for just under half of a Californian's blue-green water footprint and that require the most water of any food group on both a caloric and gravimetric basis. Another change is wasting less food, which is a shared responsibility among consumers, producers and retailers; however, consumers' actions and preferences ultimately drive much of the waste. Personal water footprints suggest a role for individuals in conserving local water resources that is neither readily obvious nor a major focus of most conservation programs.

  20. Simple Model for Identifying Critical Regions in Atrial Fibrillation

    NASA Astrophysics Data System (ADS)

    Christensen, Kim; Manani, Kishan A.; Peters, Nicholas S.

    2015-01-01

    Atrial fibrillation (AF) is the most common abnormal heart rhythm and the single biggest cause of stroke. Ablation, destroying regions of the atria, is applied largely empirically and can be curative but with a disappointing clinical success rate. We design a simple model of activation wave front propagation on an anisotropic structure mimicking the branching network of heart muscle cells. This integration of phenomenological dynamics and pertinent structure shows how AF emerges spontaneously when the transverse cell-to-cell coupling decreases, as occurs with age, beyond a threshold value. We identify critical regions responsible for the initiation and maintenance of AF, the ablation of which terminates AF. The simplicity of the model allows us to calculate analytically the risk of arrhythmia and express the threshold value of transversal cell-to-cell coupling as a function of the model parameters. This threshold value decreases with increasing refractory period by reducing the number of critical regions which can initiate and sustain microreentrant circuits. These biologically testable predictions might inform ablation therapies and arrhythmic risk assessment.

  1. Building Virtual Watersheds: A Global Opportunity to Strengthen Resource Management and Conservation.

    PubMed

    Benda, Lee; Miller, Daniel; Barquin, Jose; McCleary, Richard; Cai, TiJiu; Ji, Y

    2016-03-01

    Modern land-use planning and conservation strategies at landscape to country scales worldwide require complete and accurate digital representations of river networks, encompassing all channels including the smallest headwaters. The digital river networks, integrated with widely available digital elevation models, also need to have analytical capabilities to support resource management and conservation, including attributing river segments with key stream and watershed data, characterizing topography to identify landforms, discretizing land uses at scales necessary to identify human-environment interactions, and connecting channels downstream and upstream, and to terrestrial environments. We investigate the completeness and analytical capabilities of national to regional scale digital river networks that are available in five countries: Canada, China, Russia, Spain, and United States using actual resource management and conservation projects involving 12 university, agency, and NGO organizations. In addition, we review one pan-European and one global digital river network. Based on our analysis, we conclude that the majority of the regional, national, and global scale digital river networks in our sample lack in network completeness, analytical capabilities or both. To address this limitation, we outline a general framework to build as complete as possible digital river networks and to integrate them with available digital elevation models to create robust analytical capabilities (e.g., virtual watersheds). We believe this presents a global opportunity for in-country agencies, or international players, to support creation of virtual watersheds to increase environmental problem solving, broaden access to the watershed sciences, and strengthen resource management and conservation in countries worldwide.

  2. Building Virtual Watersheds: A Global Opportunity to Strengthen Resource Management and Conservation

    NASA Astrophysics Data System (ADS)

    Benda, Lee; Miller, Daniel; Barquin, Jose; McCleary, Richard; Cai, TiJiu; Ji, Y.

    2016-03-01

    Modern land-use planning and conservation strategies at landscape to country scales worldwide require complete and accurate digital representations of river networks, encompassing all channels including the smallest headwaters. The digital river networks, integrated with widely available digital elevation models, also need to have analytical capabilities to support resource management and conservation, including attributing river segments with key stream and watershed data, characterizing topography to identify landforms, discretizing land uses at scales necessary to identify human-environment interactions, and connecting channels downstream and upstream, and to terrestrial environments. We investigate the completeness and analytical capabilities of national to regional scale digital river networks that are available in five countries: Canada, China, Russia, Spain, and United States using actual resource management and conservation projects involving 12 university, agency, and NGO organizations. In addition, we review one pan-European and one global digital river network. Based on our analysis, we conclude that the majority of the regional, national, and global scale digital river networks in our sample lack in network completeness, analytical capabilities or both. To address this limitation, we outline a general framework to build as complete as possible digital river networks and to integrate them with available digital elevation models to create robust analytical capabilities (e.g., virtual watersheds). We believe this presents a global opportunity for in-country agencies, or international players, to support creation of virtual watersheds to increase environmental problem solving, broaden access to the watershed sciences, and strengthen resource management and conservation in countries worldwide.

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

    USGS Publications Warehouse

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

    2012-01-01

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

  4. Using occupancy estimation to assess the effectiveness of a regional multiple-species conservation plan: bats in the Pacific Northwest

    Treesearch

    Theodore Weller

    2008-01-01

    Regional conservation plans are increasingly used to plan for and protect biodiversity at large spatial scales however the means of quantitatively evaluating their effectiveness are rarely specified. Multiple-species approaches, particular those which employ site-occupancy estimation, have been proposed as robust and efficient alternatives for assessing the status of...

  5. Conservation of Matrix Attachment Region-Binding Filament-Like Protein 1 among Higher Plants1

    PubMed Central

    Harder, Patricia A.; Silverstein, Rebecca A.; Meier, Iris

    2000-01-01

    The interaction of chromatin with the nuclear matrix via matrix attachment regions (MARs) on the DNA is considered to be of fundamental importance for higher-order chromatin organization and the regulation of gene expression. We have previously isolated a novel nuclear matrix-localized protein (MFP1) from tomato (Lycopersicon esculentum) that preferentially binds to MAR DNA. Tomato MFP1 has a predicted filament-protein-like structure and is associated with the nuclear envelope via an N-terminal targeting domain. Based on the antigenic relationship, we report here that MFP1 is conserved in a large number of dicot and monocot species. Several cDNAs were cloned from tobacco (Nicotiana tabacum) and shown to correspond to two tobacco MFP1 genes. Comparison of the primary and predicted secondary structures of MFP1 from tomato, tobacco, and Arabidopsis indicates a high degree of conservation of the N-terminal targeting domain, the overall putative coiled-coil structure of the protein, and the C-terminal DNA-binding domain. In addition, we show that tobacco MFP1 is regulated in an organ-specific and developmental fashion, and that this regulation occurs at the level of transcription or RNA stability. PMID:10631266

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  7. Use of inverse spatial conservation prioritization to avoid biological diversity loss outside protected areas.

    PubMed

    Kareksela, Santtu; Moilanen, Atte; Tuominen, Seppo; Kotiaho, Janne S

    2013-12-01

    Globally expanding human land use sets constantly increasing pressure for maintenance of biological diversity and functioning ecosystems. To fight the decline of biological diversity, conservation science has broken ground with methods such as the operational model of systematic conservation planning (SCP), which focuses on design and on-the-ground implementation of conservation areas. The most commonly used method in SCP is reserve selection that focuses on the spatial design of reserve networks and their expansion. We expanded these methods by introducing another form of spatial allocation of conservation effort relevant for land-use zoning at the landscape scale that avoids negative ecological effects of human land use outside protected areas. We call our method inverse spatial conservation prioritization. It can be used to identify areas suitable for economic development while simultaneously limiting total ecological and environmental effects of that development at the landscape level by identifying areas with highest economic but lowest ecological value. Our method is not based on a priori targets, and as such it is applicable to cases where the effects of land use on, for example, individual species or ecosystem types are relatively small and would not lead to violation of regional or national conservation targets. We applied our method to land-use allocation to peat mining. Our method identified a combination of profitable production areas that provides the needed area for peat production while retaining most of the landscape-level ecological value of the ecosystem. The results of this inverse spatial conservation prioritization are being used in land-use zoning in the province of Central Finland. © 2013 Society for Conservation Biology.

  8. 75 FR 23221 - Highlands Regional Study: Connecticut and Pennsylvania 2010 Update

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-03

    ... (see link below) and identifies high conservation value areas, the impacts of land use change on the... CONTACT: Martina Barnes, Regional Planner, at 212-637-3863. Individuals who use telecommunication devices...

  9. Ecosystem services-based SWOT analysis of protected areas for conservation strategies.

    PubMed

    Scolozzi, Rocco; Schirpke, Uta; Morri, Elisa; D'Amato, Dalia; Santolini, Riccardo

    2014-12-15

    An ecosystem services-based SWOT analysis is proposed in order to identify and quantify internal and external factors supporting or threatening the conservation effectiveness of protected areas. The proposed approach concerns both the ecological and the social perspective. Strengths and weaknesses, opportunities and threats were evaluated based on 12 selected environmental and socio-economic indicators for all terrestrial Italian protected areas, belonging to the Natura 2000 network, and for their 5-km buffer area. The indicators, used as criteria within a multi-criteria assessment, include: core area, cost-distance between protected areas, changes in ecosystem services values, intensification of land use, and urbanization. The results were aggregated for three biogeographical regions, Alpine, Continental, and Mediterranean, indicating that Alpine sites have more opportunities and strengths than Continental and Mediterranean sites. The results call attention to where connectivity and land-use changes may have stronger influence on protected areas, in particular, whereas urbanization or intensification of agriculture may hamper conservation goals of protected areas. The proposed SWOT analysis provides helpful information for a multiple scale perspective and for identifying conservation priorities and for defining management strategies to assure biodiversity conservation and ecosystem services provision. Copyright © 2014 Elsevier Ltd. All rights reserved.

  10. Bridging the conservation design and delivery gap for wetland bird habitat maintenance and restoration in the Midwestern United States

    USGS Publications Warehouse

    Thogmartin, W.E.; Potter, B.; Soulliere, G.

    2011-01-01

    The U.S. Fish and Wildlife Service's adoption of Strategic Habitat Conservation is intended to increase the effectiveness and efficiency of conservation delivery by targeting effort in areas where biological benefits are greatest. Conservation funding has not often been allocated in accordance with explicit biological endpoints, and the gap between conservation design (the identification of conservation priority areas) and delivery needs to be bridged to better meet conservation goals for multiple species and landscapes. We introduce a regional prioritization scheme for North American Wetlands Conservation Act funding which explicitly addresses Midwest regional goals for wetland-dependent birds. We developed decision-support maps to guide conservation of breeding and non-breeding wetland bird habitat. This exercise suggested ~55% of the Midwest consists of potential wetland bird habitat, and areas suited for maintenance (protection) were distinguished from those most suited to restoration. Areas with greater maintenance focus were identified for central Minnesota, southeastern Wisconsin, the Upper Mississippi and Illinois rivers, and the shore of western Lake Erie and Saginaw Bay. The shores of Lakes Michigan and Superior accommodated fewer waterbird species overall, but were also important for wetland bird habitat maintenance. Abundant areas suited for wetland restoration occurred in agricultural regions of central Illinois, western Iowa, and northern Indiana and Ohio. Use of this prioritization scheme can increase effectiveness, efficiency, transparency, and credibility to land and water conservation efforts for wetland birds in the Midwestern United States.

  11. Credibility and advocacy in conservation science.

    PubMed

    Horton, Cristi C; Peterson, Tarla Rai; Banerjee, Paulami; Peterson, Markus J

    2016-02-01

    Conservation policy sits at the nexus of natural science and politics. On the one hand, conservation scientists strive to maintain scientific credibility by emphasizing that their research findings are the result of disinterested observations of reality. On the other hand, conservation scientists are committed to conservation even if they do not advocate a particular policy. The professional conservation literature offers guidance on negotiating the relationship between scientific objectivity and political advocacy without damaging conservation science's credibility. The value of this guidance, however, may be restricted by limited recognition of credibility's multidimensionality and emergent nature: it emerges through perceptions of expertise, goodwill, and trustworthiness. We used content analysis of the literature to determine how credibility is framed in conservation science as it relates to apparent contradictions between science and advocacy. Credibility typically was framed as a static entity lacking dimensionality. Authors identified expertise or trustworthiness as important, but rarely mentioned goodwill. They usually did not identify expertise, goodwill, or trustworthiness as dimensions of credibility or recognize interactions among these 3 dimensions of credibility. This oversimplification may limit the ability of conservation scientists to contribute to biodiversity conservation. Accounting for the emergent quality and multidimensionality of credibility should enable conservation scientists to advance biodiversity conservation more effectively. © 2015 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

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

    PubMed

    Ocampo-Peñuela, Natalia; Pimm, Stuart L

    2014-10-01

    We aspired to set conservation priorities in ways that lead to direct conservation actions. Very large-scale strategic mapping leads to familiar conservation priorities exemplified by biodiversity hotspots. In contrast, tactical conservation actions unfold on much smaller geographical extents and they need to reflect the habitat loss and fragmentation that have sharply restricted where species now live. Our aspirations for direct, practical actions were demanding. First, we identified the global, strategic conservation priorities and then downscaled to practical local actions within the selected priorities. In doing this, we recognized the limitations of incomplete information. We started such a process in Colombia and used the results presented here to implement reforestation of degraded land to prevent the isolation of a large area of cloud forest. We used existing range maps of 171 bird species to identify priority conservation areas that would conserve the greatest number of species at risk in Colombia. By at risk species, we mean those that are endemic and have small ranges. The Western Andes had the highest concentrations of such species-100 in total-but the lowest densities of national parks. We then adjusted the priorities for this region by refining these species ranges by selecting only areas of suitable elevation and remaining habitat. The estimated ranges of these species shrank by 18-100% after accounting for habitat and suitable elevation. Setting conservation priorities on the basis of currently available range maps excluded priority areas in the Western Andes and, by extension, likely elsewhere and for other taxa. By incorporating detailed maps of remaining natural habitats, we made practical recommendations for conservation actions. One recommendation was to restore forest connections to a patch of cloud forest about to become isolated from the main Andes. © 2014 Society for Conservation Biology.

  13. Credibility and advocacy in conservation science

    PubMed Central

    Horton, Cristi C.; Peterson, Tarla Rai; Banerjee, Paulami

    2015-01-01

    Abstract Conservation policy sits at the nexus of natural science and politics. On the one hand, conservation scientists strive to maintain scientific credibility by emphasizing that their research findings are the result of disinterested observations of reality. On the other hand, conservation scientists are committed to conservation even if they do not advocate a particular policy. The professional conservation literature offers guidance on negotiating the relationship between scientific objectivity and political advocacy without damaging conservation science's credibility. The value of this guidance, however, may be restricted by limited recognition of credibility's multidimensionality and emergent nature: it emerges through perceptions of expertise, goodwill, and trustworthiness. We used content analysis of the literature to determine how credibility is framed in conservation science as it relates to apparent contradictions between science and advocacy. Credibility typically was framed as a static entity lacking dimensionality. Authors identified expertise or trustworthiness as important, but rarely mentioned goodwill. They usually did not identify expertise, goodwill, or trustworthiness as dimensions of credibility or recognize interactions among these 3 dimensions of credibility. This oversimplification may limit the ability of conservation scientists to contribute to biodiversity conservation. Accounting for the emergent quality and multidimensionality of credibility should enable conservation scientists to advance biodiversity conservation more effectively. PMID:26041036

  14. Prediction of Human Disease Genes by Human-Mouse Conserved Coexpression Analysis

    PubMed Central

    Grassi, Elena; Damasco, Christian; Silengo, Lorenzo; Oti, Martin; Provero, Paolo; Di Cunto, Ferdinando

    2008-01-01

    Background Even in the post-genomic era, the identification of candidate genes within loci associated with human genetic diseases is a very demanding task, because the critical region may typically contain hundreds of positional candidates. Since genes implicated in similar phenotypes tend to share very similar expression profiles, high throughput gene expression data may represent a very important resource to identify the best candidates for sequencing. However, so far, gene coexpression has not been used very successfully to prioritize positional candidates. Methodology/Principal Findings We show that it is possible to reliably identify disease-relevant relationships among genes from massive microarray datasets by concentrating only on genes sharing similar expression profiles in both human and mouse. Moreover, we show systematically that the integration of human-mouse conserved coexpression with a phenotype similarity map allows the efficient identification of disease genes in large genomic regions. Finally, using this approach on 850 OMIM loci characterized by an unknown molecular basis, we propose high-probability candidates for 81 genetic diseases. Conclusion Our results demonstrate that conserved coexpression, even at the human-mouse phylogenetic distance, represents a very strong criterion to predict disease-relevant relationships among human genes. PMID:18369433

  15. Conservation planning under uncertainty in urban development and vegetation dynamics

    PubMed Central

    Carmel, Yohay

    2018-01-01

    Systematic conservation planning is a framework for optimally locating and prioritizing areas for conservation. An often-noted shortcoming of most conservation planning studies is that they do not address future uncertainty. The selection of protected areas that are intended to ensure the long-term persistence of biodiversity is often based on a snapshot of the current situation, ignoring processes such as climate change. Scenarios, in the sense of being accounts of plausible futures, can be utilized to identify conservation area portfolios that are robust to future uncertainty. We compared three approaches for utilizing scenarios in conservation area selection: considering a full set of scenarios (all-scenarios portfolio), assuming the realization of specific scenarios, and a reference strategy based on the current situation (current distributions portfolio). Our objective was to compare the robustness of these approaches in terms of their relative performance across future scenarios. We focused on breeding bird species in Israel’s Mediterranean region. We simulated urban development and vegetation dynamics scenarios 60 years into the future using DINAMICA-EGO, a cellular-automata simulation model. For each scenario, we mapped the target species’ available habitat distribution, identified conservation priority areas using the site-selection software MARXAN, and constructed conservation area portfolios using the three aforementioned strategies. We then assessed portfolio performance based on the number of species for which representation targets were met in each scenario. The all-scenarios portfolio consistently outperformed the other portfolios, and was more robust to ‘errors’ (e.g., when an assumed specific scenario did not occur). On average, the all-scenarios portfolio achieved representation targets for five additional species compared with the current distributions portfolio (approximately 33 versus 28 species). Our findings highlight the importance

  16. Conservation planning under uncertainty in urban development and vegetation dynamics.

    PubMed

    Troupin, David; Carmel, Yohay

    2018-01-01

    Systematic conservation planning is a framework for optimally locating and prioritizing areas for conservation. An often-noted shortcoming of most conservation planning studies is that they do not address future uncertainty. The selection of protected areas that are intended to ensure the long-term persistence of biodiversity is often based on a snapshot of the current situation, ignoring processes such as climate change. Scenarios, in the sense of being accounts of plausible futures, can be utilized to identify conservation area portfolios that are robust to future uncertainty. We compared three approaches for utilizing scenarios in conservation area selection: considering a full set of scenarios (all-scenarios portfolio), assuming the realization of specific scenarios, and a reference strategy based on the current situation (current distributions portfolio). Our objective was to compare the robustness of these approaches in terms of their relative performance across future scenarios. We focused on breeding bird species in Israel's Mediterranean region. We simulated urban development and vegetation dynamics scenarios 60 years into the future using DINAMICA-EGO, a cellular-automata simulation model. For each scenario, we mapped the target species' available habitat distribution, identified conservation priority areas using the site-selection software MARXAN, and constructed conservation area portfolios using the three aforementioned strategies. We then assessed portfolio performance based on the number of species for which representation targets were met in each scenario. The all-scenarios portfolio consistently outperformed the other portfolios, and was more robust to 'errors' (e.g., when an assumed specific scenario did not occur). On average, the all-scenarios portfolio achieved representation targets for five additional species compared with the current distributions portfolio (approximately 33 versus 28 species). Our findings highlight the importance of

  17. Conservation Status of the Family Orchidaceae in Spain Based on European, National, and Regional Catalogues of Protected Species

    PubMed Central

    2018-01-01

    This report reviews the European, National, and Regional catalogues of protected species, focusing specifically on the Orchidaceae family to determine which species seem to be well-protected and where they are protected. Moreover, this examination highlights which species appear to be underprotected and therefore need to be included in some catalogues of protection or be catalogued under some category of protection. The national and regional catalogues that should be implemented are shown, as well as what species should be included within them. This report should be a helpful guideline for environmental policies about orchid's conservation in Spain, at least at the regional and national level. Around 76% of the Spanish orchid flora are listed with any figure of protection or included in any red list, either nationally (about 12–17%) or regionally (72%). PMID:29643757

  18. Identifying Potential Regions of Copy Number Variation for Bipolar Disorder

    PubMed Central

    Chen, Yi-Hsuan; Lu, Ru-Band; Hung, Hung; Kuo, Po-Hsiu

    2014-01-01

    Bipolar disorder is a complex psychiatric disorder with high heritability, but its genetic determinants are still largely unknown. Copy number variation (CNV) is one of the sources to explain part of the heritability. However, it is a challenge to estimate discrete values of the copy numbers using continuous signals calling from a set of markers, and to simultaneously perform association testing between CNVs and phenotypic outcomes. The goal of the present study is to perform a series of data filtering and analysis procedures using a DNA pooling strategy to identify potential CNV regions that are related to bipolar disorder. A total of 200 normal controls and 200 clinically diagnosed bipolar patients were recruited in this study, and were randomly divided into eight control and eight case pools. Genome-wide genotyping was employed using Illumina Human Omni1-Quad array with approximately one million markers for CNV calling. We aimed at setting a series of criteria to filter out the signal noise of marker data and to reduce the chance of false-positive findings for CNV regions. We first defined CNV regions for each pool. Potential CNV regions were reported based on the different patterns of CNV status between cases and controls. Genes that were mapped into the potential CNV regions were examined with association testing, Gene Ontology enrichment analysis, and checked with existing literature for their associations with bipolar disorder. We reported several CNV regions that are related to bipolar disorder. Two CNV regions on chromosome 11 and 22 showed significant signal differences between cases and controls (p < 0.05). Another five CNV regions on chromosome 6, 9, and 19 were overlapped with results in previous CNV studies. Experimental validation of two CNV regions lent some support to our reported findings. Further experimental and replication studies could be designed for these selected regions. PMID:27605030

  19. 77 FR 18856 - Atchafalaya National Wildlife Refuge, LA; Final Comprehensive Conservation Plan and Finding of No...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-28

    ... local, state, and regional newspapers, six online media outlets, and two local radio networks. Copies of... Atchafalaya; The Nature Conservancy; Gulf Restoration Network; Atchafalaya Basinkeeper; Louisiana Crawfish... Environmental Action Network; and local citizens. Selected Alternative The Draft CCP/EA identified and evaluated...

  20. Estimating climate resilience for conservation across geophysical settings.

    PubMed

    Anderson, Mark G; Clark, Melissa; Sheldon, Arlene Olivero

    2014-08-01

    Conservationists need methods to conserve biological diversity while allowing species and communities to rearrange in response to a changing climate. We developed and tested such a method for northeastern North America that we based on physical features associated with ecological diversity and site resilience to climate change. We comprehensively mapped 30 distinct geophysical settings based on geology and elevation. Within each geophysical setting, we identified sites that were both connected by natural cover and that had relatively more microclimates indicated by diverse topography and elevation gradients. We did this by scoring every 405 ha hexagon in the region for these two characteristics and selecting those that scored >SD 0.5 above the mean combined score for each setting. We hypothesized that these high-scoring sites had the greatest resilience to climate change, and we compared them with sites selected by The Nature Conservancy for their high-quality rare species populations and natural community occurrences. High-scoring sites captured significantly more of the biodiversity sites than expected by chance (p < 0.0001): 75% of the 414 target species, 49% of the 4592 target species locations, and 53% of the 2170 target community locations. Calcareous bedrock, coarse sand, and fine silt settings scored markedly lower for estimated resilience and had low levels of permanent land protection (average 7%). Because our method identifies-for every geophysical setting-sites that are the most likely to retain species and functions longer under a changing climate, it reveals natural strongholds for future conservation that would also capture substantial existing biodiversity and correct the bias in current secured lands. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

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

    PubMed

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

    2012-05-01

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

  2. Identifying Ancient Settlement Patterns through LiDAR in the Mosquitia Region of Honduras.

    PubMed

    Fisher, Christopher T; Fernández-Diaz, Juan Carlos; Cohen, Anna S; Neil Cruz, Oscar; Gonzáles, Alicia M; Leisz, Stephen J; Pezzutti, Florencia; Shrestha, Ramesh; Carter, William

    2016-01-01

    The Mosquitia ecosystem of Honduras occupies the fulcrum between the American continents and as such constitutes a critical region for understanding past patterns of socio-political development and interaction. Heavy vegetation, rugged topography, and remoteness have limited scientific investigation. This paper presents prehistoric patterns of settlement and landuse for a critical valley within the Mosquitia derived from airborne LiDAR scanning and field investigation. We show that (i) though today the valley is a wilderness it was densely inhabited in the past; (ii) that this population was organized into a three-tiered system composed of 19 settlements dominated by a city; and, (iii) that this occupation was embedded within a human engineered landscape. We also add to a growing body of literature that demonstrates the utility of LiDAR as means for rapid cultural assessments in undocumented regions for analysis and conservation. Our ultimate hope is for our work to promote protections to safeguard the unique and critically endangered Mosquitia ecosystem and other similar areas in need of preservation.

  3. Identifying Ancient Settlement Patterns through LiDAR in the Mosquitia Region of Honduras

    PubMed Central

    Fernández-Diaz, Juan Carlos; Cohen, Anna S.; Neil Cruz, Oscar; Gonzáles, Alicia M.; Leisz, Stephen J.; Pezzutti, Florencia; Shrestha, Ramesh; Carter, William

    2016-01-01

    The Mosquitia ecosystem of Honduras occupies the fulcrum between the American continents and as such constitutes a critical region for understanding past patterns of socio-political development and interaction. Heavy vegetation, rugged topography, and remoteness have limited scientific investigation. This paper presents prehistoric patterns of settlement and landuse for a critical valley within the Mosquitia derived from airborne LiDAR scanning and field investigation. We show that (i) though today the valley is a wilderness it was densely inhabited in the past; (ii) that this population was organized into a three-tiered system composed of 19 settlements dominated by a city; and, (iii) that this occupation was embedded within a human engineered landscape. We also add to a growing body of literature that demonstrates the utility of LiDAR as means for rapid cultural assessments in undocumented regions for analysis and conservation. Our ultimate hope is for our work to promote protections to safeguard the unique and critically endangered Mosquitia ecosystem and other similar areas in need of preservation. PMID:27560962

  4. Teaching for a World Conservation Strategy.

    ERIC Educational Resources Information Center

    Kirk, John J.

    1982-01-01

    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…

  5. Conservation challenges for the Austral and Neotropical America section.

    PubMed

    Ceballos, Gerardo; Vale, Mariana M; Bonacic, Cristian; Calvo-Alvarado, Julio; List, Rurik; Bynum, Nora; Medellín, Rodrigo A; Simonetti, Javier A; Rodríguez, Jon Paul

    2009-08-01

    The Austral and Neotropical America (ANA) section of the Society for Conservation Biology includes a vast territory with some of the largest relatively pristine ecosystems in the world. With more than 573 million people, the economic growth of the region still depends strongly on natural resource exploitation and still has high rates of environmental degradation and biodiversity loss. A survey among the ANA section membership, with more than 700 members, including most of the section's prominent ecologists and conservationists, indicates that lack of capacity building for conservation, corruption, and threats such as deforestation and illegal trade of species, are among the most urgent problems that need to be addressed to improve conservation in the region. There are, however, strong universities and ecology groups taking the lead in environmental research and conservation, a most important issue to enhance the ability of the region to solve conservation and development conflicts.

  6. Fine-resolution conservation planning with limited climate-change information.

    PubMed

    Shah, Payal; Mallory, Mindy L; Ando, Amy W; Guntenspergen, Glenn R

    2017-04-01

    Climate-change induced uncertainties in future spatial patterns of conservation-related outcomes make it difficult to implement standard conservation-planning paradigms. A recent study translates Markowitz's risk-diversification strategy from finance to conservation settings, enabling conservation agents to use this diversification strategy for allocating conservation and restoration investments across space to minimize the risk associated with such uncertainty. However, this method is information intensive and requires a large number of forecasts of ecological outcomes associated with possible climate-change scenarios for carrying out fine-resolution conservation planning. We developed a technique for iterative, spatial portfolio analysis that can be used to allocate scarce conservation resources across a desired level of subregions in a planning landscape in the absence of a sufficient number of ecological forecasts. We applied our technique to the Prairie Pothole Region in central North America. A lack of sufficient future climate information prevented attainment of the most efficient risk-return conservation outcomes in the Prairie Pothole Region. The difference in expected conservation returns between conservation planning with limited climate-change information and full climate-change information was as large as 30% for the Prairie Pothole Region even when the most efficient iterative approach was used. However, our iterative approach allowed finer resolution portfolio allocation with limited climate-change forecasts such that the best possible risk-return combinations were obtained. With our most efficient iterative approach, the expected loss in conservation outcomes owing to limited climate-change information could be reduced by 17% relative to other iterative approaches. © 2016 Society for Conservation Biology.

  7. Conserved noncoding sequences conserve biological networks and influence genome evolution.

    PubMed

    Xie, Jianbo; Qian, Kecheng; Si, Jingna; Xiao, Liang; Ci, Dong; Zhang, Deqiang

    2018-05-01

    Comparative genomics approaches have identified numerous conserved cis-regulatory sequences near genes in plant genomes. Despite the identification of these conserved noncoding sequences (CNSs), our knowledge of their functional importance and selection remains limited. Here, we used a combination of DNA methylome analysis, microarray expression analyses, and functional annotation to study these sequences in the model tree Populus trichocarpa. Methylation in CG contexts and non-CG contexts was lower in CNSs, particularly CNSs in the 5'-upstream regions of genes, compared with other sites in the genome. We observed that CNSs are enriched in genes with transcription and binding functions, and this also associated with syntenic genes and those from whole-genome duplications, suggesting that cis-regulatory sequences play a key role in genome evolution. We detected a significant positive correlation between CNS number and protein interactions, suggesting that CNSs may have roles in the evolution and maintenance of biological networks. The divergence of CNSs indicates that duplication-degeneration-complementation drives the subfunctionalization of a proportion of duplicated genes from whole-genome duplication. Furthermore, population genomics confirmed that most CNSs are under strong purifying selection and only a small subset of CNSs shows evidence of adaptive evolution. These findings provide a foundation for future studies exploring these key genomic features in the maintenance of biological networks, local adaptation, and transcription.

  8. Monitoring for conservation

    USGS Publications Warehouse

    Nichols, J.D.; Williams, B.K.

    2006-01-01

    Human-mediated environmental changes have resulted in appropriate concern for the conservation of ecological systems and have led to the development of many ecological monitoring programs worldwide. Many programs that are identified with the purpose of `surveillance? represent an inefficient use of conservation funds and effort. Here, we revisit the 1964 paper by Platt and argue that his recommendations about the conduct of science are equally relevant to the conduct of ecological monitoring programs. In particular, we argue that monitoring should not be viewed as a stand-alone activity, but instead as a component of a larger process of either conservation-oriented science or management. Corresponding changes in monitoring focus and design would lead to substantial increases in the efficiency and usefulness of monitoring results in conservation.

  9. Setting priorities for private land conservation in fire-prone landscapes: Are fire risk reduction and biodiversity conservation competing or compatible objectives?

    USGS Publications Warehouse

    Syphard, Alexandra D.; Butsic, Van; Bar-Massada, Avi; Keeley, Jon E.; Tracey, Jeff A.; Fisher, Robert N.

    2016-01-01

    Although wildfire plays an important role in maintaining biodiversity in many ecosystems, fire management to protect human assets is often carried out by different agencies than those tasked for conserving biodiversity. In fact, fire risk reduction and biodiversity conservation are often viewed as competing objectives. Here we explored the role of management through private land conservation and asked whether we could identify private land acquisition strategies that fulfill the mutual objectives of biodiversity conservation and fire risk reduction, or whether the maximization of one objective comes at a detriment to the other. Using a fixed budget and number of homes slated for development, we simulated 20 years of housing growth under alternative conservation selection strategies, and then projected the mean risk of fires destroying structures and the area and configuration of important habitat types in San Diego County, California, USA. We found clear differences in both fire risk projections and biodiversity impacts based on the way conservation lands are prioritized for selection, but these differences were split between two distinct groupings. If no conservation lands were purchased, or if purchases were prioritized based on cost or likelihood of development, both the projected fire risk and biodiversity impacts were much higher than if conservation lands were purchased in areas with high fire hazard or high species richness. Thus, conserving land focused on either of the two objectives resulted in nearly equivalent mutual benefits for both. These benefits not only resulted from preventing development in sensitive areas, but they were also due to the different housing patterns and arrangements that occurred as development was displaced from those areas. Although biodiversity conflicts may still arise using other fire management strategies, this study shows that mutual objectives can be attained through land-use planning in this region. These results likely

  10. Comparison of theoretical proteomes: identification of COGs with conserved and variable pI within the multimodal pI distribution.

    PubMed

    Nandi, Soumyadeep; Mehra, Nipun; Lynn, Andrew M; Bhattacharya, Alok

    2005-09-09

    Theoretical proteome analysis, generated by plotting theoretical isoelectric points (pI) against molecular masses of all proteins encoded by the genome show a multimodal distribution for pI. This multimodal distribution is an effect of allowed combinations of the charged amino acids, and not due to evolutionary causes. The variation in this distribution can be correlated to the organisms ecological niche. Contributions to this variation maybe mapped to individual proteins by studying the variation in pI of orthologs across microorganism genomes. The distribution of ortholog pI values showed trimodal distributions for all prokaryotic genomes analyzed, similar to whole proteome plots. Pairwise analysis of pI variation show that a few COGs are conserved within, but most vary between, the acidic and basic regions of the distribution, while molecular mass is more highly conserved. At the level of functional grouping of orthologs, five groups vary significantly from the population of orthologs, which is attributed to either conservation at the level of sequences or a bias for either positively or negatively charged residues contributing to the function. Individual COGs conserved in both the acidic and basic regions of the trimodal distribution are identified, and orthologs that best represent the variation in levels of the acidic and basic regions are listed. The analysis of pI distribution by using orthologs provides a basis for resolution of theoretical proteome comparison at the level of individual proteins. Orthologs identified that significantly vary between the major acidic and basic regions maybe used as representative of the variation of the entire proteome.

  11. Comparison of theoretical proteomes: Identification of COGs with conserved and variable pI within the multimodal pI distribution

    PubMed Central

    Nandi, Soumyadeep; Mehra, Nipun; Lynn, Andrew M; Bhattacharya, Alok

    2005-01-01

    Background Theoretical proteome analysis, generated by plotting theoretical isoelectric points (pI) against molecular masses of all proteins encoded by the genome show a multimodal distribution for pI. This multimodal distribution is an effect of allowed combinations of the charged amino acids, and not due to evolutionary causes. The variation in this distribution can be correlated to the organisms ecological niche. Contributions to this variation maybe mapped to individual proteins by studying the variation in pI of orthologs across microorganism genomes. Results The distribution of ortholog pI values showed trimodal distributions for all prokaryotic genomes analyzed, similar to whole proteome plots. Pairwise analysis of pI variation show that a few COGs are conserved within, but most vary between, the acidic and basic regions of the distribution, while molecular mass is more highly conserved. At the level of functional grouping of orthologs, five groups vary significantly from the population of orthologs, which is attributed to either conservation at the level of sequences or a bias for either positively or negatively charged residues contributing to the function. Individual COGs conserved in both the acidic and basic regions of the trimodal distribution are identified, and orthologs that best represent the variation in levels of the acidic and basic regions are listed. Conclusion The analysis of pI distribution by using orthologs provides a basis for resolution of theoretical proteome comparison at the level of individual proteins. Orthologs identified that significantly vary between the major acidic and basic regions maybe used as representative of the variation of the entire proteome. PMID:16150155

  12. Conservation Genetics of the Philippine Tarsier: Cryptic Genetic Variation Restructures Conservation Priorities for an Island Archipelago Primate

    PubMed Central

    Brown, Rafe M.; Weghorst, Jennifer A.; Olson, Karen V.; Duya, Mariano R. M.; Barley, Anthony J.; Duya, Melizar V.; Shekelle, Myron; Neri-Arboleda, Irene; Esselstyn, Jacob A.; Dominy, Nathaniel J.; Ong, Perry S.; Moritz, Gillian L.; Luczon, Adrian; Diesmos, Mae Lowe L.; Diesmos, Arvin C.; Siler, Cameron D.

    2014-01-01

    Establishment of conservation priorities for primates is a particular concern in the island archipelagos of Southeast Asia, where rates of habitat destruction are among the highest in the world. Conservation programs require knowledge of taxonomic diversity to ensure success. The Philippine tarsier is a flagship species that promotes environmental awareness and a thriving ecotourism economy in the Philippines. However, assessment of its conservation status has been impeded by taxonomic uncertainty, a paucity of field studies, and a lack of vouchered specimens and genetic samples available for study in biodiversity repositories. Consequently, conservation priorities are unclear. In this study we use mitochondrial and nuclear DNA to empirically infer geographic partitioning of genetic variation and to identify evolutionarily distinct lineages for conservation action. The distribution of Philippine tarsier genetic diversity is neither congruent with expectations based on biogeographical patterns documented in other Philippine vertebrates, nor does it agree with the most recent Philippine tarsier taxonomic arrangement. We identify three principal evolutionary lineages that do not correspond to the currently recognized subspecies, highlight the discovery of a novel cryptic and range-restricted subcenter of genetic variation in an unanticipated part of the archipelago, and identify additional geographically structured genetic variation that should be the focus of future studies and conservation action. Conservation of this flagship species necessitates establishment of protected areas and targeted conservation programs within the range of each genetically distinct variant of the Philippine tarsier. PMID:25136854

  13. Phylodiversity to inform conservation policy: An Australian example.

    PubMed

    Laity, Tania; Laffan, Shawn W; González-Orozco, Carlos E; Faith, Daniel P; Rosauer, Dan F; Byrne, Margaret; Miller, Joseph T; Crayn, Darren; Costion, Craig; Moritz, Craig C; Newport, Karl

    2015-11-15

    Phylodiversity measures summarise the phylogenetic diversity patterns of groups of organisms. By using branches of the tree of life, rather than its tips (e.g., species), phylodiversity measures provide important additional information about biodiversity that can improve conservation policy and outcomes. As a biodiverse nation with a strong legislative and policy framework, Australia provides an opportunity to use phylogenetic information to inform conservation decision-making. We explored the application of phylodiversity measures across Australia with a focus on two highly biodiverse regions, the south west of Western Australia (SWWA) and the South East Queensland bioregion (SEQ). We analysed seven diverse groups of organisms spanning five separate phyla on the evolutionary tree of life, the plant genera Acacia and Daviesia, mammals, hylid frogs, myobatrachid frogs, passerine birds, and camaenid land snails. We measured species richness, weighted species endemism (WE) and two phylodiversity measures, phylogenetic diversity (PD) and phylogenetic endemism (PE), as well as their respective complementarity scores (a measure of gains and losses) at 20 km resolution. Higher PD was identified within SEQ for all fauna groups, whereas more PD was found in SWWA for both plant groups. PD and PD complementarity were strongly correlated with species richness and species complementarity for most groups but less so for plants. PD and PE were found to complement traditional species-based measures for all groups studied: PD and PE follow similar spatial patterns to richness and WE, but highlighted different areas that would not be identified by conventional species-based biodiversity analyses alone. The application of phylodiversity measures, particularly the novel weighted complementary measures considered here, in conservation can enhance protection of the evolutionary history that contributes to present day biodiversity values of areas. Phylogenetic measures in conservation

  14. Patterns of genetic differentiation at MHC class I genes and microsatellites identify conservation units in the giant panda.

    PubMed

    Zhu, Ying; Wan, Qiu-Hong; Yu, Bin; Ge, Yun-Fa; Fang, Sheng-Guo

    2013-10-22

    Evaluating patterns of genetic variation is important to identify conservation units (i.e., evolutionarily significant units [ESUs], management units [MUs], and adaptive units [AUs]) in endangered species. While neutral markers could be used to infer population history, their application in the estimation of adaptive variation is limited. The capacity to adapt to various environments is vital for the long-term survival of endangered species. Hence, analysis of adaptive loci, such as the major histocompatibility complex (MHC) genes, is critical for conservation genetics studies. Here, we investigated 4 classical MHC class I genes (Aime-C, Aime-F, Aime-I, and Aime-L) and 8 microsatellites to infer patterns of genetic variation in the giant panda (Ailuropoda melanoleuca) and to further define conservation units. Overall, we identified 24 haplotypes (9 for Aime-C, 1 for Aime-F, 7 for Aime-I, and 7 for Aime-L) from 218 individuals obtained from 6 populations of giant panda. We found that the Xiaoxiangling population had the highest genetic variation at microsatellites among the 6 giant panda populations and higher genetic variation at Aime-MHC class I genes than other larger populations (Qinling, Qionglai, and Minshan populations). Differentiation index (FST)-based phylogenetic and Bayesian clustering analyses for Aime-MHC-I and microsatellite loci both supported that most populations were highly differentiated. The Qinling population was the most genetically differentiated. The giant panda showed a relatively higher level of genetic diversity at MHC class I genes compared with endangered felids. Using all of the loci, we found that the 6 giant panda populations fell into 2 ESUs: Qinling and non-Qinling populations. We defined 3 MUs based on microsatellites: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. We also recommended 3 possible AUs based on MHC loci: Qinling, Minshan-Qionglai, and Daxiangling-Xiaoxiangling-Liangshan. Furthermore, we recommend

  15. An evolutionarily conserved motif in the TAB1 C-terminal region is necessary for interaction with and activation of TAK1 MAPKKK.

    PubMed

    Ono, K; Ohtomo, T; Sato, S; Sugamata, Y; Suzuki, M; Hisamoto, N; Ninomiya-Tsuji, J; Tsuchiya, M; Matsumoto, K

    2001-06-29

    TAK1, a member of the MAPKKK family, is involved in the intracellular signaling pathways mediated by transforming growth factor beta, interleukin 1, and Wnt. TAK1 kinase activity is specifically activated by the TAK1-binding protein TAB1. The C-terminal 68-amino acid sequence of TAB1 (TAB1-C68) is sufficient for TAK1 interaction and activation. Analysis of various truncated versions of TAB1-C68 defined a C-terminal 30-amino acid sequence (TAB1-C30) necessary for TAK1 binding and activation. NMR studies revealed that the TAB1-C30 region has a unique alpha-helical structure. We identified a conserved sequence motif, PYVDXA/TXF, in the C-terminal domain of mammalian TAB1, Xenopus TAB1, and its Caenorhabditis elegans homolog TAP-1, suggesting that this motif constitutes a specific TAK1 docking site. Alanine substitution mutagenesis showed that TAB1 Phe-484, located in the conserved motif, is crucial for TAK1 binding and activation. The C. elegans homolog of TAB1, TAP-1, was able to interact with and activate the C. elegans homolog of TAK1, MOM-4. However, the site in TAP-1 corresponding to Phe-484 of TAB1 is an alanine residue (Ala-364), and changing this residue to Phe abrogates the ability of TAP-1 to interact with and activate MOM-4. These results suggest that the Phe or Ala residue within the conserved motif of the TAB1-related proteins is important for interaction with and activation of specific TAK1 MAPKKK family members in vivo.

  16. DMRfinder: efficiently identifying differentially methylated regions from MethylC-seq data.

    PubMed

    Gaspar, John M; Hart, Ronald P

    2017-11-29

    DNA methylation is an epigenetic modification that is studied at a single-base resolution with bisulfite treatment followed by high-throughput sequencing. After alignment of the sequence reads to a reference genome, methylation counts are analyzed to determine genomic regions that are differentially methylated between two or more biological conditions. Even though a variety of software packages is available for different aspects of the bioinformatics analysis, they often produce results that are biased or require excessive computational requirements. DMRfinder is a novel computational pipeline that identifies differentially methylated regions efficiently. Following alignment, DMRfinder extracts methylation counts and performs a modified single-linkage clustering of methylation sites into genomic regions. It then compares methylation levels using beta-binomial hierarchical modeling and Wald tests. Among its innovative attributes are the analyses of novel methylation sites and methylation linkage, as well as the simultaneous statistical analysis of multiple sample groups. To demonstrate its efficiency, DMRfinder is benchmarked against other computational approaches using a large published dataset. Contrasting two replicates of the same sample yielded minimal genomic regions with DMRfinder, whereas two alternative software packages reported a substantial number of false positives. Further analyses of biological samples revealed fundamental differences between DMRfinder and another software package, despite the fact that they utilize the same underlying statistical basis. For each step, DMRfinder completed the analysis in a fraction of the time required by other software. Among the computational approaches for identifying differentially methylated regions from high-throughput bisulfite sequencing datasets, DMRfinder is the first that integrates all the post-alignment steps in a single package. Compared to other software, DMRfinder is extremely efficient and unbiased in

  17. Water management, purification, and conservation in arid climates. Volume 3: Water conservation

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Goosen, M.F.A.; Shayya, W.H.

    1999-07-01

    Arid regions are already feeling the severe restraining effects of potable water shortages. In coming years, humid and sub-humid regions of the world will also have to face many of these same problems. In the future, serious conflicts may arise not because of a lack of oil, but due to water shortages. Are there solutions to these problems? Aside from increasing public awareness about the importance of water, society needs to take a three pronged approach: water needs to be effectively managed, it needs to be economically purified, and it needs to be conserved. Only by doing these three thingsmore » in unison can they hope to alleviate the water problems faced by arid regions of the world. This book presents information valuable to seeking, finding and using current technologies to help solve these problems now. Volume 3 addresses aspects of water conservation and includes rainwater harvesting and wastewater reuse and reclamation.« less

  18. Expression screening using a Medaka cDNA library identifies evolutionarily conserved regulators of the p53/Mdm2 pathway.

    PubMed

    Zhang, Ping; Kratz, Anne Sophie; Salama, Mohammed; Elabd, Seham; Heinrich, Thorsten; Wittbrodt, Joachim; Blattner, Christine; Davidson, Gary

    2015-10-08

    The p53 tumor suppressor protein is mainly regulated by alterations in the half-life of the protein, resulting in significant differences in p53 protein levels in cells. The major regulator of this process is Mdm2, which ubiquitinates p53 and targets it for proteasomal degradation. This process can be enhanced or reduced by proteins that associate with p53 or Mdm2 and several proteins have been identified with such an activity. Furthermore, additional ubiquitin ligases for p53 have been identified in recent years. Nevertheless, our understanding of how p53 abundance and Mdm2 activity are regulated remains incomplete. Here we describe a cell culture based overexpression screen to identify evolutionarily conserved regulators of the p53/Mdm2 circuit. The results from this large-scale screening method will contribute to a better understanding of the regulation of these important proteins. Expression screening was based on co-transfection of H1299 cells with pools of cDNA's from a Medaka library together with p53, Mdm2 and, as internal control, Ror2. After cell lysis, SDS-PAGE/WB analysis was used to detect alterations in these proteins. More than one hundred hits that altered the abundance of either p53, Mdm2, or both were identified in the primary screen. Subscreening of the library pools that were identified in the primary screen identified several potential novel regulators of p53 and/or Mdm2. We also tested whether the human orthologues of the Medaka genes regulate p53 and/or Mdm2 abundance. All human orthologues regulated p53 and/or Mdm2 abundance in the same manner as the proteins from Medaka, which underscores the suitability of this screening methodology for the identification of new modifiers of p53 and Mdm2. Despite enormous efforts in the last two decades, many unknown regulators for p53 and Mdm2 abundance are predicted to exist. This cross-species approach to identify evolutionarily conserved regulators demonstrates that our Medaka unigene cDNA library

  19. Ten things to get right for marine conservation planning in the Coral Triangle

    PubMed Central

    Weeks, Rebecca; Pressey, Robert L.; Wilson, Joanne R.; Knight, Maurice; Horigue, Vera; Abesamis, Rene A.; Acosta, Renerio; Jompa, Jamaluddin

    2015-01-01

    Systematic conservation planning increasingly underpins the conservation and management of marine and coastal ecosystems worldwide. Amongst other benefits, conservation planning provides transparency in decision-making, efficiency in the use of limited resources, the ability to minimise conflict between diverse objectives, and to guide strategic expansion of local actions to maximise their cumulative impact. The Coral Triangle has long been recognised as a global marine conservation priority, and has been the subject of huge investment in conservation during the last five years through the Coral Triangle Initiative on Coral Reefs, Fisheries and Food Security. Yet conservation planning has had relatively little influence in this region. To explore why this is the case, we identify and discuss 10 challenges that must be resolved if conservation planning is to effectively inform management actions in the Coral Triangle. These are: making conservation planning accessible; integrating with other planning processes; building local capacity for conservation planning; institutionalising conservation planning within governments; integrating plans across governance levels; planning across governance boundaries; planning for multiple tools and objectives; understanding limitations of data; developing better measures of progress and effectiveness; and making a long term commitment. Most important is a conceptual shift from conservation planning undertaken as a project, to planning undertaken as a process, with dedicated financial and human resources committed to long-term engagement. PMID:25110579

  20. Ten things to get right for marine conservation planning in the Coral Triangle.

    PubMed

    Weeks, Rebecca; Pressey, Robert L; Wilson, Joanne R; Knight, Maurice; Horigue, Vera; Abesamis, Rene A; Acosta, Renerio; Jompa, Jamaluddin

    2014-01-01

    Systematic conservation planning increasingly underpins the conservation and management of marine and coastal ecosystems worldwide. Amongst other benefits, conservation planning provides transparency in decision-making, efficiency in the use of limited resources, the ability to minimise conflict between diverse objectives, and to guide strategic expansion of local actions to maximise their cumulative impact. The Coral Triangle has long been recognised as a global marine conservation priority, and has been the subject of huge investment in conservation during the last five years through the Coral Triangle Initiative on Coral Reefs, Fisheries and Food Security. Yet conservation planning has had relatively little influence in this region. To explore why this is the case, we identify and discuss 10 challenges that must be resolved if conservation planning is to effectively inform management actions in the Coral Triangle. These are: making conservation planning accessible; integrating with other planning processes; building local capacity for conservation planning; institutionalising conservation planning within governments; integrating plans across governance levels; planning across governance boundaries; planning for multiple tools and objectives; understanding limitations of data; developing better measures of progress and effectiveness; and making a long term commitment. Most important is a conceptual shift from conservation planning undertaken as a project, to planning undertaken as a process, with dedicated financial and human resources committed to long-term engagement.

  1. Quantifying the relative contribution of an ecological reserve to conservation objectives

    USGS Publications Warehouse

    Aagaard, Kevin; Lyons, James E.; Thogmartin, Wayne E.

    2017-01-01

    Evaluating the role public lands play in meeting conservation goals is an essential step in good governance. We present a tool for comparing the regional contribution of each of a suite of wildlife management units to conservation goals. We use weighted summation (simple additive weighting) to compute a Unit Contribution Index (UCI) based on species richness, population abundance, and a conservation score based on IUCN Red List classified threat levels. We evaluate UCI for a subset of the 729 participating wetlands of the Integrated Waterbird Management and Monitoring (IWMM) Program across U.S. Fish and Wildlife Service Regions 3 (Midwest USA), 4 (Southeast USA), and 5 (Northeast USA). We found that the median across-Region UCI for Region 5 was greater than Regions 3 and 4, while Region 4 had the greatest within-Region UCI median. This index is a powerful tool for wildlife managers to evaluate the performance of units within the conservation estate.

  2. Utilization of manual therapy to the lumbar spine in conjunction with traditional conservative care for individuals with bilateral lower extremity complex regional pain syndrome: A case series.

    PubMed

    Walston, Zachary; Hernandez, Luis; Yake, Dale

    2018-06-06

    Conservative therapies for complex regional pain syndrome (CRPS) have traditionally focused on exercise and desensitization techniques targeted at the involved extremity. The primary purpose of this case series is to report on the potential benefit of utilizing manual therapy to the lumbar spine in conjunction with traditional conservative care when treating patients with lower extremity CRPS. Two patients with the diagnosis of lower extremity CRPS were treated with manual therapy to the lumbar spine in conjunction with education, exercise, desensitization, and soft tissue techniques for the extremity. Patient 1 received 13 sessions over 6 weeks resulting in a 34-point improvement in oswestry disability index (ODI) and 35-point improvement in lower extremity functional scale (LEFS). Patient 2 received 21 sessions over 12 weeks resulting in a 28-point improvement in ODI and a 41-point improvement in LEFS. Both patients exhibited reductions in pain and clinically meaningful improvements in function. Manual therapies when applied to the lumbar spine in these patients as part of a comprehensive treatment plan resulted in improved spinal mobility, decreased pain, and reduction is distal referred symptoms. Although one cannot infer a cause and effect relationship from a case series, this report identifies meaningful clinical outcomes potentially associated with manual physical therapy to the lumbar spine for two patients with complex regional pain syndrome type 1.

  3. Cooperative drought adaptation: Integrating infrastructure development, conservation, and water transfers into adaptive policy pathways

    NASA Astrophysics Data System (ADS)

    Zeff, Harrison B.; Herman, Jonathan D.; Reed, Patrick M.; Characklis, Gregory W.

    2016-09-01

    A considerable fraction of urban water supply capacity serves primarily as a hedge against drought. Water utilities can reduce their dependence on firm capacity and forestall the development of new supplies using short-term drought management actions, such as conservation and transfers. Nevertheless, new supplies will often be needed, especially as demands rise due to population growth and economic development. Planning decisions regarding when and how to integrate new supply projects are fundamentally shaped by the way in which short-term adaptive drought management strategies are employed. To date, the challenges posed by long-term infrastructure sequencing and adaptive short-term drought management are treated independently, neglecting important feedbacks between planning and management actions. This work contributes a risk-based framework that uses continuously updating risk-of-failure (ROF) triggers to capture the feedbacks between short-term drought management actions (e.g., conservation and water transfers) and the selection and sequencing of a set of regional supply infrastructure options over the long term. Probabilistic regional water supply pathways are discovered for four water utilities in the "Research Triangle" region of North Carolina. Furthermore, this study distinguishes the status-quo planning path of independent action (encompassing utility-specific conservation and new supply infrastructure only) from two cooperative formulations: "weak" cooperation, which combines utility-specific conservation and infrastructure development with regional transfers, and "strong" cooperation, which also includes jointly developed regional infrastructure to support transfers. Results suggest that strong cooperation aids utilities in meeting their individual objectives at substantially lower costs and with less overall development. These benefits demonstrate how an adaptive, rule-based decision framework can coordinate integrated solutions that would not be

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

    PubMed Central

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

    2013-01-01

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

  5. Knowledge co-production and boundary work to promote implementation of conservation plans.

    PubMed

    Nel, Jeanne L; Roux, Dirk J; Driver, Amanda; Hill, Liesl; Maherry, Ashton C; Snaddon, Kate; Petersen, Chantel R; Smith-Adao, Lindie B; Van Deventer, Heidi; Reyers, Belinda

    2016-02-01

    Knowledge co-production and boundary work offer planners a new frame for critically designing a social process that fosters collaborative implementation of resulting plans. Knowledge co-production involves stakeholders from diverse knowledge systems working iteratively toward common vision and action. Boundary work is a means of creating permeable knowledge boundaries that satisfy the needs of multiple social groups while guarding the functional integrity of contributing knowledge systems. Resulting products are boundary objects of mutual interest that maintain coherence across all knowledge boundaries. We examined how knowledge co-production and boundary work can bridge the gap between planning and implementation and promote cross-sectoral cooperation. We applied these concepts to well-established stages in regional conservation planning within a national scale conservation planning project aimed at identifying areas for conserving rivers and wetlands of South Africa and developing an institutional environment for promoting their conservation. Knowledge co-production occurred iteratively over 4 years in interactive stake-holder workshops that included co-development of national freshwater conservation goals and spatial data on freshwater biodiversity and local conservation feasibility; translation of goals into quantitative inputs that were used in Marxan to select draft priority conservation areas; review of draft priority areas; and packaging of resulting map products into an atlas and implementation manual to promote application of the priority area maps in 37 different decision-making contexts. Knowledge co-production stimulated dialogue and negotiation and built capacity for multi-scale implementation beyond the project. The resulting maps and information integrated diverse knowledge types of over 450 stakeholders and represented >1000 years of collective experience. The maps provided a consistent national source of information on priority conservation areas

  6. Identifying Unstable Regions of Proteins Involved in Misfolding Diseases

    NASA Astrophysics Data System (ADS)

    Guest, Will; Cashman, Neil; Plotkin, Steven

    2009-05-01

    Protein misfolding is a necessary step in the pathogenesis of many diseases, including Creutzfeldt-Jakob disease (CJD) and familial amyotrophic lateral sclerosis (fALS). Identifying unstable structural elements in their causative proteins elucidates the early events of misfolding and presents targets for inhibition of the disease process. An algorithm was developed to calculate the Gibbs free energy of unfolding for all sequence-contiguous regions of a protein using three methods to parameterize energy changes: a modified G=o model, changes in solvent-accessible surface area, and all-atoms molecular dynamics. The entropic effects of disulfide bonds and post-translational modifications are treated analytically. It incorporates a novel method for finding local dielectric constants inside a protein to accurately handle charge effects. We have predicted the unstable parts of prion protein and superoxide dismutase 1, the proteins involved in CJD and fALS respectively, and have used these regions as epitopes to prepare antibodies that are specific to the misfolded conformation and show promise as therapeutic agents.

  7. A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize

    PubMed Central

    Musungu, Bryan; Bhatnagar, Deepak; Brown, Robert L.; Fakhoury, Ahmad M.; Geisler, Matt

    2015-01-01

    Interactomes are genome-wide roadmaps of protein-protein interactions. They have been produced for humans, yeast, the fruit fly, and Arabidopsis thaliana and have become invaluable tools for generating and testing hypotheses. A predicted interactome for Zea mays (PiZeaM) is presented here as an aid to the research community for this valuable crop species. PiZeaM was built using a proven method of interologs (interacting orthologs) that were identified using both one-to-one and many-to-many orthology between genomes of maize and reference species. Where both maize orthologs occurred for an experimentally determined interaction in the reference species, we predicted a likely interaction in maize. A total of 49,026 unique interactions for 6004 maize proteins were predicted. These interactions are enriched for processes that are evolutionarily conserved, but include many otherwise poorly annotated proteins in maize. The predicted maize interactions were further analyzed by comparing annotation of interacting proteins, including different layers of ontology. A map of pairwise gene co-expression was also generated and compared to predicted interactions. Two global subnetworks were constructed for highly conserved interactions. These subnetworks showed clear clustering of proteins by function. Another subnetwork was created for disease response using a bait and prey strategy to capture interacting partners for proteins that respond to other organisms. Closer examination of this subnetwork revealed the connectivity between biotic and abiotic hormone stress pathways. We believe PiZeaM will provide a useful tool for the prediction of protein function and analysis of pathways for Z. mays researchers and is presented in this paper as a reference tool for the exploration of protein interactions in maize. PMID:26089837

  8. Right practice, right place: A conservation planning toolbox for meeting water quality goals in the Corn Belt

    USDA-ARS?s Scientific Manuscript database

    With increasing recognition that regional nutrient pollution problems will only be solved using edge-of-field and beyond-field practices, conservation planners now face the challenge of identifying the most appropriate practices and practice locations to deliver water quality outcomes. We have deve...

  9. On the formation of a conservation hotspot for juvenile North Pacific loggerhead sea turtles (Caretta caretta)

    NASA Astrophysics Data System (ADS)

    Wingfield, Dana K.

    2009-12-01

    This research examined the incorporation of highly productive regions within the marine system. I combined historical conservation literature, remotely sensed oceanography, ship based surveys, satellite tagged animals, and statistical models to explore an integrated approach to the identification of key oceanic regions that require incorporation into current marine conservation strategies. In my first chapter, I undertook a literature review of the term "hotspot", one of the most common ways by which scientists ascribe conservation prioritization in the marine and terrestrial systems. My results showed that marine literature has identified important areas of biodiversity and productivity (i.e. high primary production that results in trophic linkages and species aggregations) are in need of protection from human threats. However, current non-governmental organizations focus primarily on biodiversity, thus missing important areas of productivity for marine conservation. In my second chapter, I demonstrated how remotely sensed oceanography, ship-based surveys, and satellite tagged animals can help to identify the formation of such a "productivity hotspot". Specifically, I examined the connection between physical forcing (surface winds and vertical Ekman upwelling), sea-surface temperature, primary production (chlorophyll-a concentrations), retentive features of fronts and dynamic height, and prey abundance (red crabs) in the spatial and temporal concentration of the critically endangered North Pacific juvenile loggerhead sea turtle (Caretta caretta) within its foraging habitat off the Pacific coast of Baja California. Finally, in my third chapter, I identified habitat selection of loggerheads to better understand the species preference within suitable habitat. I sampled several environmental variables (depth, sea-surface temperature, and chlorophyll- a) within 'preferred' versus 'avoided' turtle habitat. Results from a generalized additive model showed the statistical

  10. Whole genome association study identifies regions of the bovine genome and biological pathways involved in carcass trait performance in Holstein-Friesian cattle.

    PubMed

    Doran, Anthony G; Berry, Donagh P; Creevey, Christopher J

    2014-10-01

    Four traits related to carcass performance have been identified as economically important in beef production: carcass weight, carcass fat, carcass conformation of progeny and cull cow carcass weight. Although Holstein-Friesian cattle are primarily utilized for milk production, they are also an important source of meat for beef production and export. Because of this, there is great interest in understanding the underlying genomic structure influencing these traits. Several genome-wide association studies have identified regions of the bovine genome associated with growth or carcass traits, however, little is known about the mechanisms or underlying biological pathways involved. This study aims to detect regions of the bovine genome associated with carcass performance traits (employing a panel of 54,001 SNPs) using measures of genetic merit (as predicted transmitting abilities) for 5,705 Irish Holstein-Friesian animals. Candidate genes and biological pathways were then identified for each trait under investigation. Following adjustment for false discovery (q-value < 0.05), 479 quantitative trait loci (QTL) were associated with at least one of the four carcass traits using a single SNP regression approach. Using a Bayesian approach, 46 QTL were associated (posterior probability > 0.5) with at least one of the four traits. In total, 557 unique bovine genes, which mapped to 426 human orthologs, were within 500kbs of QTL found associated with a trait using the Bayesian approach. Using this information, 24 significantly over-represented pathways were identified across all traits. The most significantly over-represented biological pathway was the peroxisome proliferator-activated receptor (PPAR) signaling pathway. A large number of genomic regions putatively associated with bovine carcass traits were detected using two different statistical approaches. Notably, several significant associations were detected in close proximity to genes with a known role in animal growth

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

    PubMed Central

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

    2014-01-01

    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

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

    PubMed

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

    2014-01-01

    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

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

    PubMed Central

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

    2012-01-01

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

  14. A study on using texture analysis methods for identifying lobar fissure regions in isotropic CT images.

    PubMed

    Wei, Q; Hu, Y

    2009-01-01

    The major hurdle for segmenting lung lobes in computed tomographic (CT) images is to identify fissure regions, which encase lobar fissures. Accurate identification of these regions is difficult due to the variable shape and appearance of the fissures, along with the low contrast and high noise associated with CT images. This paper studies the effectiveness of two texture analysis methods - the gray level co-occurrence matrix (GLCM) and the gray level run length matrix (GLRLM) - in identifying fissure regions from isotropic CT image stacks. To classify GLCM and GLRLM texture features, we applied a feed-forward back-propagation neural network and achieved the best classification accuracy utilizing 16 quantized levels for computing the GLCM and GLRLM texture features and 64 neurons in the input/hidden layers of the neural network. Tested on isotropic CT image stacks of 24 patients with the pathologic lungs, we obtained accuracies of 86% and 87% for identifying fissure regions using the GLCM and GLRLM methods, respectively. These accuracies compare favorably with surgeons/radiologists' accuracy of 80% for identifying fissure regions in clinical settings. This shows promising potential for segmenting lung lobes using the GLCM and GLRLM methods.

  15. Conservation of Transcription Start Sites within Genes across a Bacterial Genus

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Shao, Wenjun; Price, Morgan N.; Deutschbauer, Adam M.

    Transcription start sites (TSSs) lying inside annotated genes, on the same or opposite strand, have been observed in diverse bacteria, but the function of these unexpected transcripts is unclear. Here, we use the metal-reducing bacterium Shewanella oneidensis MR-1 and its relatives to study the evolutionary conservation of unexpected TSSs. Using high-resolution tiling microarrays and 5'-end RNA sequencing, we identified 2,531 TSSs in S. oneidensis MR-1, of which 18% were located inside coding sequences (CDSs). Comparative transcriptome analysis with seven additional Shewanella species revealed that the majority (76%) of the TSSs within the upstream regions of annotated genes (gTSSs) were conserved.more » Thirty percent of the TSSs that were inside genes and on the sense strand (iTSSs) were also conserved. Sequence analysis around these iTSSs showed conserved promoter motifs, suggesting that many iTSS are under purifying selection. Furthermore, conserved iTSSs are enriched for regulatory motifs, suggesting that they are regulated, and they tend to eliminate polar effects, which confirms that they are functional. In contrast, the transcription of antisense TSSs located inside CDSs (aTSSs) was significantly less likely to be conserved (22%). However, aTSSs whose transcription was conserved often have conserved promoter motifs and drive the expression of nearby genes. Overall, our findings demonstrate that some internal TSSs are conserved and drive protein expression despite their unusual locations, but the majority are not conserved and may reflect noisy initiation of transcription rather than a biological function.« less

  16. Ranching and conservation in the Santa Cruz River Region, Sonora: Milpillas Case Study (Ganaderia y Conservacion en la Region del Rio Santa Cruz, Sonora: El Caso del Grupo Milpillas)

    Treesearch

    Joaquin Murrieta-Saldivar

    2006-01-01

    The Sonoran Institute (SI) is a non-profit organization working with people toward common conservation goals. Two objectives guide the work of the Sonoran Institute in the Santa Cruz River Region in Sonora, Mexico: to establish projects with community participation that can result in tangible and long-lasting benefits to the environment, and to ensure success by...

  17. Using strategic foresight to assess conservation opportunity.

    PubMed

    Cook, Carly N; Wintle, Bonnie C; Aldrich, Stephen C; Wintle, Brendan A

    2014-12-01

    The nature of conservation challenges can foster a reactive, rather than proactive approach to decision making. Failure to anticipate problems before they escalate results in the need for more costly and time-consuming solutions. Proactive conservation requires forward-looking approaches to decision making that consider possible futures without being overly constrained by the past. Strategic foresight provides a structured process for considering the most desirable future and for mapping the most efficient and effective approaches to promoting that future with tools that facilitate creative thinking. The process involves 6 steps: setting the scope, collecting inputs, analyzing signals, interpreting the information, determining how to act, and implementing the outcomes. Strategic foresight is ideal for seeking, recognizing, and realizing conservation opportunities because it explicitly encourages a broad-minded, forward-looking perspective on an issue. Despite its potential value, the foresight process is rarely used to address conservation issues, and previous attempts have generally failed to influence policy. We present the strategic foresight process as it can be used for proactive conservation planning, describing some of the key tools in the foresight tool kit and how they can be used to identify and exploit different types of conservation opportunities. Scanning is an important tool for collecting and organizing diverse streams of information and can be used to recognize new opportunities and those that could be created. Scenario planning explores how current trends, drivers of change, and key uncertainties might influence the future and can be used to identify barriers to opportunities. Backcasting is used to map out a path to a goal and can determine how to remove barriers to opportunities. We highlight how the foresight process was used to identify conservation opportunities during the development of a strategic plan to address climate change in New York

  18. Genetic conservation planning for forest tree species in Western North America under future climate change: Employing a novel approach to identify conservation gaps

    Treesearch

    L.K. Gray; E.J. Russell; Q.E. Barber; A. Hamann

    2017-01-01

    Among the 17 provinces, territories, and states that comprise western North America, approximately 18 percent of the 8.4 million km2 of forested land base is designated as protected areas to ensure the in situ conservation of forest biodiversity. Jurisdictions vary substantially however, in their responsibilities, protected area coverage, and conservation policies....

  19. The Role of DNA Barcodes in Understanding and Conservation of Mammal Diversity in Southeast Asia

    PubMed Central

    Francis, Charles M.; Borisenko, Alex V.; Ivanova, Natalia V.; Eger, Judith L.; Lim, Burton K.; Guillén-Servent, Antonio; Kruskop, Sergei V.; Mackie, Iain; Hebert, Paul D. N.

    2010-01-01

    Background Southeast Asia is recognized as a region of very high biodiversity, much of which is currently at risk due to habitat loss and other threats. However, many aspects of this diversity, even for relatively well-known groups such as mammals, are poorly known, limiting ability to develop conservation plans. This study examines the value of DNA barcodes, sequences of the mitochondrial COI gene, to enhance understanding of mammalian diversity in the region and hence to aid conservation planning. Methodology and Principal Findings DNA barcodes were obtained from nearly 1900 specimens representing 165 recognized species of bats. All morphologically or acoustically distinct species, based on classical taxonomy, could be discriminated with DNA barcodes except four closely allied species pairs. Many currently recognized species contained multiple barcode lineages, often with deep divergence suggesting unrecognized species. In addition, most widespread species showed substantial genetic differentiation across their distributions. Our results suggest that mammal species richness within the region may be underestimated by at least 50%, and there are higher levels of endemism and greater intra-specific population structure than previously recognized. Conclusions DNA barcodes can aid conservation and research by assisting field workers in identifying species, by helping taxonomists determine species groups needing more detailed analysis, and by facilitating the recognition of the appropriate units and scales for conservation planning. PMID:20838635

  20. Kortright Centre for Conservation: Forestry Theme.

    ERIC Educational Resources Information Center

    Foster, Allan

    One of a series of four reports on specific conservation themes, this report on forestry is intended to consolidate techniques which will best communicate the legislation, role, objectives and practices of the Metropolitan Toronto and Region Conservation Authority in retaining forest cover and extending it over additional areas. Facilities and…

  1. Building robust conservation plans.

    PubMed

    Visconti, Piero; Joppa, Lucas

    2015-04-01

    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 χ, 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. © 2014 Society for Conservation Biology.

  2. Practical method to identify orbital anomaly as spacecraft breakup in the geostationary region

    NASA Astrophysics Data System (ADS)

    Hanada, Toshiya; Uetsuhara, Masahiko; Nakaniwa, Yoshitaka

    2012-07-01

    Identifying a spacecraft breakup is an essential issue to define the current orbital debris environment. This paper proposes a practical method to identify an orbital anomaly, which appears as a significant discontinuity in the observation data, as a spacecraft breakup. The proposed method is applicable to orbital anomalies in the geostationary region. Long-term orbital evolutions of breakup fragments may conclude that their orbital planes will converge into several corresponding regions in inertial space even if the breakup epoch is not specified. This empirical method combines the aforementioned conclusion with the search strategy developed at Kyushu University, which can identify origins of observed objects as fragments released from a specified spacecraft. This practical method starts with selecting a spacecraft that experienced an orbital anomaly, and formulates a hypothesis to generate fragments from the anomaly. Then, the search strategy is applied to predict the behavior of groups of fragments hypothetically generated. Outcome of this predictive analysis specifies effectively when, where and how we should conduct optical measurements using ground-based telescopes. Objects detected based on the outcome are supposed to be from the anomaly, so that we can confirm the anomaly as a spacecraft breakup to release the detected objects. This paper also demonstrates observation planning for a spacecraft anomaly in the geostationary region.

  3. Using occupancy models of forest breeding birds to prioritize conservation planning

    USGS Publications Warehouse

    De Wan, A. A.; Sullivan, P.J.; Lembo, A.J.; Smith, C.R.; Maerz, J.C.; Lassoie, J.P.; Richmond, M.E.

    2009-01-01

    As urban development continues to encroach on the natural and rural landscape, land-use planners struggle to identify high priority conservation areas for protection. Although knowing where urban-sensitive species may be occurring on the landscape would facilitate conservation planning, research efforts are often not sufficiently designed to make quality predictions at unknown locations. Recent advances in occupancy modeling allow for more precise estimates of occupancy by accounting for differences in detectability. We applied these techniques to produce robust estimates of habitat occupancy for a subset of forest breeding birds, a group that has been shown to be sensitive to urbanization, in a rapidly urbanizing yet biological diverse region of New York State. We found that detection probability ranged widely across species, from 0.05 to 0.8. Our models suggest that detection probability declined with increasing forest fragmentation. We also found that the probability of occupancy of forest breeding birds is negatively influenced by increasing perimeter-area ratio of forest fragments and urbanization in the surrounding habitat matrix. We capitalized on our random sampling design to produce spatially explicit models that predict high priority conservation areas across the entire region, where interior-species were most likely to occur. Finally, we use our predictive maps to demonstrate how a strict sampling design coupled with occupancy modeling can be a valuable tool for prioritizing biodiversity conservation in land-use planning. ?? 2009 Elsevier Ltd.

  4. Structural flexibility of a conserved antigenic region in hepatitis C virus glycoprotein E2 recognized by broadly neutralizing antibodies.

    PubMed

    Meola, Annalisa; Tarr, Alexander W; England, Patrick; Meredith, Luke W; McClure, C Patrick; Foung, Steven K H; McKeating, Jane A; Ball, Jonathan K; Rey, Felix A; Krey, Thomas

    2015-02-01

    Neutralizing antibodies (NAbs) targeting glycoprotein E2 are important for the control of hepatitis C virus (HCV) infection. One conserved antigenic site (amino acids 412 to 423) is disordered in the reported E2 structure, but a synthetic peptide mimicking this site forms a β-hairpin in complex with three independent NAbs. Our structure of the same peptide in complex with NAb 3/11 demonstrates a strikingly different extended conformation. We also show that residues 412 to 423 are essential for virus entry but not for E2 folding. Together with the neutralizing capacity of the 3/11 Fab fragment, this indicates an unexpected structural flexibility within this epitope. NAbs 3/11 and AP33 (recognizing the extended and β-hairpin conformations, respectively) display similar neutralizing activities despite converse binding kinetics. Our results suggest that HCV utilizes conformational flexibility as an immune evasion strategy, contributing to the limited immunogenicity of this epitope in patients, similar to the conformational flexibility described for other enveloped and nonenveloped viruses. Approximately 180 million people worldwide are infected with hepatitis C virus (HCV), and neutralizing antibodies play an important role in controlling the replication of this major human pathogen. We show here that one of the most conserved antigenic sites within the major glycoprotein E2 (amino acids 412 to 423), which is disordered in the recently reported crystal structure of an E2 core fragment, can adopt different conformations in the context of the infectious virus particle. Recombinant Fab fragments recognizing different conformations of this antigenic site have similar neutralization activities in spite of converse kinetic binding parameters. Of note, an antibody response targeting this antigenic region is less frequent than those targeting other more immunogenic regions in E2. Our results suggest that the observed conformational flexibility in this conserved antigenic

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

    USGS Publications Warehouse

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

    2008-01-01

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

  6. Watershed prioritization in the upper Han River basin for soil and water conservation in the South-to-North Water Transfer Project (middle route) of China.

    PubMed

    Wu, Haibing

    2018-01-01

    Watershed prioritization with the objective of identifying critical areas to undertake soil and water conservation measures was conducted in the upper Han River basin, the water source area of approximately 95,000 km 2 for the middle route of China's South-to-North Water Transfer Project. Based on the estimated soil erosion intensity in uplands and clustering analysis of measured nutrient concentrations in rivers, the basin was grouped into very-high-, high-, moderate-, and low-priority regions for water and soil conservation, respectively. The results indicated that soil erosion was primarily controlled by topography, and nutrients in rivers were associated with land use and land cover in uplands. Also, there was large spatial disparity between soil erosion intensity in the uplands and nutrient concentrations in the rivers across the basin. Analysis was then performed to prioritize the basin by the integration of the soil erosion intensity and water quality on a GIS platform in order to identify critical areas for water and soil conservation in the basin. The identified high-priority regions which occupy 5.74% of the drainage areas need immediate attention for soil and water conservation treatments, of which 5.28% is critical for soil erosion prevention and 0.46% for water conservation. Understandings of the basin environment and pollutant loading with spatial explicit are critical to the soil and water resource conservation for the interbasin water transfer project.

  7. Current conserving theory at the operator level

    NASA Astrophysics Data System (ADS)

    Yuan, Jiangtao; Wang, Yin; Wang, Jian

    The basic assumption of quantum transport in mesoscopic systems is that the total charge inside the scattering region is zero. This means that the potential deep inside reservoirs is effectively screened and therefore the electric field at interface of scattering region is zero. Thus the current conservation condition can be satisfied automatically which is an important condition in mesoscopic transport. So far the current conserving ac theory is well developed by considering the displacement current which is due to Coulomb interaction if we just focus on the average current. However, the frequency dependent shot noise does not satisfy the conservation condition since we do not consider the current conservation at the operator level. In this work, we formulate a generalized current conserving theory at the operator level using non-equilibrium Green's function theory which could be applied to both average current and frequency dependent shot noise. A displacement operator is derived for the first time so that the frequency dependent correlation of displacement currents could be investigated. Moreover, the equilibrium shot noise is investigated and a generalized fluctuation-dissipation relationship is presented.

  8. Ecological and socio-cultural factors influencing in situ conservation of crop diversity by traditional Andean households in Peru

    PubMed Central

    2011-01-01

    Background The Peruvian Andean region is a main center of plant domestication of the world. There, several tuber species were domesticated and the area lodges one of the most important reservoirs of their varieties and wild relatives. It is also the setting of traditional cultures using and conserving them. However, crop genetic erosion has been reported in the region since several decades ago; therefore, understanding factors influencing both loss and maintenance of crop variation is relevant to design conservation policies. Previous researches have examined factors influencing agrobiodiversity conservation in the region but additional case studies are recognized to be still necessary for a deeper understanding of causes of genetic erosion and for policy design to prevent and remedy it. Our study focused on analyzing (1) variation in richness of traditional varieties of tubers cultivated among households, (2) changes in varieties richness occurred in four consecutive agricultural cycles, and (3) ecological, social, and cultural factors influencing loss and conservation of varieties. Methods Richness of farmer varieties of tuber species cultivated by 28 peasant households was monitored in communities of Cajamarca and Huánuco, Peru during four consecutive agricultural cycles (from 2001 to 2005). In-depth interviews were conducted with 12 of the households with higher reputation as conservationists, in order to document farmers' perception of tubers qualities in ecological, social, economic, technological and culinary aspects and how these influence their decisions of conservation priorities. Traditional varieties were identified according to their local names, which were then confronted among farmers and with scientific catalogues in order to identify synonyms. Based on the information documented, indexes of ecological and socio-cultural factors affecting agricultural practices were designed, and their linear correlations and multivariate relations with varieties

  9. Ecological and socio-cultural factors influencing in situ conservation of crop diversity by traditional Andean households in Peru.

    PubMed

    Velásquez-Milla, Dora; Casas, Alejandro; Torres-Guevara, Juan; Cruz-Soriano, Aldo

    2011-12-06

    The Peruvian Andean region is a main center of plant domestication of the world. There, several tuber species were domesticated and the area lodges one of the most important reservoirs of their varieties and wild relatives. It is also the setting of traditional cultures using and conserving them. However, crop genetic erosion has been reported in the region since several decades ago; therefore, understanding factors influencing both loss and maintenance of crop variation is relevant to design conservation policies. Previous researches have examined factors influencing agrobiodiversity conservation in the region but additional case studies are recognized to be still necessary for a deeper understanding of causes of genetic erosion and for policy design to prevent and remedy it. Our study focused on analyzing (1) variation in richness of traditional varieties of tubers cultivated among households, (2) changes in varieties richness occurred in four consecutive agricultural cycles, and (3) ecological, social, and cultural factors influencing loss and conservation of varieties. Richness of farmer varieties of tuber species cultivated by 28 peasant households was monitored in communities of Cajamarca and Huánuco, Peru during four consecutive agricultural cycles (from 2001 to 2005). In-depth interviews were conducted with 12 of the households with higher reputation as conservationists, in order to document farmers' perception of tubers qualities in ecological, social, economic, technological and culinary aspects and how these influence their decisions of conservation priorities. Traditional varieties were identified according to their local names, which were then confronted among farmers and with scientific catalogues in order to identify synonyms. Based on the information documented, indexes of ecological and socio-cultural factors affecting agricultural practices were designed, and their linear correlations and multivariate relations with varieties richness managed per

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

    PubMed Central

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

    2013-01-01

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

  11. Land Conservation Plan from the New Hampshire’s Coastal Watersheds (Piscataqua Region Estuaries Partnership)

    EPA Pesticide Factsheets

    The overarching goal of this land conservation plan is to focus conservation on those lands and waters that are most important for conserving living resources - native plants, animals and natural communities - and water quality in the coastal watersheds.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Yeo, U. J.; Supple, J. R.; Franich, R. D.

    2013-10-15

    Purpose: Deformable image registration (DIR) has become a key tool for adaptive radiotherapy to account for inter- and intrafraction organ deformation. Of contemporary interest, the application to deformable dose accumulation requires accurate deformation even in low contrast regions where dose gradients may exist within near-uniform tissues. One expects high-contrast features to generally be deformed more accurately by DIR algorithms. The authors systematically assess the accuracy of 12 DIR algorithms and quantitatively examine, in particular, low-contrast regions, where accuracy has not previously been established.Methods: This work investigates DIR algorithms in three dimensions using deformable gel (DEFGEL) [U. J. Yeo, M. L.more » 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

  13. In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus

    PubMed Central

    2012-01-01

    Background MicroRNAs (miRNAs) are small RNAs (21-24 bp) providing an RNA-based system of gene regulation highly conserved in plants and animals. In plants, miRNAs control mRNA degradation or restrain translation, affecting development and responses to stresses. Plant miRNAs show imperfect but extensive complementarity to mRNA targets, making their computational prediction possible, useful when data mining is applied on different species. In this study we used a comparative approach to identify both miRNAs and their targets, in artichoke and safflower. Results Two complete expressed sequence tags (ESTs) datasets from artichoke (3.6·104 entries) and safflower (4.2·104), were analysed with a bioinformatic pipeline and in vitro experiments, identifying 17 potential miRNAs. For each EST, using RNAhybrid program and 953 non redundant miRNA mature sequences, available in mirBase as reference, we searched matching putative targets. 8730 out of 42011 ESTs from safflower and 7145 of 36323 ESTs from artichoke showed at least one predicted miRNA target. BLAST analysis showed that 75% of all ESTs shared at least a common homologous region (E-value < 10-4) and about 50% of these displayed 400 bp or longer aligned sequences as conserved homologous/orthologous (COS) regions. 960 and 890 ESTs of safflower and artichoke organized in COS shared 79 different miRNA targets, considered functionally conserved, and statistically significant when compared with random sequences (signal to noise ratio > 2 and specificity ≥ 0.85). Four highly significant miRNAs selected from in silico data were experimentally validated in globe artichoke leaves. Conclusions Mature miRNAs and targets were predicted within EST sequences of safflower and artichoke. Most of the miRNA targets appeared highly/moderately conserved, highlighting an important and conserved function. In this study we introduce a stringent parameter for the comparative sequence analysis, represented by the identification of the same

  14. Understanding the effects of different social data on selecting priority conservation areas.

    PubMed

    Karimi, Azadeh; Tulloch, Ayesha I T; Brown, Greg; Hockings, Marc

    2017-12-01

    Conservation success is contingent on assessing social and environmental factors so that cost-effective implementation of strategies and actions can be placed in a broad social-ecological context. Until now, the focus has been on how to include spatially explicit social data in conservation planning, whereas the value of different kinds of social data has received limited attention. In a regional systematic conservation planning case study in Australia, we examined the spatial concurrence of a range of spatially explicit social values and land-use preferences collected using a public participation geographic information system and biological data. We used Zonation to integrate the social data with the biological data in a series of spatial-prioritization scenarios to determine the effect of the different types of social data on spatial prioritization compared with biological data alone. The type of social data (i.e., conservation opportunities or constraints) significantly affected spatial prioritization outcomes. The integration of social values and land-use preferences under different scenarios was highly variable and generated spatial prioritizations 1.2-51% different from those based on biological data alone. The inclusion of conservation-compatible values and preferences added relatively few new areas to conservation priorities, whereas including noncompatible economic values and development preferences as costs significantly changed conservation priority areas (48.2% and 47.4%, respectively). Based on our results, a multifaceted conservation prioritization approach that combines spatially explicit social data with biological data can help conservation planners identify the type of social data to collect for more effective and feasible conservation actions. © 2017 Society for Conservation Biology.

  15. Fine‐resolution conservation planning with limited climate‐change information

    USGS Publications Warehouse

    Shah, Payal; Mallory, Mindy L.; Ando , Amy W.; Guntenspergen, Glenn R.

    2017-01-01

    Climate‐change induced uncertainties in future spatial patterns of conservation‐related outcomes make it difficult to implement standard conservation‐planning paradigms. A recent study translates Markowitz's risk‐diversification strategy from finance to conservation settings, enabling conservation agents to use this diversification strategy for allocating conservation and restoration investments across space to minimize the risk associated with such uncertainty. However, this method is information intensive and requires a large number of forecasts of ecological outcomes associated with possible climate‐change scenarios for carrying out fine‐resolution conservation planning. We developed a technique for iterative, spatial portfolio analysis that can be used to allocate scarce conservation resources across a desired level of subregions in a planning landscape in the absence of a sufficient number of ecological forecasts. We applied our technique to the Prairie Pothole Region in central North America. A lack of sufficient future climate information prevented attainment of the most efficient risk‐return conservation outcomes in the Prairie Pothole Region. The difference in expected conservation returns between conservation planning with limited climate‐change information and full climate‐change information was as large as 30% for the Prairie Pothole Region even when the most efficient iterative approach was used. However, our iterative approach allowed finer resolution portfolio allocation with limited climate‐change forecasts such that the best possible risk‐return combinations were obtained. With our most efficient iterative approach, the expected loss in conservation outcomes owing to limited climate‐change information could be reduced by 17% relative to other iterative approaches.

  16. A similarity based approach to identify homogeneous regions for seasonal forecasting

    NASA Astrophysics Data System (ADS)

    Schick, Simon; Rössler, Ole; Weingartner, Rolf

    2015-04-01

    Seasonal runoff forecasting using statistical models is challenged by a large number of candidate predictors and a general weak predictor-predictand relationship. As the area of the target basin increases, often also the available data sets do, thus reinforcing the predictor selection challenge. We propose an approach which follows the idea of 'divide and conquer' as developed in computational sciences and machine learning: First, the macroscale target basin is partitioned into homogeneous regions using all its gauged mesoscale subbasins. Second, one representative subbasin per homogeneous region is identified, for which models are fitted and applied. Third, the resulting forecasts are combined at the scale of the macroscale target basin. This approach requires a suitable method to identify homogeneous regions and representative subbasins. We suggest a way based on hydrological similarity, as catchment similarity estimated with respect to physiographic-climatic descriptors does not necessarily imply similar runoff response. Each descriptor is derived from daily runoff series and aimed to reflect a specific catchment characteristic: autocorrelation coefficient, parameters of fitted Gamma distribution and low/high flow indices (based on daily runoff values) fluctuation of the standard deviation within the yearly cycle (based on weekly runoff values) dominant harmonics obtained from the discrete Fourier transform (based on monthly runoff values) long term trend (based on yearly runoff values) Where necessary, the runoff series first need to be standardized, aggregated, detrended or deseasonalized. As a preliminary study we present the results of a cluster analysis for the Swiss Rhine River as macroscale target basin, which leads to about 40 mesoscale subbasins with runoff series for the period 1991-2010. Problems we have to address include the choice of a clustering algorithm, the identification of an appropriate number of regions and the selection of representative

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

    NASA Astrophysics Data System (ADS)

    Wu, N.; Zhang, X.

    2015-08-01

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

  18. Comparative Genomics of 12 Strains of Erwinia amylovora Identifies a Pan-Genome with a Large Conserved Core

    PubMed Central

    Mann, Rachel A.; Smits, Theo H. M.; Bühlmann, Andreas; Blom, Jochen; Goesmann, Alexander; Frey, Jürg E.; Plummer, Kim M.; Beer, Steven V.; Luck, Joanne; Duffy, Brion; Rodoni, Brendan

    2013-01-01

    The plant pathogen Erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the Rosaceae subfamily Spiraeoideae (e.g., Malus, Pyrus, Crataegus, Sorbus) and strains infecting Rubus (raspberries and blackberries). Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of E. amylovora was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and Rubus-infecting strains (and among individual Rubus-infecting strains), the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the Rubus-infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of E. amylovora than it was to the other Rubus-infecting strains. Analysis of the accessory genomes of Spiraeoideae- and Rubus-infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1Ea and a putative secondary metabolite pathway only present in Rubus-infecting strains. PMID:23409014

  19. Comparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.

    PubMed

    Mann, Rachel A; Smits, Theo H M; Bühlmann, Andreas; Blom, Jochen; Goesmann, Alexander; Frey, Jürg E; Plummer, Kim M; Beer, Steven V; Luck, Joanne; Duffy, Brion; Rodoni, Brendan

    2013-01-01

    The plant pathogen Erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the Rosaceae subfamily Spiraeoideae (e.g., Malus, Pyrus, Crataegus, Sorbus) and strains infecting Rubus (raspberries and blackberries). Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of E. amylovora was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and Rubus-infecting strains (and among individual Rubus-infecting strains), the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the Rubus-infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of E. amylovora than it was to the other Rubus-infecting strains. Analysis of the accessory genomes of Spiraeoideae- and Rubus-infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1(Ea) and a putative secondary metabolite pathway only present in Rubus-infecting strains.

  20. 50 CFR 622.179 - Conservation measures for protected resources.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 50 Wildlife and Fisheries 12 2014-10-01 2014-10-01 false Conservation measures for protected resources. 622.179 Section 622.179 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL..., AND SOUTH ATLANTIC Snapper-Grouper Fishery of the South Atlantic Region § 622.179 Conservation...

  1. 50 CFR 622.179 - Conservation measures for protected resources.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 50 Wildlife and Fisheries 12 2013-10-01 2013-10-01 false Conservation measures for protected resources. 622.179 Section 622.179 Wildlife and Fisheries FISHERY CONSERVATION AND MANAGEMENT, NATIONAL..., AND SOUTH ATLANTIC Snapper-Grouper Fishery of the South Atlantic Region § 622.179 Conservation...

  2. Practitioner and scientist perceptions of successful amphibian conservation.

    PubMed

    Meredith, Helen M R; St John, Freya A V; Collen, Ben; Black, Simon A; Griffiths, Richard A

    2018-04-01

    Conservation requires successful outcomes. However, success is perceived in many different ways depending on the desired outcome. Through a questionnaire survey, we examined perceptions of success among 355 scientists and practitioners working on amphibian conservation from over 150 organizations in more than 50 countries. We also sought to identify how different types of conservation actions and respondent experience and background influenced perceptions. Respondents identified 4 types of success: species and habitat improvements (84% of respondents); effective program management (36%); outreach initiatives such as education and public engagement (25%); and the application of science-based conservation (15%). The most significant factor influencing overall perceived success was reducing threats. Capacity building was rated least important. Perceptions were influenced by experience, professional affiliation, involvement in conservation practice, and country of residence. More experienced practitioners associated success with improvements to species and habitats and less so with education and engagement initiatives. Although science-based conservation was rated as important, this factor declined in importance as the number of programs a respondent participated in increased, particularly among those from less economically developed countries. The ultimate measure of conservation success-population recovery-may be difficult to measure in many amphibians; difficult to relate to the conservation actions intended to drive it; and difficult to achieve within conventional funding time frames. The relaunched Amphibian Conservation Action Plan provides a framework for capturing lower level processes and outcomes, identifying gaps, and measuring progress. © 2017 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

  3. Fanconi Anemia Core Complex Gene Promoters Harbor Conserved Transcription Regulatory Elements

    PubMed Central

    Meier, Daniel; Schindler, Detlev

    2011-01-01

    The Fanconi anemia (FA) gene family is a recent addition to the complex network of proteins that respond to and repair certain types of DNA damage in the human genome. Since little is known about the regulation of this novel group of genes at the DNA level, we characterized the promoters of the eight genes (FANCA, B, C, E, F, G, L and M) that compose the FA core complex. The promoters of these genes show the characteristic attributes of housekeeping genes, such as a high GC content and CpG islands, a lack of TATA boxes and a low conservation. The promoters functioned in a monodirectional way and were, in their most active regions, comparable in strength to the SV40 promoter in our reporter plasmids. They were also marked by a distinctive transcriptional start site (TSS). In the 5′ region of each promoter, we identified a region that was able to negatively regulate the promoter activity in HeLa and HEK 293 cells in isolation. The central and 3′ regions of the promoter sequences harbor binding sites for several common and rare transcription factors, including STAT, SMAD, E2F, AP1 and YY1, which indicates that there may be cross-connections to several established regulatory pathways. Electrophoretic mobility shift assays and siRNA experiments confirmed the shared regulatory responses between the prominent members of the TGF-β and JAK/STAT pathways and members of the FA core complex. Although the promoters are not well conserved, they share region and sequence specific regulatory motifs and transcription factor binding sites (TBFs), and we identified a bi-partite nature to these promoters. These results support a hypothesis based on the co-evolution of the FA core complex genes that was expanded to include their promoters. PMID:21826217

  4. Fanconi anemia core complex gene promoters harbor conserved transcription regulatory elements.

    PubMed

    Meier, Daniel; Schindler, Detlev

    2011-01-01

    The Fanconi anemia (FA) gene family is a recent addition to the complex network of proteins that respond to and repair certain types of DNA damage in the human genome. Since little is known about the regulation of this novel group of genes at the DNA level, we characterized the promoters of the eight genes (FANCA, B, C, E, F, G, L and M) that compose the FA core complex. The promoters of these genes show the characteristic attributes of housekeeping genes, such as a high GC content and CpG islands, a lack of TATA boxes and a low conservation. The promoters functioned in a monodirectional way and were, in their most active regions, comparable in strength to the SV40 promoter in our reporter plasmids. They were also marked by a distinctive transcriptional start site (TSS). In the 5' region of each promoter, we identified a region that was able to negatively regulate the promoter activity in HeLa and HEK 293 cells in isolation. The central and 3' regions of the promoter sequences harbor binding sites for several common and rare transcription factors, including STAT, SMAD, E2F, AP1 and YY1, which indicates that there may be cross-connections to several established regulatory pathways. Electrophoretic mobility shift assays and siRNA experiments confirmed the shared regulatory responses between the prominent members of the TGF-β and JAK/STAT pathways and members of the FA core complex. Although the promoters are not well conserved, they share region and sequence specific regulatory motifs and transcription factor binding sites (TBFs), and we identified a bi-partite nature to these promoters. These results support a hypothesis based on the co-evolution of the FA core complex genes that was expanded to include their promoters.

  5. Identifying species at extinction risk using global models of anthropogenic impact.

    PubMed

    Peters, Howard; O'Leary, Bethan C; Hawkins, Julie P; Roberts, Callum M

    2015-02-01

    The International Union for Conservation of Nature Red List of Endangered Species employs a robust, standardized approach to assess extinction threat focussed on taxa approaching an end-point in population decline. Used alone, we argue this enforces a reactive approach to conservation. Species not assessed as threatened but which occur predominantly in areas with high levels of anthropogenic impact may require proactive conservation management to prevent loss. We matched distribution and bathymetric range data from the global Red List assessment of 632 species of marine cone snails with human impacts and projected ocean thermal stress and aragonite saturation (a proxy for ocean acidification). Our results show 67 species categorized as 'Least Concern' have 70% or more of their occupancy in places subject to high and very high levels of human impact with 18 highly restricted species (range <100 km(2)) living exclusively in such places. Using a range-rarity scoring method we identified where clusters of endemic species are subject to all three stressors: high human impact, declining aragonite saturation levels and elevated thermal stress. Our approach reinforces Red List threatened status, highlights candidate species for reassessment, contributes important evidential data to minimize data deficiency and identifies regions and species for proactive conservation. © 2014 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

  6. National Proceedings: Forest and Conservation Nursery Associations-2008

    Treesearch

    R. K. Dumroese; L. E. Riley

    2009-01-01

    These proceedings are a compilation of 27 papers that were presented at the regional meetings of the forest and conservation nursery associations in the United States in 2008. The Western Forest and Conservation Nursery Association meeting was held at the DoubleTree Hotel in Missoula, Montana, on June 23 to 25. The meeting was hosted by the Montana Conservation...

  7. Multiscale habitat suitability index models for priority landbirds in the Central Hardwoods and West Gulf Coastal Plain/Ouachitas Bird Conservation Regions

    Treesearch

    John M. Tirpak; D. Todd Jones-Farrand; Frank R., III Thompson; Daniel J. Twedt; William B., III Uihlein

    2009-01-01

    Habitat Suitability Index (HSI) models were developed to assess habitat quality for 40 priority bird species in the Central Hardwoods and West Gulf Coastal Plain/Ouachitas Bird Conservation Regions. The models incorporated both site and landscape environmental variables from one of six nationally consistent datasets. Potential habitat was first defined from unique...

  8. An Fe-S cluster in the conserved Cys-rich region in the catalytic subunit of FAD-dependent dehydrogenase complexes.

    PubMed

    Shiota, Masaki; Yamazaki, Tomohiko; Yoshimatsu, Keiichi; Kojima, Katsuhiro; Tsugawa, Wakako; Ferri, Stefano; Sode, Koji

    2016-12-01

    Several bacterial flavin adenine dinucleotide (FAD)-harboring dehydrogenase complexes comprise three distinct subunits: a catalytic subunit with FAD, a cytochrome c subunit containing three hemes, and a small subunit. Owing to the cytochrome c subunit, these dehydrogenase complexes have the potential to transfer electrons directly to an electrode. Despite various electrochemical applications and engineering studies of FAD-dependent dehydrogenase complexes, the intra/inter-molecular electron transfer pathway has not yet been revealed. In this study, we focused on the conserved Cys-rich region in the catalytic subunits using the catalytic subunit of FAD dependent glucose dehydrogenase complex (FADGDH) as a model, and site-directed mutagenesis and electron paramagnetic resonance (EPR) were performed. By co-expressing a hitch-hiker protein (γ-subunit) and a catalytic subunit (α-subunit), FADGDH γα complexes were prepared, and the properties of the catalytic subunit of both wild type and mutant FADGDHs were investigated. Substitution of the conserved Cys residues with Ser resulted in the loss of dye-mediated glucose dehydrogenase activity. ICP-AEM and EPR analyses of the wild-type FADGDH catalytic subunit revealed the presence of a 3Fe-4S-type iron-sulfur cluster, whereas none of the Ser-substituted mutants showed the EPR spectrum characteristic for this cluster. The results suggested that three Cys residues in the Cys-rich region constitute an iron-sulfur cluster that may play an important role in the electron transfer from FAD (intra-molecular) to the multi-heme cytochrome c subunit (inter-molecular) electron transfer pathway. These features appear to be conserved in the other three-subunit dehydrogenases having an FAD cofactor. Copyright © 2016 Elsevier B.V. All rights reserved.

  9. Indicator-driven conservation planning across terrestrial, freshwater aquatic, and marine ecosystems of the south Atlantic, USA

    USGS Publications Warehouse

    Pickens, Bradley A.; Mordecai, Rua S.; Drew, C. Ashton; Alexander-Vaughn, Louise B.; Keister, Amy S.; Morris, Hilary L.C.; Collazo, Jaime A.

    2017-01-01

    Systematic conservation planning, a widely used approach to identify priority lands and waters, uses efficient, defensible, and transparent methods aimed at conserving biodiversity and ecological systems. Limited financial resources and competing land uses can be major impediments to conservation; therefore, participation of diverse stakeholders in the planning process is advantageous to help address broad-scale threats and challenges of the 21st century. Although a broad extent is needed to identify core areas and corridors for fish and wildlife populations, a fine-scale resolution is needed to manage for multiple, interconnected ecosystems. Here, we developed a conservation plan using a systematic approach to promote landscape-level conservation within the extent of the South Atlantic Landscape Conservation Cooperative. Our objective was to identify the highest-ranked 30% of lands and waters within the South Atlantic deemed necessary to conserve ecological and cultural integrity for the 10 primary ecosystems of the southeastern United States. These environments varied from terrestrial, freshwater aquatic, and marine. The planning process was driven by indicators of ecosystem integrity at a 4-ha resolution. We used the program Zonation and 28 indicators to optimize the identification of lands and waters to meet the stated objective. A novel part of our study was the prioritization of multiple ecosystems, and we discuss the advantages and disadvantages of this approach. The evaluation of indicator representation within prioritizations was a useful method to show where improvements could be made; some indicators dictated hotspots, some had a limited extent and were well represented, and others had a limited effect. Overall, we demonstrate that a broad-scale (408,276 km2 of terrestrial and 411,239 km2 of marine environments) conservation plan can be realized at a fine-scale resolution, which will allow implementation of the regional plan at a local level relevant

  10. Identifying effective actions to guide volunteer-based and nationwide conservation efforts for a ground-nesting farmland bird.

    PubMed

    Santangeli, Andrea; Arroyo, Beatriz; Millon, Alexandre; Bretagnolle, Vincent

    2015-08-01

    1. Modern farming practices threaten wildlife in different ways, and failure to identify the complexity of multiple threats acting in synergy may result in ineffective management. To protect ground-nesting birds in farmland, monitoring and mitigating impacts of mechanical harvesting is crucial. 2. Here, we use 6 years of data from a nationwide volunteer-based monitoring scheme of the Montagu's harrier, a ground-nesting raptor, in French farmlands. We assess the effectiveness of alternative nest protection measures and map their potential benefit to the species. 3. We show that unprotected nests in cultivated land are strongly negatively affected by harvesting and thus require active management. Further, we show that protection from harvesting alone (e.g. by leaving a small unharvested buffer around the nest) is impaired by post-harvest predation at nests that become highly conspicuous after harvest. Measures that simultaneously protect from harvesting and predation (by adding a fence around the nest) significantly enhance nest productivity. 4. The map of expected gain from nest protection in relation to available volunteers' workforce pinpoints large areas of high expected gain from nest protection that are not matched by equally high workforce availability. This mismatch suggests that the impact of nest protection can be further improved by increasing volunteer efforts in key areas where they are low relative to the expected gain they could have. 5. Synthesis and applications . This study shows that synergistic interplay of multiple factors (e.g. mechanical harvesting and predation) may completely undermine the success of well-intentioned conservation efforts. However, identifying areas where the greatest expected gains can be achieved relative to effort expended can minimize the risk of wasted volunteer actions. Overall, this study underscores the importance of citizen science for collecting large-scale data useful for producing science and ultimately informs

  11. Prioritizing Tiger Conservation through Landscape Genetics and Habitat Linkages

    PubMed Central

    Yumnam, Bibek; Jhala, Yadvendradev V.; Qureshi, Qamar; Maldonado, Jesus E.; Gopal, Rajesh; Saini, Swati; Srinivas, Y.; Fleischer, Robert C.

    2014-01-01

    Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km2 of forest habitat was found to be only 21,290 km2. After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (F ST) between populations were better explained by modeled linkage costs (r>0.5, p<0.05) compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should provide legal status to

  12. Prioritizing tiger conservation through landscape genetics and habitat linkages.

    PubMed

    Yumnam, Bibek; Jhala, Yadvendradev V; Qureshi, Qamar; Maldonado, Jesus E; Gopal, Rajesh; Saini, Swati; Srinivas, Y; Fleischer, Robert C

    2014-01-01

    Even with global support for tiger (Panthera tigris) conservation their survival is threatened by poaching, habitat loss and isolation. Currently about 3,000 wild tigers persist in small fragmented populations within seven percent of their historic range. Identifying and securing habitat linkages that connect source populations for maintaining landscape-level gene flow is an important long-term conservation strategy for endangered carnivores. However, habitat corridors that link regional tiger populations are often lost to development projects due to lack of objective evidence on their importance. Here, we use individual based genetic analysis in combination with landscape permeability models to identify and prioritize movement corridors across seven tiger populations within the Central Indian Landscape. By using a panel of 11 microsatellites we identified 169 individual tigers from 587 scat and 17 tissue samples. We detected four genetic clusters within Central India with limited gene flow among three of them. Bayesian and likelihood analyses identified 17 tigers as having recent immigrant ancestry. Spatially explicit tiger occupancy obtained from extensive landscape-scale surveys across 76,913 km(2) of forest habitat was found to be only 21,290 km(2). After accounting for detection bias, the covariates that best explained tiger occupancy were large, remote, dense forest patches; large ungulate abundance, and low human footprint. We used tiger occupancy probability to parameterize habitat permeability for modeling habitat linkages using least-cost and circuit theory pathway analyses. Pairwise genetic differences (FST) between populations were better explained by modeled linkage costs (r>0.5, p<0.05) compared to Euclidean distances, which was in consonance with observed habitat fragmentation. The results of our study highlight that many corridors may still be functional as there is evidence of contemporary migration. Conservation efforts should provide legal status

  13. Using regional bird density distribution models to evaluate protected area networks and inform conservation planning

    Treesearch

    John D. Alexander; Jaime L. Stephens; Sam Veloz; Leo Salas; Josée S. Rousseau; C. John Ralph; Daniel A. Sarr

    2017-01-01

    As data about populations of indicator species become available, proactive strategies that improve representation of biological diversity within protected area networks should consider finer-scaled evaluations, especially in regions identified as important through course-scale analyses. We use density distribution models derived from a robust regional bird...

  14. A view of the global conservation job market and how to succeed in it.

    PubMed

    Lucas, Jane; Gora, Evan; Alonso, Alfonso

    2017-12-01

    The high demand for conservation work is creating a need for conservation-focused training of scientists. Although many people with postsecondary degrees in biology are finding careers outside academia, many programs and mentors continue to prepare students to follow-in-the-footsteps of their professors. Unfortunately, information regarding how to prepare for today's conservation-based job market is limited in detail and scope. This problem is complicated by the differing needs of conservation organizations in both economically developed and developing regions worldwide. To help scientists identify the tools needed for conservation positions worldwide, we reviewed the current global conservation job market and identified skills required for success in careers in academia, government, nonprofit, and for-profit organizations. We also interviewed conservation professionals across all conservation sectors. Positions in nonprofit organizations were the most abundant, whereas academic jobs were only 10% of the current job market. The most common skills required across sectors were a strong disciplinary background, followed by analytical and technical skills. Academic positions differed the most from other types of positions in that they emphasized teaching as a top skill. Nonacademic jobs emphasized the need for excellent written and oral communication, as well as project-management experience. Furthermore, we found distinct differences across job locations. Positions in developing countries emphasized language and interpersonal skills, whereas positions in countries with advanced economies focused on publication history and technical skills. Our results were corroborated by the conservation professionals we interviewed. Based on our results, we compiled a nondefinitive list of conservation-based training programs that are likely to provide training for the current job market. Using the results of this study, scientists may be better able to tailor their training to

  15. HABITAT DISTRIBUTION MODELS FOR 37 VERTEBRATE SPECIES ADDRESSED BY THE MULTI-SPECIES HABITAT CONSERVATION PLAN OF CLARK COUNTY, NEVADA

    EPA Science Inventory

    Thirty-seven species identified in the Clark County Multi-Species Habitat Conservation Plan were

    previously modeled through the Southwest Regional Gap Analysis Project. Existing SWReGAP habitat

    models and modeling databases were used to facilitate the revision of mo...

  16. Interpreting beta-diversity components over time to conserve metacommunities in highly dynamic ecosystems.

    PubMed

    Ruhí, Albert; Datry, Thibault; Sabo, John L

    2017-12-01

    The concept of metacommunity (i.e., a set of local communities linked by dispersal) has gained great popularity among community ecologists. However, metacommunity research mostly addresses questions on spatial patterns of biodiversity at the regional scale, whereas conservation planning requires quantifying temporal variation in those metacommunities and the contributions that individual (local) sites make to regional dynamics. We propose that recent advances in diversity-partitioning methods may allow for a better understanding of metacommunity dynamics and the identification of keystone sites. We used time series of the 2 components of beta diversity (richness and replacement) and the contributions of local sites to these components to examine which sites controlled source-sink dynamics in a highly dynamic model system (an intermittent river). The relative importance of the richness and replacement components of beta diversity fluctuated over time, and sample aggregation led to underestimation of beta diversity by up to 35%. Our literature review revealed that research on intermittent rivers would benefit greatly from examination of beta-diversity components over time. Adequately appraising spatiotemporal variability in community composition and identifying sites that are pivotal for maintaining biodiversity at the landscape scale are key needs for conservation prioritization and planning. Thus, our framework may be used to guide conservation actions in highly dynamic ecosystems when time-series data describing biodiversity across sites connected by dispersal are available. © 2017 Society for Conservation Biology.

  17. Literature review of giant gartersnake (Thamnophis gigas) biology and conservation

    USGS Publications Warehouse

    Halstead, Brian J.; Wylie, Glenn D.; Casazza, Michael L.

    2015-08-03

    This report reviews the available literature on giant gartersnakes (Thamnophis gigas) to compile existing information on this species and identify knowledge gaps that, if addressed, would help to inform conservation efforts for giant gartersnakes.  Giant gartersnakes comprise a species of semi-aquatic snake precinctive to wetlands in the Central Valley of California.  The diversion of surface water and conversion of wetlands to agricultural and other land uses resulted in the loss of more than 90 percent of natural giant gartersnake habitats.  Because of this habitat loss, giant gartersnakes are now listed by the United States and California Endangered Species Acts as Threatened.  Most extant populations occur in the rice-growing regions of the Sacramento Valley, which comprises the northern portion of the giant gartersnake’s former range.  The huge demand for water in California for agriculture, industry, recreation, and other human consumption, combined with periodic severe drought, places remaining giant gartersnake habitats at increased risk of degradation and loss.  This literature review summarizes the available information on giant gartersnake distribution, habitat relations, behavior, demography, and other aspects of its biology relevant to conservation.  This information is then compiled into a graphical conceptual model that indicates the importance of different aspects of giant gartersnake biology for maintaining positive population growth, and identifies those areas for which important information relevant for conservation is lacking.  Directing research efforts toward these aspects of giant gartersnake ecology will likely result in improvements to conserving this unique species while meeting the high demands for water in California.

  18. Comparative Sequence and X-Inactivation Analyses of a Domain of Escape in Human Xp11.2 and the Conserved Segment in Mouse

    PubMed Central

    Tsuchiya, Karen D.; Greally, John M.; Yi, Yajun; Noel, Kevin P.; Truong, Jean-Pierre; Disteche, Christine M.

    2004-01-01

    We have performed X-inactivation and sequence analyses on 350 kb of sequence from human Xp11.2, a region shown previously to contain a cluster of genes that escape X inactivation, and we compared this region with the region of conserved synteny in mouse. We identified several new transcripts from this region in human and in mouse, which defined the full extent of the domain escaping X inactivation in both species. In human, escape from X inactivation involves an uninterrupted 235-kb domain of multiple genes. Despite highly conserved gene content and order between the two species, Smcx is the only mouse gene from the conserved segment that escapes inactivation. As repetitive sequences are believed to facilitate spreading of X inactivation along the chromosome, we compared the repetitive sequence composition of this region between the two species. We found that long terminal repeats (LTRs) were decreased in the human domain of escape, but not in the majority of the conserved mouse region adjacent to Smcx in which genes were subject to X inactivation, suggesting that these repeats might be excluded from escape domains to prevent spreading of silencing. Our findings indicate that genomic context, as well as gene-specific regulatory elements, interact to determine expression of a gene from the inactive X-chromosome. PMID:15197169

  19. A zoological catalogue of hunted reptiles in the semiarid region of Brazil

    PubMed Central

    2012-01-01

    The variety of interactions between human cultures and herpetofauna is the subject matter of Ethnoherpetology, a subdivision of Ethnozoology. In the semi-arid region of Brazil, many reptiles interact with human communities because of their utility or because of the risks they represent. These interactions have obvious implications for the conservation of reptiles from this region.In this context, ethnoherpetology studies are crucial because they serve as subsidies for guiding strategies for the handling and conservation of reptiles. This paper presents ethnozoological and taxonomic informations of hunted reptiles in the semiarid region of Brazil and analyse the implications on conservation that are related to the interactions between people and reptiles in this region. Taxonomic keys to identifying recorded reptiles are provided. Records of humans interacting with 38 reptile species that belong to 31 genuses and 16 families have been found. The groups with the largest numbers of recorded species were snakes (18 species), and this group was followed in number by lizards (13), chelonians (4), and crocodilians (3). The reptiles that were recorded may be used for the following purposes: medicinal purposes (24 species), food (13 species), ornamental or decorative purposes (11 species), in magical/religious practices (10 species), and as pets (10 species). Some species (n = 16) may have multiple uses. Furthermore, more than half of the species (n = 19) are commonly killed because they are considered potentially dangerous. Strategies for conserving the reptiles of the Brazilian semi-arid region must reconcile and integrate human and conservation needs. PMID:22846258

  20. A zoological catalogue of hunted reptiles in the semiarid region of Brazil.

    PubMed

    Nóbrega Alves, Rômulo Romeu; Pereira Filho, Gentil Alves; Silva Vieira, Kleber; Silva Souto, Wedson Medeiros; Mendonça, Lívia Emanuelle Tavares; Montenegro, Paulofernandoguedespereira; Almeida, Waltécio de Oliveira; Silva Vieira, Washington Luiz

    2012-07-30

    The variety of interactions between human cultures and herpetofauna is the subject matter of Ethnoherpetology, a subdivision of Ethnozoology. In the semi-arid region of Brazil, many reptiles interact with human communities because of their utility or because of the risks they represent. These interactions have obvious implications for the conservation of reptiles from this region. In this context, ethnoherpetology studies are crucial because they serve as subsidies for guiding strategies for the handling and conservation of reptiles. This paper presents ethnozoological and taxonomic informations of hunted reptiles in the semiarid region of Brazil and analyse the implications on conservation that are related to the interactions between people and reptiles in this region. Taxonomic keys to identifying recorded reptiles are provided. Records of humans interacting with 38 reptile species that belong to 31 genuses and 16 families have been found. The groups with the largest numbers of recorded species were snakes (18 species), and this group was followed in number by lizards (13), chelonians (4), and crocodilians (3). The reptiles that were recorded may be used for the following purposes: medicinal purposes (24 species), food (13 species), ornamental or decorative purposes (11 species), in magical/religious practices (10 species), and as pets (10 species). Some species (n = 16) may have multiple uses. Furthermore, more than half of the species (n = 19) are commonly killed because they are considered potentially dangerous. Strategies for conserving the reptiles of the Brazilian semi-arid region must reconcile and integrate human and conservation needs.

  1. Computational approaches for identification of conserved/unique binding pockets in the A chain of ricin

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Ecale Zhou, C L; Zemla, A T; Roe, D

    2005-01-29

    Specific and sensitive ligand-based protein detection assays that employ antibodies or small molecules such as peptides, aptamers, or other small molecules require that the corresponding surface region of the protein be accessible and that there be minimal cross-reactivity with non-target proteins. To reduce the time and cost of laboratory screening efforts for diagnostic reagents, we developed new methods for evaluating and selecting protein surface regions for ligand targeting. We devised combined structure- and sequence-based methods for identifying 3D epitopes and binding pockets on the surface of the A chain of ricin that are conserved with respect to a set ofmore » ricin A chains and unique with respect to other proteins. We (1) used structure alignment software to detect structural deviations and extracted from this analysis the residue-residue correspondence, (2) devised a method to compare corresponding residues across sets of ricin structures and structures of closely related proteins, (3) devised a sequence-based approach to determine residue infrequency in local sequence context, and (4) modified a pocket-finding algorithm to identify surface crevices in close proximity to residues determined to be conserved/unique based on our structure- and sequence-based methods. In applying this combined informatics approach to ricin A we identified a conserved/unique pocket in close proximity (but not overlapping) the active site that is suitable for bi-dentate ligand development. These methods are generally applicable to identification of surface epitopes and binding pockets for development of diagnostic reagents, therapeutics, and vaccines.« less

  2. DNA barcoding for conservation, seed banking and ecological restoration of Acacia in the Midwest of Western Australia.

    PubMed

    Nevill, Paul G; Wallace, Mark J; Miller, Joseph T; Krauss, Siegfried L

    2013-11-01

    We used DNA barcoding to address an important conservation issue in the Midwest of Western Australia, working on Australia's largest genus of flowering plant. We tested whether or not currently recommended plant DNA barcoding regions (matK and rbcL) were able to discriminate Acacia taxa of varying phylogenetic distances, and ultimately identify an ambiguously labelled seed collection from a mine-site restoration project. Although matK successfully identified the unknown seed as the rare and conservation priority listed A. karina, and was able to resolve six of the eleven study species, this region was difficult to amplify and sequence. In contrast, rbcL was straightforward to recover and align, but could not determine the origin of the seed and only resolved 3 of the 11 species. Other chloroplast regions (rpl32-trnL, psbA-trnH, trnL-F and trnK) had mixed success resolving the studied taxa. In general, species were better resolved in multilocus data sets compared to single-locus data sets. We recommend using the formal barcoding regions supplemented with data from other plastid regions, particularly rpl32-trnL, for barcoding in Acacia. Our study demonstrates the novel use of DNA barcoding for seed identification and illustrates the practical potential of DNA barcoding for the growing discipline of restoration ecology. © 2013 John Wiley & Sons Ltd.

  3. Focusing ecological research for conservation.

    PubMed

    Cristescu, Bogdan; Boyce, Mark S

    2013-11-01

    Ecologists are increasingly actively involved in conservation. We identify five key topics from a broad sweep of ecology that merit research attention to meet conservation needs. We examine questions from landscape ecology, behavioral ecology, ecosystem dynamics, community ecology, and nutrient cycling related to key topics. Based on literature review and publication trend assessment, consultation with colleagues, and roundtable discussions at the 24th International Congress for Conservation Biology, focused research on the following topics could benefit conservation while advancing ecological understanding: 1. Carbon sequestration, requiring increased linkages to biodiversity conservation; 2. Ecological invasiveness, challenging our ability to find solutions to ecological aliens; 3. Individual variation, having applications in the conservation of rare species; 4. Movement of organisms, integrating ecological processes across landscapes and scales and addressing habitat fragmentation; and 5. Trophic-level interactions, driving ecological dynamics at the ecosystem-level. Addressing these will require cross-disciplinary research under the overarching framework of conservation ecology.

  4. Dominant Sequences of Human Major Histocompatibility Complex Conserved Extended Haplotypes from HLA-DQA2 to DAXX

    PubMed Central

    Larsen, Charles E.; Alford, Dennis R.; Trautwein, Michael R.; Jalloh, Yanoh K.; Tarnacki, Jennifer L.; Kunnenkeri, Sushruta K.; Fici, Dolores A.; Yunis, Edmond J.; Awdeh, Zuheir L.; Alper, Chester A.

    2014-01-01

    We resequenced and phased 27 kb of DNA within 580 kb of the MHC class II region in 158 population chromosomes, most of which were conserved extended haplotypes (CEHs) of European descent or contained their centromeric fragments. We determined the single nucleotide polymorphism and deletion-insertion polymorphism alleles of the dominant sequences from HLA-DQA2 to DAXX for these CEHs. Nine of 13 CEHs remained sufficiently intact to possess a dominant sequence extending at least to DAXX, 230 kb centromeric to HLA-DPB1. We identified the regions centromeric to HLA-DQB1 within which single instances of eight “common” European MHC haplotypes previously sequenced by the MHC Haplotype Project (MHP) were representative of those dominant CEH sequences. Only two MHP haplotypes had a dominant CEH sequence throughout the centromeric and extended class II region and one MHP haplotype did not represent a known European CEH anywhere in the region. We identified the centromeric recombination transition points of other MHP sequences from CEH representation to non-representation. Several CEH pairs or groups shared sequence identity in small blocks but had significantly different (although still conserved for each separate CEH) sequences in surrounding regions. These patterns partly explain strong calculated linkage disequilibrium over only short (tens to hundreds of kilobases) distances in the context of a finite number of observed megabase-length CEHs comprising half a population's haplotypes. Our results provide a clearer picture of European CEH class II allelic structure and population haplotype architecture, improved regional CEH markers, and raise questions concerning regional recombination hotspots. PMID:25299700

  5. [Investigation of toxigenic microcystis and microcystin pollution in Huayuankou Conservation Pool of Yellow River].

    PubMed

    Ban, Haiqun; Ba, Yue; Cheng, Xuemin; Wang, Guangzhou

    2007-09-01

    To investigate the contaminative, condition of planktonic algae, cyanobacteria, toxigenic microcystis and microcystin in Huayuankou Conservation Pool of Yellow River. From March 2005 to January 2006, water samples were taken 15 times by 2. 5L plastic sampler from Huayuankou Conservation Pool. The density of algae were counted by using blood cell counter. Phycocyanin intergenic spacer region (PC-IGS) and microcystin synthetase gene B (mcyB) of toxigenic microcystis was identified by the whole cell PCR. The concentration of microcystin was determined by ELISA kit. The positive results of PCR and ELISA were compared. Bacillariophyta, chlorophyta, cyanophyta (cyanobacteria) and euglenophyta were main algaes in Huayuankou conservation pool, and the dominant algae and cell density changed seasonally. Algae cell density and cyanobacteria cell density were higher in summer and autumn than in spring and winter. From July to November, 2005, PC-IGS and mcyB were detected positively by whole cell PCR. Microcystin was positively detected from July, the concentration of microcystin changed from 0 to 0.25microg/L, it was more higher in summer than other seasons. Toxigenic microcystis and microcystin could be detected in Huayuankou Conservation Pool of Yellow River. Whole cell PCR could be used to identify toxigenic microcystis.

  6. C&RE-SLC: Database for conservation and renewable energy activities

    NASA Astrophysics Data System (ADS)

    Cavallo, J. D.; Tompkins, M. M.; Fisher, A. G.

    1992-08-01

    The Western Area Power Administration (Western) requires all its long-term power customers to implement programs that promote the conservation of electric energy or facilitate the use of renewable energy resources. The hope is that these measures could significantly reduce the amount of environmental damage associated with electricity production. As part of preparing the environmental impact statement for Western's Electric Power Marketing Program, Argonne National Laboratory constructed a database of the conservation and renewable energy activities in which Western's Salt Lake City customers are involved. The database provides information on types of conservation and renewable energy activities and allows for comparisons of activities being conducted at different utilities in the Salt Lake City region. Sorting the database allows Western's Salt Lake City customers to be classified so the various activities offered by different classes of utilities can be identified; for example, comparisons can be made between municipal utilities and cooperatives or between large and small customers. The information included in the database was collected from customer planning documents in the files of Western's Salt Lake City office.

  7. Report: Inconsistencies With EPA Policy Identified in Region 10's Biweekly Pay Cap Waiver Process

    EPA Pesticide Factsheets

    Report #18-P-0068, January 12, 2018. We identified issues with documentation and review of biweekly pay cap waivers at Region 10, resulting from a lack of an internal policy or process. Region 10 recently issued a new procedure that addresses our concerns.

  8. Characterization of Solang valley watershed in western Himalaya for bio-resource conservation using remote sensing techniques.

    PubMed

    Kumar, Amit; Chawla, Amit; Rajkumar, S

    2011-08-01

    The development activities in mountainous region though provide comfort to the human being and enhance the socioeconomic status of the people but create pressure on the bio-resources. In this paper, the current status of land use/landcover and the vegetation communities of the Solang valley watershed in Himachal Pradesh of Indian western Himalaya has been mapped and presented using remote sensing. This watershed area was dominated by alpine and sub-alpine pastures (30.34%) followed by scree slopes (22.34%) and forests (21.06%). Many tree, shrub, and herb species identified in the study area are among the prioritized species for conservation in the Indian Himalayan Region. Thus, scientific interventions and preparation of action plans based on ecological survey are required for conservation of the Solang valley watershed.

  9. Conservation and divergence of microRNAs in Populus

    PubMed Central

    Barakat, Abdelali; Wall, Phillip K; DiLoreto, Scott; dePamphilis, Claude W; Carlson, John E

    2007-01-01

    Background MicroRNAs (miRNAs) are small RNAs (sRNA) ~21 nucleotides in length that negatively control gene expression by cleaving or inhibiting the translation of target gene transcripts. miRNAs have been extensively analyzed in Arabidopsis and rice and partially investigated in other non-model plant species. To date, 109 and 62 miRNA families have been identified in Arabidopsis and rice respectively. However, only 33 miRNAs have been identified from the genome of the model tree species (Populus trichocarpa), of which 11 are Populus specific. The low number of miRNA families previously identified in Populus, compared with the number of families identified in Arabidopsis and rice, suggests that many miRNAs still remain to be discovered in Populus. In this study, we analyzed expressed small RNAs from leaves and vegetative buds of Populus using high throughput pyrosequencing. Results Analysis of almost eighty thousand small RNA reads allowed us to identify 123 new sequences belonging to previously identified miRNA families as well as 48 new miRNA families that could be Populus-specific. Comparison of the organization of miRNA families in Populus, Arabidopsis and rice showed that miRNA family sizes were generally expanded in Populus. The putative targets of non-conserved miRNA include both previously identified targets as well as several new putative target genes involved in development, resistance to stress, and other cellular processes. Moreover, almost half of the genes predicted to be targeted by non-conserved miRNAs appear to be Populus-specific. Comparative analyses showed that genes targeted by conserved and non-conserved miRNAs are biased mainly towards development, electron transport and signal transduction processes. Similar results were found for non-conserved miRNAs from Arabidopsis. Conclusion Our results suggest that while there is a conserved set of miRNAs among plant species, a large fraction of miRNAs vary among species. The non-conserved miRNAs may

  10. Water conservation and hydrological transitions in cities in the United States

    NASA Astrophysics Data System (ADS)

    Hornberger, George M.; Hess, David J.; Gilligan, Jonathan

    2015-06-01

    Cities across the world have had to diversify and expand their water supply systems in response to demand growth, groundwater depletion and pollution, and instability and inadequacy of regional surface freshwater sources. In the U.S., these problems plague not only the arid Western cities but increasingly also cities in the Eastern portions of the country. Although cities continue to seek out new sources of water via Promethean projects of long-distance supply systems, desalinization plants, and the recharge of aquifers with surface water, they also pursue water conservation because of its low cost and other benefits. We examine water conservation as a complex sociotechnical system comprising interactions of political, sociodemographic, economic, and hydroclimatological factors. We provide quantitative data on the factors that affect more and less advanced transitions in water conservation regimes, and we show that water stress and other hydrological data can only partially predict the transition. We also provide qualitative case studies to identify institutional and political barriers to more advanced water conservation regimes. This interdisciplinary, mixed methods approach typifies the need for knowledge that informs hydrologists about how their research may or may not be adopted by decision-makers.

  11. Conserved tetramer junction in the kinetochore Ndc80 complex

    PubMed Central

    Valverde, Roberto; Ingram, Jessica; Harrison, Stephen C.

    2016-01-01

    Summary The heterotetrameric Ndc80 complex establishes connectivity along the principal longitudinal axis of a kinetochore. Its two heterodimeric subcomplexes, each with a globular end and a coiled-coil shaft, connect end-to-end to create a ∼600 Å long rod spanning the gap from centromere-proximal structures to spindle microtubules. Neither subcomplex has a known function on its own, but the heterotetrameric organization and the characteristics of the junction are conserved from yeast to man. We have determined crystal structures of two shortened (“dwarf”) Ndc80 complexes that contain the full tetramer junction and both globular ends. The junction connects two α-helical coiled coils through regions of four-chain and three-chain overlap. The complexity of its structure depends on interactions among conserved amino-acid residues, suggesting a binding site for additional cellular factor(s) not yet identified. PMID:27851957

  12. A sequence-based hybrid predictor for identifying conformationally ambivalent regions in proteins.

    PubMed

    Liu, Yu-Cheng; Yang, Meng-Han; Lin, Win-Li; Huang, Chien-Kang; Oyang, Yen-Jen

    2009-12-03

    Proteins are dynamic macromolecules which may undergo conformational transitions upon changes in environment. As it has been observed in laboratories that protein flexibility is correlated to essential biological functions, scientists have been designing various types of predictors for identifying structurally flexible regions in proteins. In this respect, there are two major categories of predictors. One category of predictors attempts to identify conformationally flexible regions through analysis of protein tertiary structures. Another category of predictors works completely based on analysis of the polypeptide sequences. As the availability of protein tertiary structures is generally limited, the design of predictors that work completely based on sequence information is crucial for advances of molecular biology research. In this article, we propose a novel approach to design a sequence-based predictor for identifying conformationally ambivalent regions in proteins. The novelty in the design stems from incorporating two classifiers based on two distinctive supervised learning algorithms that provide complementary prediction powers. Experimental results show that the overall performance delivered by the hybrid predictor proposed in this article is superior to the performance delivered by the existing predictors. Furthermore, the case study presented in this article demonstrates that the proposed hybrid predictor is capable of providing the biologists with valuable clues about the functional sites in a protein chain. The proposed hybrid predictor provides the users with two optional modes, namely, the high-sensitivity mode and the high-specificity mode. The experimental results with an independent testing data set show that the proposed hybrid predictor is capable of delivering sensitivity of 0.710 and specificity of 0.608 under the high-sensitivity mode, while delivering sensitivity of 0.451 and specificity of 0.787 under the high-specificity mode. Though

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

    PubMed

    Chiarello

    2000-05-01

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

  14. The Mid-Atlantic Regional Wetland Conservation Effects Assessment Project

    Treesearch

    Megan Lang; Greg McCarty; Mark Walbridge; Patrick Hunt; Tom Ducey; Clinton Church; Jarrod Miller; Laurel Kluber; Ali Sadeghi; Martin Rabenhorst; Amir Sharifi; In-Young Yeo; Andrew Baldwin; Margaret Palmer; Tom Fisher; Dan Fenstermaher; Sanchul Lee; Owen McDonough; Metthea Yepsen; Liza McFarland; Anne Gustafson; Rebecca Fox; Chris Palardy; William Effland; Mari-Vaughn Johnson; Judy Denver; Scott Ator; Joseph Mitchell; Dennis Whigham

    2016-01-01

    Wetlands impart many important ecosystem services, including maintenance of water quality, regulation of the climate and hydrological flows, and enhancement of biodiversity through the provision of food and habitat. The conversion of natural lands to agriculture has led to broad scale historic wetland loss, but current US Department of Agriculture conservation programs...

  15. Use of macroinvertebrates to identify cultivated wetlands in the Prairie Pothole Region

    USGS Publications Warehouse

    Euliss, Ned H.; Mushet, David M.; Johnson, Douglas H.

    2001-01-01

    We evaluated the use of macroinvertebrates as a potential tool to identify dry and intensively farmed temporary and seasonal wetlands in the Prairie Pothole Region. The techniques we designed and evaluated used the dried remains of invertebrates or their egg banks in soils as indicators of wetlands. For both the dried remains of invertebrates and their egg banks, we weighted each taxon according to its affinity for wetlands or uplands. Our study clearly demonstrated that shells, exoskeletons, head capsules, eggs, and other remains of macroinvertebrates can be used to identify wetlands, even when they are dry, intensively farmed, and difficult to identify as wetlands using standard criteria (i.e., hydrology, hydrophytic vegetation, and hydric soils). Although both dried remains and egg banks identified wetlands, the combination was more useful, especially for identifying drained or filled wetlands. We also evaluated the use of coarse taxonomic groupings to stimulate use of the technique by nonspecialists and obtained satisfactory results in most situations.

  16. How Should Beta-Diversity Inform Biodiversity Conservation?

    PubMed

    Socolar, Jacob B; Gilroy, James J; Kunin, William E; Edwards, David P

    2016-01-01

    To design robust protected area networks, accurately measure species losses, or understand the processes that maintain species diversity, conservation science must consider the organization of biodiversity in space. Central is beta-diversity--the component of regional diversity that accumulates from compositional differences between local species assemblages. We review how beta-diversity is impacted by human activities, including farming, selective logging, urbanization, species invasions, overhunting, and climate change. Beta-diversity increases, decreases, or remains unchanged by these impacts, depending on the balance of processes that cause species composition to become more different (biotic heterogenization) or more similar (biotic homogenization) between sites. While maintaining high beta-diversity is not always a desirable conservation outcome, understanding beta-diversity is essential for protecting regional diversity and can directly assist conservation planning. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Watson, J.M.; Spencer, J.A.; Graves, J.A.M.

    1990-09-01

    Eight genes, located on the long arm of the human X chromosome and present on the marsupial X chromosome, were mapped by in situ hybridization to the chromosomes of the platypus Ornithorhynchus anatinus, one of the three species of monotreme mammals. All were located on the X chromosome. The authors conclude that the long arm of the human X chromosome represents a highly conserved region that formed part of the X chromosome in a mammalian ancestor at least 150 million years ago. Since three of these genes are located on the long arm of the platypus X chromosome, which ismore » 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.« less

  18. The Intermountain West Region Waterbird Plan

    Treesearch

    Gary Ivey

    2005-01-01

    The planning process for the Intermountain West Region component of the North American Waterbird Conservation Plan began in November 2001. This is one of several region-specific plans being developed as part of the Waterbird Conservation for the Americas initiative (Kushlan et al. 2002), as called for in the North American Waterbird Conservation Plan. The plan...

  19. The most conserved genome segments for life detection on Earth and other planets.

    PubMed

    Isenbarger, Thomas A; Carr, Christopher E; Johnson, Sarah Stewart; Finney, Michael; Church, George M; Gilbert, Walter; Zuber, Maria T; Ruvkun, Gary

    2008-12-01

    On Earth, very simple but powerful methods to detect and classify broad taxa of life by the polymerase chain reaction (PCR) are now standard practice. Using DNA primers corresponding to the 16S ribosomal RNA gene, one can survey a sample from any environment for its microbial inhabitants. Due to massive meteoritic exchange between Earth and Mars (as well as other planets), a reasonable case can be made for life on Mars or other planets to be related to life on Earth. In this case, the supremely sensitive technologies used to study life on Earth, including in extreme environments, can be applied to the search for life on other planets. Though the 16S gene has become the standard for life detection on Earth, no genome comparisons have established that the ribosomal genes are, in fact, the most conserved DNA segments across the kingdoms of life. We present here a computational comparison of full genomes from 13 diverse organisms from the Archaea, Bacteria, and Eucarya to identify genetic sequences conserved across the widest divisions of life. Our results identify the 16S and 23S ribosomal RNA genes as well as other universally conserved nucleotide sequences in genes encoding particular classes of transfer RNAs and within the nucleotide binding domains of ABC transporters as the most conserved DNA sequence segments across phylogeny. This set of sequences defines a core set of DNA regions that have changed the least over billions of years of evolution and provides a means to identify and classify divergent life, including ancestrally related life on other planets.

  20. Identifying keystone habitats with a mosaic approach can improve biodiversity conservation in disturbed ecosystems.

    PubMed

    Hitchman, Sean M; Mather, Martha E; Smith, Joseph M; Fencl, Jane S

    2018-01-01

    Conserving native biodiversity in the face of human- and climate-related impacts is a challenging and globally important ecological problem that requires an understanding of spatially connected, organismal-habitat relationships. Globally, a suite of disturbances (e.g., agriculture, urbanization, climate change) degrades habitats and threatens biodiversity. A mosaic approach (in which connected, interacting collections of juxtaposed habitat patches are examined) provides a scientific foundation for addressing many disturbance-related, ecologically based conservation problems. For example, if specific habitat types disproportionately increase biodiversity, these keystones should be incorporated into research and management plans. Our sampling of fish biodiversity and aquatic habitat along ten 3-km sites within the Upper Neosho River subdrainage, KS, from June-August 2013 yielded three generalizable ecological insights. First, specific types of mesohabitat patches (i.e., pool, riffle, run, and glide) were physically distinct and created unique mosaics of mesohabitats that varied across sites. Second, species richness was higher in riffle mesohabitats when mesohabitat size reflected field availability. Furthermore, habitat mosaics that included more riffles had greater habitat diversity and more fish species. Thus, riffles (<5% of sampled area) acted as keystone habitats. Third, additional conceptual development, which we initiate here, can broaden the identification of keystone habitats across ecosystems and further operationalize this concept for research and conservation. Thus, adopting a mosaic approach can increase scientific understanding of organismal-habitat relationships, maintain natural biodiversity, advance spatial ecology, and facilitate effective conservation of native biodiversity in human-altered ecosystems. © 2017 John Wiley & Sons Ltd.

  1. Rapid Assessment for Conservation Education (RACE).

    ERIC Educational Resources Information Center

    Jacobson, Susan K.

    1997-01-01

    The Rapid Assessment for Conservation Education (RACE) provides guidelines and tools for identifying conservation education needs and recommending subsequent actions. Interviews, surveys, workshops, and public meetings are among the methods of qualitative and quantitative data collection used to gather information quickly and inexpensively.…

  2. Potential environmental effects of energy conservation measures in northwest industries

    DOE Office of Scientific and Technical Information (OSTI.GOV)

    Baechler, M C; Gygi, K F; Hendrickson, P L

    The Bonneville Power Administration (Bonneville) has identified 101 plants in the Pacific Northwest that account for 80% of the region's industrial electricity consumption. These plants offer a precise target for a conservation program. PNL determined that most of these 101 plants were represented by 11 major industries. We then reviewed 36 major conservation technologies used in these 11 industrial settings to determine their potential environmental impacts. Energy efficiency technologies designed for industrial use may result in direct or indirect environmental impacts. Effects may result from the production of the conservation measure technology, changes in the working environment due to differentmore » energy and material requirements, or changes to waste streams. Industry type, work-place conditions, worker training, and environmental conditions inside and outside the plant are all key variables that may affect environmental outcomes. To address these issues this report has three objectives: Describe potential conservation measures that Bonneville may employ in industrial programs and discuss potential primary impacts. Characterize industrial systems and processes where the measure may be employed and describe general environmental issues associated with each industry type. Review environmental permitting, licensing, and other regulatory actions required for industries and summarize the type of information available from these sources for further analysis.« less

  3. Primate occurrence across a human-impacted landscape in Guinea-Bissau and neighbouring regions in West Africa: using a systematic literature review to highlight the next conservation steps

    PubMed Central

    Bessa, Joana; Frazão-Moreira, Amélia; Biro, Dora; Hockings, Kimberley Jane

    2018-01-01

    Background West African landscapes are largely characterised by complex agroforest mosaics. Although the West African forests are considered a nonhuman primate hotspot, knowledge on the distribution of many species is often lacking and out-of-date. Considering the fast-changing nature of the landscapes in this region, up-to-date information on primate occurrence is urgently needed, particularly of taxa such as colobines, which may be more sensitive to habitat modification than others. Understanding wildlife occurrence and mechanisms of persistence in these human-dominated landscapes is fundamental for developing effective conservation strategies. Methods In this paper, we aim to review current knowledge on the distribution of three threatened primates in Guinea-Bissau and neighbouring regions, highlighting research gaps and identifying priority research and conservation action. We conducted a systematic literature review of primate studies from 1976 to 2016 in Guinea-Bissau, southern Senegal and western Guinea (Boké Region). We mapped historical observation records of chimpanzee (Pan troglodytes verus), Temminck’s red colobus (Pilicolobus badius temminckii) and king colobus (Colobus polykomos), including our preliminary survey data from Dulombi, a newly established National Park (NP) in Guinea-Bissau. Results We found 151 documents, including 87 journal articles, that contained field data on primates in this region. In Guinea-Bissau, nearly all studies focussed south of the Corubal River, including mainly Cantanhez, Cufada, and Boé NP’s. In Senegal, most of the data came from Fongoli and Niokolo-Koba NP. In Boké (Guinea) studies are few, with the most recent data coming from Sangarédi. In Dulombi NP we recorded eight primate species, including chimpanzees, red colobus and king colobus. Across the selected region, chimpanzees, red colobus and king colobus were reported in eleven, twelve and seven protected areas, respectively. Discussion Our study

  4. Anterior cingulate cortex and intuitive bias detection during number conservation.

    PubMed

    Simon, Grégory; Lubin, Amélie; Houdé, Olivier; De Neys, Wim

    2015-01-01

    Children's number conservation is often biased by misleading intuitions but the precise nature of these conservation errors is not clear. A key question is whether children detect that their erroneous conservation judgment is unwarranted. The present study reanalyzed available fMRI data to test the implication of the anterior cingulate cortex (ACC) in this detection process. We extracted mean BOLD (Blood Oxygen Level Dependent) signal values in an independently defined ACC region of interest (ROI) during presentation of classic and control number conservation problems. In classic trials, an intuitively cued visuospatial response conflicted with the correct conservation response, whereas this conflict was not present in the control trials. Results showed that ACC activation increased when solving the classic conservation problems. Critically, this increase did not differ between participants who solved the classic problems correctly (i.e., so-called conservers) and incorrectly (i.e., so-called non-conservers). Additional control analyses of inferior and lateral prefrontal ROIs showed that the group of conservers did show stronger activation in the right inferior frontal gyrus and right lateral middle frontal gyrus. In line with recent behavioral findings, these data lend credence to the hypothesis that even non-conserving children detect the biased nature of their judgment. The key difference between conservers and non-conservers seems to lie in a differential recruitment of inferior and lateral prefrontal regions associated with inhibitory control.

  5. Tourism and the conservation of critically endangered frogs.

    PubMed

    Morrison, Clare; Simpkins, Clay; Castley, J Guy; Buckley, Ralf C

    2012-01-01

    Protected areas are critical for the conservation of many threatened species. Despite this, many protected areas are acutely underfunded, which reduces their effectiveness significantly. Tourism is one mechanism to promote and fund conservation in protected areas, but there are few studies analyzing its tangible conservation outcomes for threatened species. This study uses the 415 IUCN critically endangered frog species to evaluate the contribution of protected area tourism revenue to conservation. Contributions were calculated for each species as the proportion of geographic range inside protected areas multiplied by the proportion of protected area revenues derived from tourism. Geographic ranges were determined from IUCN Extent of Occurrence maps. Almost 60% (239) of critically endangered frog species occur in protected areas. Higher proportions of total range are protected in Nearctic, Australasian and Afrotopical regions. Tourism contributions to protected area budgets ranged from 5-100%. These financial contributions are highest for developing countries in the Afrotropical, Indomalayan and Neotropical regions. Data for both geographic range and budget are available for 201 critically endangered frog species with proportional contributions from tourism to species protection ranging from 0.8-99%. Tourism's financial contributions to critically endangered frog species protection are highest in the Afrotropical region. This study uses a coarse measure but at the global scale it demonstrates that tourism has significant potential to contribute to global frog conservation efforts.

  6. Tourism and the Conservation of Critically Endangered Frogs

    PubMed Central

    Morrison, Clare; Simpkins, Clay; Castley, J. Guy; Buckley, Ralf C.

    2012-01-01

    Protected areas are critical for the conservation of many threatened species. Despite this, many protected areas are acutely underfunded, which reduces their effectiveness significantly. Tourism is one mechanism to promote and fund conservation in protected areas, but there are few studies analyzing its tangible conservation outcomes for threatened species. This study uses the 415 IUCN critically endangered frog species to evaluate the contribution of protected area tourism revenue to conservation. Contributions were calculated for each species as the proportion of geographic range inside protected areas multiplied by the proportion of protected area revenues derived from tourism. Geographic ranges were determined from IUCN Extent of Occurrence maps. Almost 60% (239) of critically endangered frog species occur in protected areas. Higher proportions of total range are protected in Nearctic, Australasian and Afrotopical regions. Tourism contributions to protected area budgets ranged from 5–100%. These financial contributions are highest for developing countries in the Afrotropical, Indomalayan and Neotropical regions. Data for both geographic range and budget are available for 201 critically endangered frog species with proportional contributions from tourism to species protection ranging from 0.8–99%. Tourism's financial contributions to critically endangered frog species protection are highest in the Afrotropical region. This study uses a coarse measure but at the global scale it demonstrates that tourism has significant potential to contribute to global frog conservation efforts. PMID:22984440

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

    PubMed Central

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

    2010-01-01

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

  8. Identifying Possible Pheromones of Cerambycid Beetles by Field Testing Known Pheromone Components in Four Widely Separated Regions of the United States

    Treesearch

    Jocelyn G Millar; Robert F Mitchell; Judith A Mongold-Diers; Yunfan Zou; Carlos E Bográn; Melissa K Fierke; Matthew D Ginzel; Crawford W Johnson; James R Meeker; Therese M Poland; Iral Ragenovich; Lawrence M Hanks

    2017-01-01

    The pheromone components of many cerambycid beetles appear to be broadly shared among related species, including species native to different regions of the world. This apparent conservation of pheromone structures within the family suggests that field trials of common pheromone components could be used as a means of attracting multiple species, which then could be...

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

    PubMed

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

    2012-06-01

    Understanding habitat requirements and identifying landscape linkages are essential for the survival of isolated populations of endangered species. Currently, some of the giant panda populations are isolated, which threatens their long-term survival, particularly in the Xiaoxiangling mountains. In the present study, we quantified niche requirements and then identified potential linkages of giant panda subpopulations in the most isolated region, using ecological niche factor analysis and a least-cost path model. Giant pandas preferred habitat with conifer forest and gentle slopes (>20 to ≤30°). Based on spatial distribution of suitable habitat, linkages were identified for the Yele subpopulation to 4 other subpopulations (Liziping, Matou, Xinmin and Wanba). Their lengths ranged from 15 to 54 km. The accumulated cost ranged from 693 to 3166 and conifer forest covered over 31%. However, a variety of features (e.g. major roads, human settlements and large unforested areas) might act as barriers along the linkages for giant panda dispersal. Our analysis quantified giant panda subpopulation connectivity to ensure long-term survival. © 2012 ISZS, Blackwell Publishing and IOZ/CAS.

  10. How to maximally support local and regional biodiversity in applied conservation? Insights from pond management.

    PubMed

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

    2013-01-01

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

  11. Comparative analysis of the Hrp pathogenicity island of Rubus- and Spiraeoideae-infecting Erwinia amylovora strains identifies the IT region as a remnant of an integrative conjugative element.

    PubMed

    Mann, Rachel A; Blom, Jochen; Bühlmann, Andreas; Plummer, Kim M; Beer, Steven V; Luck, Joanne E; Goesmann, Alexander; Frey, Jürg E; Rodoni, Brendan C; Duffy, Brion; Smits, Theo H M

    2012-08-01

    The Hrp pathogenicity island (hrpPAI) of Erwinia amylovora not only encodes a type III secretion system (T3SS) and other genes required for pathogenesis on host plants, but also includes the so-called island transfer (IT) region, a region that originates from an integrative conjugative element (ICE). Comparative genomic analysis of the IT regions of two Spiraeoideae- and three Rubus-infecting strains revealed that the regions in Spiraeoideae-infecting strains were syntenic and highly conserved in length and genetic information, but that the IT regions of the Rubus-infecting strains varied in gene content and length, showing a mosaic structure. None of the ICEs in E. amylovora strains were complete, as conserved ICE genes and the left border were missing, probably due to reductive genome evolution. Comparison of the hrpPAI region of E. amylovora strains to syntenic regions from other Erwinia spp. indicates that the hrpPAI and the IT regions are the result of several insertion and deletion events that have occurred within the ICE. It also suggests that the T3SS was present in a common ancestor of the pathoadapted Erwinia spp. and that insertion and deletion events in the IT region occurred during speciation. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. San Diego Multiple Species Conservation Program (MSCP) Rare Plant Monitoring Review and Revision

    USGS Publications Warehouse

    McEachern, Kathryn; Pavlik, Bruce M.; Rebman, Jon; Sutter, Rob

    2007-01-01

    Introduction The San Diego Multiple Species Conservation Program (MSCP) was developed for the conservation of plants and animals in the south part of San Diego County, under the California Natural Community Conservation Planning Act of 1991 (California Department of Fish and Game) and the Federal Endangered Species Act of 1973, as amended (16 U.S. Code 1531-1544.) The Program is on the leading edge of conservation, as it seeks to both guide development and conserve at-risk species with the oversight of both State and Federal agencies. Lands were identified for inclusion in the MSCP based on their value as habitat for at-risk plants or plant communities (Natural Community Conservation Planning, 2005). Since its inception in the mid-1990s the Program has protected over 100,000 acres, involving 15 jurisdictions and the U.S. Fish and Wildlife Service (USFWS) and California Department of Fish and Game (CDFG) in the conservation of 87 taxa. Surveys for covered species have been conducted, and management and monitoring have been implemented at some high priority sites. Each jurisdiction or agency manages and monitors their conservation areas independently, while collaborating regionally for long-term protection. The San Diego MSCP is on the forefront of conservation, in one of the most rapidly growing urban areas of the country. The planning effort that developed the MSCP was state-of-the-art, using expert knowledge, spatial habitat modeling, and principles of preserve design to identify and prioritize areas for protection. Land acquisition and protection are ahead of schedule for most jurisdictions. Surveys have verified the locations of many rare plant populations known from earlier collections, and they provide general information on population size and health useful for further conservation planning. Management plans have been written or are in development for most MSCP parcels under jurisdictional control. Several agencies are developing databases for implementation

  13. EPA Region 7 Aquatic Focus Areas (ECO_RES.R7_AQUATIC_FOCUS_AREAS)

    EPA Pesticide Factsheets

    This shapefile consists of 347 individual Aquatic Ecological System (AES) polygons that are the Aquatic Conservation Focus Areas for EPA Region 7. The focus areas are those areas within each aquatic ecological system types that, if preserved, would maintain the biological and ecological diversity extant within that ecological system type. The layer consists of those polygons from the R7_AES.shp shapefile that had the highest ranks. The AES polygons in the Missouri portion of the file were appended and are those that contain the 158 aquatic conservation opportunity areas identified in Missouri as part of another project (Missouri Department of Conservation Aquatic Biodiversity Assessment 2005). Note that the identifiers in the Missouri portion of this file will not match the ID's in any Missouri specific files.

  14. Mechanisms of aquatic species invasions across the South Atlantic Landscape Conservation Cooperative region

    USGS Publications Warehouse

    Benson, Amy J.; Stith, Bradley M.; Engel, Victor C.

    2016-12-15

    Invasive species are a global issue, and the southeastern United States is not immune to the problems they present. Therefore, various analyses using modeling and exploratory statistics were performed on the U.S. Geological Survey Nonindigenous Aquatic Species (NAS) Database with the primary objective of determining the most appropriate use of presence-only data as related to invasive species in the South Atlantic Landscape Conservation Cooperative (SALCC) region. A hierarchical model approach showed that a relatively small amount of high-quality data from planned surveys can be used to leverage the information in presence-only observations, having a broad spatial coverage and high biases of observer detection and in site selection. Because a variety of sampling protocols can be used in planned surveys, this approach to the analysis of presence-only data is widely applicable. An important part of the management of natural landscapes is the preservation of designated protected areas. When the hydrologic connection was considered in this analysis, the number of potential invaders that could spread to each protected area within the SALCC region was greatly increased, with a mean exceeding 30 species and the maximum reaching 57 species. Nearly all protected areas are hydrologically connected to at least 20 nonindigenous aquatic species. To examine possible factors which may contribute to nonindigenous aquatic species richness in the SALCC region, a set of exploratory statistics was employed. The best statistical model that included a combination of three anthropogenic variables (densities of housing, roads, and reservoirs) and two environmental variables (elevation range and longitude) explained approximately 62 percent of the variation in introduced species richness. Highest nonindigenous aquatic species richness occurred in the more upland, mountainous regions, where elevation range favored reservoirs and attracted urban centers. Lastly, patterns seen in a diffusion

  15. A Screen for Modifiers of Hedgehog Signaling in Drosophila melanogaster Identifies swm and mts

    PubMed Central

    Casso, David J.; Liu, Songmei; Iwaki, D. David; Ogden, Stacey K.; Kornberg, Thomas B.

    2008-01-01

    Signaling by Hedgehog (Hh) proteins shapes most tissues and organs in both vertebrates and invertebrates, and its misregulation has been implicated in many human diseases. Although components of the signaling pathway have been identified, key aspects of the signaling mechanism and downstream targets remain to be elucidated. We performed an enhancer/suppressor screen in Drosophila to identify novel components of the pathway and identified 26 autosomal regions that modify a phenotypic readout of Hh signaling. Three of the regions include genes that contribute constituents to the pathway—patched, engrailed, and hh. One of the other regions includes the gene microtubule star (mts) that encodes a subunit of protein phosphatase 2A. We show that mts is necessary for full activation of Hh signaling. A second region includes the gene second mitotic wave missing (swm). swm is recessive lethal and is predicted to encode an evolutionarily conserved protein with RNA binding and Zn+ finger domains. Characterization of newly isolated alleles indicates that swm is a negative regulator of Hh signaling and is essential for cell polarity. PMID:18245841

  16. Modeling effects of conservation grassland losses on amphibian habitat

    USGS Publications Warehouse

    Mushet, David M.; Neau, Jordan L.; Euliss, Ned H.

    2014-01-01

    Amphibians provide many ecosystem services valued by society. However, populations have declined globally with most declines linked to habitat change. Wetlands and surrounding terrestrial grasslands form habitat for amphibians in the North American Prairie Pothole Region (PPR). Wetland drainage and grassland conversion have destroyed or degraded much amphibian habitat in the PPR. However, conservation grasslands can provide alternate habitat. In the United States, the Conservation Reserve Program (CRP) is the largest program maintaining grasslands on agricultural lands. We used an ecosystem services model (InVEST) parameterized for the PPR to quantify amphibian habitat over a six-year period (2007–2012). We then quantified changes in availability of amphibian habitat under various land-cover scenarios representing incremental losses (10%, 25%, 50%, 75%, and 100%) of CRP grasslands from 2012 levels. The area of optimal amphibian habitat in the four PPR ecoregions modeled (i.e., Northern Glaciated Plains, Northwestern Glaciated Plains, Lake Agassiz Plain, Des Moines Lobe) declined by approximately 22%, from 3.8 million ha in 2007 to 2.9 million ha in 2012. These losses were driven by the conversion of CRP grasslands to croplands, primarily for corn and soybean production. Our modeling identified an additional 0.8 million ha (26%) of optimal amphibian habitat that would be lost if remaining CRP lands are returned to crop production. An economic climate favoring commodity production over conservation has resulted in substantial losses of amphibian habitat across the PPR that will likely continue into the future. Other regions of the world face similar challenges to maintaining amphibian habitats.

  17. Habitat assessment for giant pandas in the Qinling Mountain region of China

    USGS Publications Warehouse

    Feng, Tian-Tian; Van Manen, Frank T.; Zhao, Na-Xun; Li, Ming; Wei, Fu-Wen

    2009-01-01

    Because habitat loss and fragmentation threaten giant pandas (Ailuropoda melanoleuca), habitat protection and restoration are important conservation measures for this endangered species. However, distribution and value of potential habitat to giant pandas on a regional scale are not fully known. Therefore, we identified and ranked giant panda habitat in Foping Nature Reserve, Guanyinshan Nature Reserve, and adjacent areas in the Qinling Mountains of China. We used Mahalanobis distance and 11 digital habitat layers to develop a multivariate habitat signature associated with 247 surveyed giant panda locations, which we then applied to the study region. We identified approximately 128 km2 of giant panda habitat in Foping Nature Reserve (43.6% of the reserve) and 49 km2 in Guanyinshan Nature Reserve (33.6% of the reserve). We defined core habitat areas by incorporating a minimum patch-size criterion (5.5 km2) based on home-range size. Percentage of core habitat area was higher in Foping Nature Reserve (41.8% of the reserve) than Guanyinshan Nature Reserve (26.3% of the reserve). Within the larger analysis region, Foping Nature Reserve contained 32.7% of all core habitat areas we identified, indicating regional importance of the reserve. We observed a negative relationship between distribution of core areas and presence of roads and small villages. Protection of giant panda habitat at lower elevations and improvement of habitat linkages among core habitat areas are important in a regional approach to giant panda conservation.

  18. 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

    Eng, Thomas; Guacci, Vincent; Koshland, Doug

    2014-01-01

    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

  19. Comparative analysis on the structural features of the 5' flanking region of κ-casein genes from six different species

    PubMed Central

    Gerencsér, Ákos; Barta, Endre; Boa, Simon; Kastanis, Petros; Bösze, Zsuzsanna; Whitelaw, C Bruce A

    2002-01-01

    κ-casein plays an essential role in the formation, stabilisation and aggregation of milk micelles. Control of κ-casein expression reflects this essential role, although an understanding of the mechanisms involved lags behind that of the other milk protein genes. We determined the 5'-flanking sequences for the murine, rabbit and human κ-casein genes and compared them to the published ruminant sequences. The most conserved region was not the proximal promoter region but an approximately 400 bp long region centred 800 bp upstream of the TATA box. This region contained two highly conserved MGF/STAT5 sites with common spacing relative to each other. In this region, six conserved short stretches of similarity were also found which did not correspond to known transcription factor consensus sites. On the contrary to ruminant and human 5' regulatory sequences, the rabbit and murine 5'-flanking regions did not harbour any kind of repetitive elements. We generated a phylogenetic tree of the six species based on multiple alignment of the κ-casein sequences. This study identified conserved candidate transcriptional regulatory elements within the κ-casein gene promoter. PMID:11929628

  20. InterB multigenic family, a gene repertoire associated with subterminal chromosome regions of Encephalitozoon cuniculi and conserved in several human-infecting microsporidian species.

    PubMed

    Dia, Ndongo; Lavie, Laurence; Méténier, Guy; Toguebaye, Bhen S; Vivarès, Christian P; Cornillot, Emmanuel

    2007-03-01

    Microsporidia are fungi-related obligate intracellular parasites that infect numerous animals, including man. Encephalitozoon cuniculi harbours a very small genome (2.9 Mbp) with about 2,000 coding sequences (CDSs). Most repeated CDSs are of unknown function and are distributed in subterminal regions that mark the transitions between subtelomeric rDNA units and chromosome cores. A potential multigenic family (interB) encoding proteins within a size range of 579-641 aa was investigated by PCR and RT-PCR. Thirty members were finally assigned to the E. cuniculi interB family and a predominant interB transcript was found to originate from a newly identified gene on chromosome III. Microsporidian species from eight different genera infecting insects, fishes or mammals, were tested for a possible intra-phylum conservation of interB genes. Only representatives of the Encephalitozoon, Vittaforma and Brachiola genera, differing in host range but all able to invade humans, were positive. Molecular karyotyping of Brachiola algerae showed a complex set of chromosome bands, providing a haploid genome size estimate of 15-20 Mbp. In spite of this large difference in genome complexity, B. algerae and E. cuniculi shared some similar interB gene copies and a common location of interB genes in near-rDNA subterminal regions.

  1. Multiobjective hedging rules for flood water conservation

    NASA Astrophysics Data System (ADS)

    Ding, Wei; Zhang, Chi; Cai, Ximing; Li, Yu; Zhou, Huicheng

    2017-03-01

    Flood water conservation can be beneficial for water uses especially in areas with water stress but also can pose additional flood risk. The potential of flood water conservation is affected by many factors, especially decision makers' preference for water conservation and reservoir inflow forecast uncertainty. This paper discusses the individual and joint effects of these two factors on the trade-off between flood control and water conservation, using a multiobjective, two-stage reservoir optimal operation model. It is shown that hedging between current water conservation and future flood control exists only when forecast uncertainty or decision makers' preference is within a certain range, beyond which, hedging is trivial and the multiobjective optimization problem is reduced to a single objective problem with either flood control or water conservation. Different types of hedging rules are identified with different levels of flood water conservation preference, forecast uncertainties, acceptable flood risk, and reservoir storage capacity. Critical values of decision preference (represented by a weight) and inflow forecast uncertainty (represented by standard deviation) are identified. These inform reservoir managers with a feasible range of their preference to water conservation and thresholds of forecast uncertainty, specifying possible water conservation within the thresholds. The analysis also provides inputs for setting up an optimization model by providing the range of objective weights and the choice of hedging rule types. A case study is conducted to illustrate the concepts and analyses.

  2. Broadly neutralizing antibodies from human survivors target a conserved site in the Ebola virus glycoprotein HR2-MPER region.

    PubMed

    Flyak, Andrew I; Kuzmina, Natalia; Murin, Charles D; Bryan, Christopher; Davidson, Edgar; Gilchuk, Pavlo; Gulka, Christopher P; Ilinykh, Philipp A; Shen, Xiaoli; Huang, Kai; Ramanathan, Palaniappan; Turner, Hannah; Fusco, Marnie L; Lampley, Rebecca; Kose, Nurgun; King, Hannah; Sapparapu, Gopal; Doranz, Benjamin J; Ksiazek, Thomas G; Wright, David W; Saphire, Erica Ollmann; Ward, Andrew B; Bukreyev, Alexander; Crowe, James E

    2018-05-07

    Ebola virus (EBOV) in humans causes a severe illness with high mortality rates. Several strategies have been developed in the past to treat EBOV infection, including the antibody cocktail ZMapp, which has been shown to be effective in nonhuman primate models of infection 1 and has been used under compassionate-treatment protocols in humans 2 . ZMapp is a mixture of three chimerized murine monoclonal antibodies (mAbs) 3-6 that target EBOV-specific epitopes on the surface glycoprotein 7,8 . However, ZMapp mAbs do not neutralize other species from the genus Ebolavirus, such as Bundibugyo virus (BDBV), Reston virus (RESTV) or Sudan virus (SUDV). Here, we describe three naturally occurring human cross-neutralizing mAbs, from BDBV survivors, that target an antigenic site in the canonical heptad repeat 2 (HR2) region near the membrane-proximal external region (MPER) of the glycoprotein. The identification of a conserved neutralizing antigenic site in the glycoprotein suggests that these mAbs could be used to design universal antibody therapeutics against diverse ebolavirus species. Furthermore, we found that immunization with a peptide comprising the HR2-MPER antigenic site elicits neutralizing antibodies in rabbits. Structural features determined by conserved residues in the antigenic site described here could inform an epitope-based vaccine design against infection caused by diverse ebolavirus species.

  3. Molecular forensics in avian conservation: a DNA-based approach for identifying mammalian predators of ground-nesting birds and eggs.

    PubMed

    Hopken, Matthew W; Orning, Elizabeth K; Young, Julie K; Piaggio, Antoinette J

    2016-01-07

    The greater sage-grouse (Centrocercus urophasianus) is a ground-nesting bird from the Northern Rocky Mountains and a species at risk of extinction in in multiple U.S. states and Canada. Herein we report results from a proof of concept that mitochondrial and nuclear DNAs from mammalian predator saliva could be non-invasively collected from depredated greater sage-grouse eggshells and carcasses and used for predator species identification. Molecular forensic approaches have been applied to identify predators from depredated remains as one strategy to better understand predator-prey dynamics and guide management strategies. This can aid conservation efforts by correctly identifying predators most likely to impact threatened and endangered species. DNA isolated from non-invasive samples around nesting sites (e.g. fecal or hair samples) is one method that can increase the success and accuracy of predator species identification when compared to relying on nest remains alone. Predator saliva DNA was collected from depredated eggshells and carcasses using swabs. We sequenced two partial fragments of two mitochondrial genes and obtained microsatellite genotypes using canid specific primers for species and individual identification, respectively. Using this multilocus approach we were able to identify predators, at least down to family, from 11 out of 14 nests (79%) and three out of seven carcasses (47%). Predators detected most frequently were canids (86%), while other taxa included rodents, a striped skunk, and cattle. We attempted to match the genotypes of individual coyotes obtained from eggshells and carcasses with those obtained from fecal samples and coyotes collected in the areas, but no genotype matches were found. Predation is a main cause of nest failure in ground-nesting birds and can impact reproduction and recruitment. To inform predator management for ground-nesting bird conservation, accurate identification of predator species is necessary. Considering

  4. Defining the demands and meeting the challenges of integrated bird conservation

    Treesearch

    Charles K. Baxter

    2005-01-01

    Understanding the demands of integration bird conservation begins with a critical assessment of the North American Bird Conservation Initiative's (NABCI) goal."Regionally-based, biologically-driven, landscape oriented partnerships delivering the full spectrum of bird conservation across the entirety of North America."

  5. Determining coding CpG islands by identifying regions significant for pattern statistics on Markov chains.

    PubMed

    Singer, Meromit; Engström, Alexander; Schönhuth, Alexander; Pachter, Lior

    2011-09-23

    Recent experimental and computational work confirms that CpGs can be unmethylated inside coding exons, thereby showing that codons may be subjected to both genomic and epigenomic constraint. It is therefore of interest to identify coding CpG islands (CCGIs) that are regions inside exons enriched for CpGs. The difficulty in identifying such islands is that coding exons exhibit sequence biases determined by codon usage and constraints that must be taken into account. We present a method for finding CCGIs that showcases a novel approach we have developed for identifying regions of interest that are significant (with respect to a Markov chain) for the counts of any pattern. Our method begins with the exact computation of tail probabilities for the number of CpGs in all regions contained in coding exons, and then applies a greedy algorithm for selecting islands from among the regions. We show that the greedy algorithm provably optimizes a biologically motivated criterion for selecting islands while controlling the false discovery rate. We applied this approach to the human genome (hg18) and annotated CpG islands in coding exons. The statistical criterion we apply to evaluating islands reduces the number of false positives in existing annotations, while our approach to defining islands reveals significant numbers of undiscovered CCGIs in coding exons. Many of these appear to be examples of functional epigenetic specialization in coding exons.

  6. Identification of evolutionarily conserved Momordica charantia microRNAs using computational approach and its utility in phylogeny analysis.

    PubMed

    Thirugnanasambantham, Krishnaraj; Saravanan, Subramanian; Karikalan, Kulandaivelu; Bharanidharan, Rajaraman; Lalitha, Perumal; Ilango, S; HairulIslam, Villianur Ibrahim

    2015-10-01

    Momordica charantia (bitter gourd, bitter melon) is a monoecious Cucurbitaceae with anti-oxidant, anti-microbial, anti-viral and anti-diabetic potential. Molecular studies on this economically valuable plant are very essential to understand its phylogeny and evolution. MicroRNAs (miRNAs) are conserved, small, non-coding RNA with ability to regulate gene expression by bind the 3' UTR region of target mRNA and are evolved at different rates in different plant species. In this study we have utilized homology based computational approach and identified 27 mature miRNAs for the first time from this bio-medically important plant. The phylogenetic tree developed from binary data derived from the data on presence/absence of the identified miRNAs were noticed to be uncertain and biased. Most of the identified miRNAs were highly conserved among the plant species and sequence based phylogeny analysis of miRNAs resolved the above difficulties in phylogeny approach using miRNA. Predicted gene targets of the identified miRNAs revealed their importance in regulation of plant developmental process. Reported miRNAs held sequence conservation in mature miRNAs and the detailed phylogeny analysis of pre-miRNA sequences revealed genus specific segregation of clusters. Copyright © 2015 Elsevier Ltd. All rights reserved.

  7. Learning from conservation planning for the U.S. National Wildlife Refuges.

    PubMed

    Meretsky, Vicky J; Fischman, Robert L

    2014-10-01

    The U.S. National Wildlife Refuge System has nearly completed its first round of unit-level, comprehensive conservation plans (CCPs) and will soon begin required revisions. Laws and policies governing refuge planning emphasize ecological integrity, landscape-scale conservation, and adaptive management. We evaluated 185 CCPs completed during 2005-2011, which cover 324 of 555 national wildlife refuges. We reviewed CCP prescriptions addressing 5 common conservation issues (habitat and game, nongame, imperiled, and invasive species) and 3 specialized topics (landscape-scale conservation, climate change, and environmental quality). Common conservation issues received prescriptions in >90% of CCPs. Specialized topics received more variable treatment. Prescriptions for aquatic connectivity, water quantity, and climate-change impacts increased over the study period. Except for climate change, direct actions were the most common type of management prescription, followed by plans or studies. Most CCPs stated a commitment to adaptive management and prescribed monitoring for common conservation objectives; other aspects of planning for adaptive management were often lacking, despite strong support for adaptive management in the conservation planning literature. To better address refuge-specific threats, we recommend that revised plans explicitly match identified refuge issues with prescriptions, particularly for under-represented concerns such as novel pests and pathogens. We recommend incorporating triggers into monitoring frameworks and specifying actions that will occur when threshold values are reached to improve support for adaptive management. Revised CCPs should better reflect work that refuges already undertake to extend conservation objectives beyond their borders and better engage with regional conservation efforts to continue this work. More thorough landscape-scale threat assessments and explicit prioritization of planned actions would further improve conservation

  8. Global Invasion of Lantana camara: Has the Climatic Niche Been Conserved across Continents?

    PubMed Central

    Duarte, Milén; Bustamante, Ramiro O.; Lampo, Margarita; Velásquez, Grisel; Sharma, Gyan P.; García-Rangel, Shaenandhoa

    2014-01-01

    Lantana camara, a native plant from tropical America, is considered one of the most harmful invasive species worldwide. Several studies have identified potentially invasible areas under scenarios of global change, on the assumption that niche is conserved during the invasion process. Recent studies, however, suggest that many invasive plants do not conserve their niches. Using Principal Components Analyses (PCA), we tested the hypothesis of niche conservatism for L. camara by comparing its native niche in South America with its expressed niche in Africa, Australia and India. Using MaxEnt, the estimated niche for the native region was projected onto each invaded region to generate potential distributions there. Our results demonstrate that while L. camara occupied subsets of its original native niche in Africa and Australia, in India its niche shifted significantly. There, 34% of the occurrences were detected in warmer habitats nonexistent in its native range. The estimated niche for India was also projected onto Africa and Australia to identify other vulnerable areas predicted from the observed niche shift detected in India. As a result, new potentially invasible areas were identified in central Africa and southern Australia. Our findings do not support the hypothesis of niche conservatism for the invasion of L. camara. The mechanisms that allow this species to expand its niche need to be investigated in order to improve our capacity to predict long-term geographic changes in the face of global climatic changes. PMID:25343481

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

    NASA Astrophysics Data System (ADS)

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

    2011-12-01

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

  10. Forest gene conservation from the perspective of the international community

    Treesearch

    M. Hosny El-Lakany

    2017-01-01

    conservation of forest genetic resources (FGR). After presenting internationally adopted definitions of some terms related to FGR, the characteristics of the current state of FGR conservation from a global perspective are summarized. Many international and regional organizations and institutions are engaged in the conservation of FGR at degrees ranging from...

  11. Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.

    PubMed

    Elam, W Austin; Schrank, Travis P; Campagnolo, Andrew J; Hilser, Vincent J

    2013-04-01

    Intrinsically disordered (ID) proteins function in the absence of a unique stable structure and appear to challenge the classic structure-function paradigm. The extent to which ID proteins take advantage of subtle conformational biases to perform functions, and whether signals for such mechanism can be identified in proteome-wide studies is not well understood. Of particular interest is the polyproline II (PII) conformation, suggested to be highly populated in unfolded proteins. We experimentally determine a complete calorimetric propensity scale for the PII conformation. Projection of the scale into representative eukaryotic proteomes reveals significant PII bias in regions coding for ID proteins. Importantly, enrichment of PII in ID proteins, or protein segments, is also captured by other PII scales, indicating that this enrichment is robustly encoded and universally detectable regardless of the method of PII propensity determination. Gene ontology (GO) terms obtained using our PII scale and other scales demonstrate a consensus for molecular functions performed by high PII proteins across the proteome. Perhaps the most striking result of the GO analysis is conserved enrichment (P < 10(-8) ) of phosphorylation sites in high PII regions found by all PII scales. Subsequent conformational analysis reveals a phosphorylation-dependent modulation of PII, suggestive of a conserved "tunability" within these regions. In summary, the application of an experimentally determined polyproline II (PII) propensity scale to proteome-wide sequence analysis and gene ontology reveals an enrichment of PII bias near disordered phosphorylation sites that is conserved throughout eukaryotes. Copyright © 2013 The Protein Society.

  12. A conserved domain in the NH2 terminus important for assembly and functional expression of pacemaker channels.

    PubMed

    Tran, Neil; Proenza, Catherine; Macri, Vincenzo; Petigara, Fiona; Sloan, Erin; Samler, Shannon; Accili, Eric A

    2002-11-15

    Pacemaker channels are formed by co-assembly of hyperpolarization-activated cyclic nucleotide-gated (HCN) subunits. Previously, we suggested that the NH(2) termini of the mouse HCN2 isoform were important for subunit co-assembly and functional channel expression. Using an alignment strategy together with yeast two-hybrid assays, patch clamp electrophysiology, and confocal imaging, we have now identified a domain within the NH(2) terminus of the HCN2 subunit that is responsible for interactions between NH(2) termini and promoting the trafficking of functional channels to the plasma membrane. This domain is composed of 52 amino acids, is located adjacent to the putative first transmembrane segment, and is highly conserved among the mammalian HCN isoforms. This conserved domain, but not the remaining unconserved NH(2)-terminal regions of HCN2, specifically interacted with itself in yeast two-hybrid assays. Moreover, the conserved domain was important for expression of currents. Whereas relatively normal whole cell HCN2 currents were produced by channels containing only the conserved domain, further deletion of this region, leaving only a more polar and putative coiled-coil segment, eliminated HCN2 currents and resulted in proteins that localized predominantly in perinuclear compartments. Thus, we suggest that this conserved domain is the critical NH(2)-terminal determinant of subunit co-assembly and trafficking of pacemaker channels.

  13. Geospatial Information Informs Bonobo (pan Paniscus) Conservation Efforts in the Democratic Republic of the Congo

    NASA Astrophysics Data System (ADS)

    Nackoney, J.; Hickey, J.; Williams, D.; Facheux, C.; Dupain, J.

    2014-12-01

    The bonobo (Pan paniscus), a great ape that is endemic to the Democratic Republic of the Congo (DRC), has been listed as Endangered on the IUCN Red List since 2007. Hunting and habitat loss are primary threats. Two recent wars and ongoing conflicts in the DRC have resulted in political and economic instability that hampers on-the-ground work, thereby accentuating the importance of spatial data and maps as tools for monitoring threats remotely and prioritizing locations for safeguarding bonobo habitat. Several regional and rangewide efforts have leveraged the utility of existing spatial data to help focus limited resources for effective broad-scale conservation of these great apes. At local scales, we developed spatial models to identify locations of highest hunting pressure, predict future human settlement and agricultural expansion, map areas of highest conservation value to bonobos, and identify the connective corridors linking them. We identified 42 least-disturbed wildland blocks meeting the minimum home range size needed for bonobos, and 32 potential corridors. At the range-wide scale, we developed a first range-wide spatial model of suitable conditions for the bonobo; this was a major contribution to the development of a Bonobo Conservation Strategy for 2012-2022, recently published by IUCN. The model used a forest edge density metric and other biotic and abiotic variables in conjunction with bonobo nest data collected during 2003-2010 by over 40 bonobo researchers. Approximately 28% of the range was predicted suitable; of that, about 27.5% was located in official protected areas. Highlighting these examples, this presentation will discuss the conservation status of bonobos and how spatial data and models are being utilized for the formation of strategic conservation plans.

  14. The NASA Energy Conservation Program

    NASA Technical Reports Server (NTRS)

    Gaffney, G. P.

    1977-01-01

    Large energy-intensive research and test equipment at NASA installations is identified, and methods for reducing energy consumption outlined. However, some of the research facilities are involved in developing more efficient, fuel-conserving aircraft, and tradeoffs between immediate and long-term conservation may be necessary. Major programs for conservation include: computer-based systems to automatically monitor and control utility consumption; a steam-producing solid waste incinerator; and a computer-based cost analysis technique to engineer more efficient heating and cooling of buildings. Alternate energy sources in operation or under evaluation include: solar collectors; electric vehicles; and ultrasonically emulsified fuel to attain higher combustion efficiency. Management support, cooperative participation by employees, and effective reporting systems for conservation programs, are also discussed.

  15. Identifying open magnetic field regions of the Sun and their heliospheric counterparts

    NASA Astrophysics Data System (ADS)

    Krista, L. D.; Reinard, A.

    2017-12-01

    Open magnetic regions on the Sun are either long-lived (coronal holes) or transient (dimmings) in nature. Both phenomena are fundamental to our understanding of the solar behavior as a whole. Coronal holes are the sources of high-speed solar wind streams that cause recurrent geomagnetic storms. Furthermore, the variation of coronal hole properties (area, location, magnetic field strength) over the solar activity cycle is an important marker of the global evolution of the solar magnetic field. Dimming regions, on the other hand, are short-lived coronal holes that often emerge in the wake of solar eruptions. By analyzing their physical properties and their temporal evolution, we aim to understand their connection with their eruptive counterparts (flares and coronal mass ejections) and predict the possibility of a geomagnetic storm. The author developed the Coronal Hole Automated Recognition and Monitoring (CHARM) and the Coronal Dimming Tracker (CoDiT) algorithms. These tools not only identify but track the evolution of open magnetic field regions. CHARM also provides daily coronal hole maps, that are used for forecasts at the NOAA Space Weather Prediction Center. Our goal is to better understand the processes that give rise to eruptive and non-eruptive open field regions and investigate how these regions evolve over time and influence space weather.

  16. Conservation priorities for mammals in megadiverse Mexico: the efficiency of reserve networks.

    PubMed

    Ceballos, Gerardo

    2007-03-01

    A major goal of conservation biologists is to identify critical areas for the conservation of biological diversity and then strategically include them in an efficient system of reserves. In general, however, reserve networks have been selected for different objectives, and most countries lack an evaluation of their reserves' ability to represent a percentage of the national diversity. This paper evaluates the effectiveness of a network of reserves to represent the species of mammals in Mexico. The focus of the analyses is on species and site level, evaluating the representation of all terrestrial mammals in the 30 most important reserves. The representation of all species, endemic species, endangered species, and species with restricted distributions in the reserves was assessed and compared. Endemic or endangered species with restricted distributions were expected to be less represented in reserves than were widespread species. The most important reserves for the conservation of mammals were determined with the use of complementarity analyses. Priority sites for the representation of all the species currently absent from the reserve network were then selected. The results have broad applications for conservation. First, 82% of the mammal species from Mexico were represented in the reserve network, which covers a small portion (3.8%) of the country. Second, this percentage is certainly larger as several reserves were not evaluated due to a lack of data. A priority for a national conservation strategy could be to conduct biological surveys in those reserves lacking inventories to evaluate their contribution to conservation. Third, in spite of its demonstrated value, Mexico's reserve network can be improved by designating complementary areas. Additional priority sites, where reserves are required to represent most gap species in the network, were identified. Finally, it is clear that this reserve network has limitations for maintaining biodiversity and ecosystem

  17. Sequence analysis of the L protein of the Ebola 2014 outbreak: Insight into conserved regions and mutations.

    PubMed

    Ayub, Gohar; Waheed, Yasir

    2016-06-01

    The 2014 Ebola outbreak was one of the largest that have occurred; it started in Guinea and spread to Nigeria, Liberia and Sierra Leone. Phylogenetic analysis of the current virus species indicated that this outbreak is the result of a divergent lineage of the Zaire ebolavirus. The L protein of Ebola virus (EBOV) is the catalytic subunit of the RNA‑dependent RNA polymerase complex, which, with VP35, is key for the replication and transcription of viral RNA. Earlier sequence analysis demonstrated that the L protein of all non‑segmented negative‑sense (NNS) RNA viruses consists of six domains containing conserved functional motifs. The aim of the present study was to analyze the presence of these motifs in 2014 EBOV isolates, highlight their function and how they may contribute to the overall pathogenicity of the isolates. For this purpose, 81 2014 EBOV L protein sequences were aligned with 475 other NNS RNA viruses, including Paramyxoviridae and Rhabdoviridae viruses. Phylogenetic analysis of all EBOV outbreak L protein sequences was also performed. Analysis of the amino acid substitutions in the 2014 EBOV outbreak was conducted using sequence analysis. The alignment demonstrated the presence of previously conserved motifs in the 2014 EBOV isolates and novel residues. Notably, all the mutations identified in the 2014 EBOV isolates were tolerant, they were pathogenic with certain examples occurring within previously determined functional conserved motifs, possibly altering viral pathogenicity, replication and virulence. The phylogenetic analysis demonstrated that all sequences with the exception of the 2014 EBOV sequences were clustered together. The 2014 EBOV outbreak has acquired a great number of mutations, which may explain the reasons behind this unprecedented outbreak. Certain residues critical to the function of the polymerase remain conserved and may be targets for the development of antiviral therapeutic agents.

  18. Trading Water Conservation Credits: A Coordinative Approach for Enhanced Urban Water Reliability

    NASA Astrophysics Data System (ADS)

    Gonzales, P.; Ajami, N. K.

    2016-12-01

    Water utilities in arid and semi-arid regions are increasingly relying on water use efficiency and conservation to extend the availability of supplies. Despite spatial and institutional inter-dependency of many service providers, these demand-side management initiatives have traditionally been tackled by individual utilities operating in a silo. In this study, we introduce a new approach to water conservation that addresses regional synergies—a novel system of tradable water conservation credits. Under the proposed approach, utilities have the flexibility to invest in water conservation measures that are appropriate for their specific service area. When utilities have insufficient capacity for local cost-effective measures, they may opt to purchase credits, contributing to fund subsidies for utilities that do have that capacity and can provide the credits, while the region as whole benefits from more reliable water supplies. While similar programs have been used to address water quality concerns, to our knowledge this is one of the first studies proposing tradable credits for incentivizing water conservation. Through mathematical optimization, this study estimates the potential benefits of a trading program and demonstrates the institutional and economic characteristics needed for such a policy to be viable, including a proposed web platform to facilitate transparent regional planning, data-driven decision-making, and enhanced coordination of utilities. We explore the impacts of defining conservation targets tailored to local realities of utilities, setting credit prices, and different policy configurations. We apply these models to the case study of water utility members of the Bay Area Water Supply and Conservation Agency. Preliminary work shows that the diverse characteristics of these utilities present opportunities for the region to achieve conservation goals while maximizing the benefits to individual utilities through more flexible coordinative efforts.

  19. Identifying Markers of Dignity-Conserving Care in Long-Term Care: A Modified Delphi Study

    PubMed Central

    Thompson, Genevieve N.; McArthur, Jennifer; Doupe, Malcolm

    2016-01-01

    Ensuring that people living in nursing homes (NHs) are afforded with dignity in their daily lives is an essential and humane concern. Promoting dignity-conserving care is fundamentally important. By nature, however, this care is all-encompassing and holistic, and from current knowledge it is challenging to create explicit strategies for measuring dignity-conserving care. In practice the majority of current NH indicators of quality care are derived from information that is routinely collected on NH residents using the RAI-Minimum Data Set (MDS). In this regard, issues that are more tangible to resident dignity such as being treated with respect, compassion, and having opportunities to engage with others are not adequately captured in current NH quality of care indicators. An initial set of markers was created by conducting an integrative literature review of existing markers and indicators of dignity in the NH setting. A modified Delphi process was used to prioritize essential dignity-conserving care markers for use by NH providers, based on factors such as the importance to fostering a culture of dignity, the impact it may have on the residents, and how achievable it is in practice. Through this consensus building technique, we were able to develop a comprehensive set of markers that capture the range and diversity of important dignity-conserving care strategies for use in NHs. The final 10 markers were judged as having high face validity by experts in the field and have explicit implications for enhancing the provision of daily dignified care to NH residents. These markers make an important addition to the traditional quality indicators used in the NH setting and as such, bridge an important gap in addressing the psychosocial and the less easily quantified needs of NH residents. PMID:27304853

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

    PubMed

    Spiteri, Arian; Nepal, Sanjay K

    2008-09-01

    Protected areas are integral to the global effort to conserve biodiversity, and, over the past two decades, protected area managers have begun to recognize that conservation objectives are next to impossible to achieve without considering the needs and concerns of local communities. Incentive-based programs (IBPs) have become a favored approach to protected area management, geared at fostering local stewardship by delivering benefits tied to conservation to local people. Effective IBPs require benefits to accrue to and be recognized by those experiencing the greatest consequences as a result of the protected area, and those likely to continue extractive activities if their livelihood needs are compromised. This research examines dispersal of IBP benefits, as perceived by local residents in Nepal's Annapurna Conservation Area. Results reported here are based on questionnaire interviews with 188 households conducted between September and December 2004. Results indicate that local residents primarily identify benefits from social development activities, provisions for resource extraction, and economic opportunities. Overall, benefits have been dispersed equally to households in villages on and off the main tourist route, and regardless of a household's participation in tourism. However, benefits are not effectively targeted to poorer residents, those highly dependent on natural resources, and those experiencing the most crop damage and livestock loss from protected wildlife. This article provides several suggestions for improving the delivery of conservation incentives.

  1. The existence of High Conservation Value Forest (HCVF) in Perum Perhutani KPH Kendal to support Implementation of FSC Certification

    NASA Astrophysics Data System (ADS)

    Sulistyowati, Sri; Hadi, Sudharto P.

    2018-02-01

    High Conservation Value Forest (HCVF) is the identification of High Conservation Values that are important and need to be protected. Under FSC certification mechanism, HCVF becomes one of Principles and Criteria to attain certification. In this study, we identify the existence of HCVF in Perum Perhutani KPH Kendal to support implementation process of FSC certification. Qualitative method was conducted through observation and secondary data from Perum Perhutani KPH Kendal. Data analysis showed through ecolabel certification, Perum Perhutani KPH Kendal has been identified HCVF area covering 2,715.5 hectares consists of HCV 1 until 6. Secondary Natural Forest (HAS) Subah and Kaliwungu for Ulolanang and Pagerwunung Nature Reserve buffer zone include as HCV 1.1, conservation area of leopard (Panthera pardus melas) and Pangolin (Manis javanica).for HCV 1.2, conservation area of lutung (Trachypiyhecus auratus) as endemic species for CITES App I and Critically Endangered species include as HCV 1.3, Goa kiskendo for bats species habitat include as HCV 1.4, regions of interest species for Deer (Cervus timorensis) and Kepodang (Oriolus chinensis) as HCV 2.3, Germplasm Protection Region/ KPPN area with high biodiversity include as HCV 3, river border area and water springs for HCV 4. While, utilization of firewood, grass for cattle fodder include as HCV 5 and 14 cultural sites include as HCV 6. From monitoring and evaluation of HCVF data, showed that in 2011-2015 the level of diversity for flora and fauna were increased.

  2. Modelling conservation in the Amazon basin.

    PubMed

    Soares-Filho, Britaldo Silveira; Nepstad, Daniel Curtis; Curran, Lisa M; Cerqueira, Gustavo Coutinho; Garcia, Ricardo Alexandrino; Ramos, Claudia Azevedo; Voll, Eliane; McDonald, Alice; Lefebvre, Paul; Schlesinger, Peter

    2006-03-23

    Expansion of the cattle and soy industries in the Amazon basin has increased deforestation rates and will soon push all-weather highways into the region's core. In the face of this growing pressure, a comprehensive conservation strategy for the Amazon basin should protect its watersheds, the full range of species and ecosystem diversity, and the stability of regional climates. Here we report that protected areas in the Amazon basin--the central feature of prevailing conservation approaches--are an important but insufficient component of this strategy, based on policy-sensitive simulations of future deforestation. By 2050, current trends in agricultural expansion will eliminate a total of 40% of Amazon forests, including at least two-thirds of the forest cover of six major watersheds and 12 ecoregions, releasing 32 +/- 8 Pg of carbon to the atmosphere. One-quarter of the 382 mammalian species examined will lose more than 40% of the forest within their Amazon ranges. Although an expanded and enforced network of protected areas could avoid as much as one-third of this projected forest loss, conservation on private lands is also essential. Expanding market pressures for sound land management and prevention of forest clearing on lands unsuitable for agriculture are critical ingredients of a strategy for comprehensive conservation.

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

    PubMed

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

    2008-06-01

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

  4. 76 FR 28060 - Regional Habitat Conservation Plan, Hays County, TX

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-05-13

    ... alternative features the acquisition of a modestly sized, pre-determined preserve system and limits the amount... under Alternative B, this alternative involves a conservation program that utilizes a pre-determined..., adaptive management, and other strategies designed to avoid and minimize harm to the covered species and...

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

    PubMed

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

    2015-07-01

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

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

    USGS Publications Warehouse

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

    2015-01-01

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

  7. Combining landscape-level conservation planning and biodiversity offset programs: a case study.

    PubMed

    Underwood, Jared G

    2011-01-01

    Habitat loss is a major factor in the endangerment and extinction of species around the world. One promising strategy to balance continued habitat loss and biodiversity conservation is that of biodiversity offsets. However, a major concern with offset programs is their consistency with landscape-level conservation goals. While merging offset policies and landscape-level conservation planning is thought to provide advantages over a traditional disconnected approach, few such landscape-level conservation-offset plans have been designed and implemented, so the effectiveness of such a strategy remains uncertain. In this study, we quantitatively assess the conservation impact of combining landscape-level conservation planning and biodiversity offset programs by comparing regions of San Diego County, USA with the combined approach to regions with only an offset program. This comparison is generally very difficult due to a variety of complicating factors. We overcome these complications and quantify the benefits to rare and threatened species of implementing a combined approach by assessing the amount of each species' predicted distribution, and the number of documented locations, conserved in comparison to the same metric for areas with an offset policy alone. We found that adoption of the combined approach has increased conservation for many rare species, often 5-10 times more than in the comparison area, and that conservation has been focused in the areas most important for these species. The level of conservation achieved reduces uncertainty that these species will persist in the region into the future. This San Diego County example demonstrates the potential benefits of combining landscape-level conservation planning and biodiversity offset programs.

  8. COORDINATING, COMMUNICATING AND PERFORMING COMPLEX RESEARCH THAT IDENTIFIES VULNERABLE STREAM ECOSYSTEM IN THE MID-ATLANTIC REGION

    EPA Science Inventory

    The USEPA's Regional Vulnerability Assessment (ReVA) program was created to advance the scientific basis for protecting vulnerable ecosystems at a regional scale. As a first step, the ReVa program will coordinate, communicate and perform complex research that will identify vulner...

  9. NetCoffee: a fast and accurate global alignment approach to identify functionally conserved proteins in multiple networks.

    PubMed

    Hu, Jialu; Kehr, Birte; Reinert, Knut

    2014-02-15

    Owing to recent advancements in high-throughput technologies, protein-protein interaction networks of more and more species become available in public databases. The question of how to identify functionally conserved proteins across species attracts a lot of attention in computational biology. Network alignments provide a systematic way to solve this problem. However, most existing alignment tools encounter limitations in tackling this problem. Therefore, the demand for faster and more efficient alignment tools is growing. We present a fast and accurate algorithm, NetCoffee, which allows to find a global alignment of multiple protein-protein interaction networks. NetCoffee searches for a global alignment by maximizing a target function using simulated annealing on a set of weighted bipartite graphs that are constructed using a triplet approach similar to T-Coffee. To assess its performance, NetCoffee was applied to four real datasets. Our results suggest that NetCoffee remedies several limitations of previous algorithms, outperforms all existing alignment tools in terms of speed and nevertheless identifies biologically meaningful alignments. The source code and data are freely available for download under the GNU GPL v3 license at https://code.google.com/p/netcoffee/.

  10. Neutral Theory is the Foundation of Conservation Genetics.

    PubMed

    Yoder, Anne D; Poelstra, Jelmer; Tiley, George P; Williams, Rachel

    2018-04-16

    Kimura's neutral theory of molecular evolution has been essential to virtually every advance in evolutionary genetics, and by extension, is foundational to the field of conservation genetics. Conservation genetics utilizes the key concepts of neutral theory to identify species and populations at risk of losing evolutionary potential by detecting patterns of inbreeding depression and low effective population size. In turn, this information can inform the management of organisms and their habitat providing hope for the long-term preservation of both. We expand upon Avise's "inventorial" and "functional" categories of conservation genetics by proposing a third category that is linked to the coalescent and that we refer to as "process-driven." It is here that connections between Kimura's theory and conservation genetics are strongest. Process-driven conservation genetics can be especially applied to large genomic datasets to identify patterns of historical risk, such as population bottlenecks, and accordingly, yield informed intuitions for future outcomes. By examining inventorial, functional, and process-driven conservation genetics in sequence, we assess the progression from theory, to data collection and analysis, and ultimately, to the production of hypotheses that can inform conservation policies.

  11. Waterfowl populations of conservation concern: learning from diverse challenges, models, and conservation strategies

    USGS Publications Warehouse

    Austin, Jane E.; Slattery, Stuart; Clark, Robert G.

    2014-01-01

    There are 30 threatened or endangered species of waterfowl worldwide, and several sub-populations are also threatened. Some of these species occur in North America, and others there are also of conservation concern due to declining population trends and their importance to hunters. Here we review conservation initiatives being undertaken for several of these latter species, along with conservation measures in place in Europe, to seek common themes and approaches that could be useful in developing broad conservation guidelines. While focal species may vary in their life histories, population threats and geopolitical context, most conservation efforts have used a systematic approach to understand factors limiting populations and o identify possible management or policy actions. This approach generally includes a priori identification of plausible hypotheses about population declines or status, incorporation of hypotheses into conceptual or quantitative planning models, and the use of some form of structured decision making and adaptive management to develop and implement conservation actions in the face of many uncertainties. A climate of collaboration among jurisdictions sharing these birds is important to the success of a conservation or management programme. The structured conservation approach exemplified herein provides an opportunity to involve stakeholders at all planning stages, allows for all views to be examined and incorporated into model structures, and yields a format for improved communication, cooperation and learning, which may ultimately be one of the greatest benefits of this strategy.

  12. The biogeography of globally threatened seabirds and island conservation opportunities.

    PubMed

    Spatz, Dena R; Newton, Kelly M; Heinz, Reina; Tershy, Bernie; Holmes, Nick D; Butchart, Stuart H M; Croll, Donald A

    2014-10-01

    Seabirds are the most threatened group of marine animals; 29% of species are at some risk of extinction. Significant threats to seabirds occur on islands where they breed, but in many cases, effective island conservation can mitigate these threats. To guide island-based seabird conservation actions, we identified all islands with extant or extirpated populations of the 98 globally threatened seabird species, as recognized on the International Union for Conservation of Nature Red List, and quantified the presence of threatening invasive species, protected areas, and human populations. We matched these results with island attributes to highlight feasible island conservation opportunities. We identified 1362 threatened breeding seabird populations on 968 islands. On 803 (83%) of these islands, we identified threatening invasive species (20%), incomplete protected area coverage (23%), or both (40%). Most islands with threatened seabirds are amenable to island-wide conservation action because they are small (57% were <1 km(2) ), uninhabited (74%), and occur in high- or middle-income countries (96%). Collectively these attributes make islands with threatened seabirds a rare opportunity for effective conservation at scale. © 2014 Society for Conservation Biology.

  13. Research Priorities from Animal Behaviour for Maximising Conservation Progress.

    PubMed

    Greggor, Alison L; Berger-Tal, Oded; Blumstein, Daniel T; Angeloni, Lisa; Bessa-Gomes, Carmen; Blackwell, Bradley F; St Clair, Colleen Cassady; Crooks, Kevin; de Silva, Shermin; Fernández-Juricic, Esteban; Goldenberg, Shifra Z; Mesnick, Sarah L; Owen, Megan; Price, Catherine J; Saltz, David; Schell, Christopher J; Suarez, Andrew V; Swaisgood, Ronald R; Winchell, Clark S; Sutherland, William J

    2016-12-01

    Poor communication between academic researchers and wildlife managers limits conservation progress and innovation. As a result, input from overlapping fields, such as animal behaviour, is underused in conservation management despite its demonstrated utility as a conservation tool and countless papers advocating its use. Communication and collaboration across these two disciplines are unlikely to improve without clearly identified management needs and demonstrable impacts of behavioural-based conservation management. To facilitate this process, a team of wildlife managers and animal behaviour researchers conducted a research prioritisation exercise, identifying 50 key questions that have great potential to resolve critical conservation and management problems. The resulting agenda highlights the diversity and extent of advances that both fields could achieve through collaboration. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  14. Comparison of conservation metrics in a case study of lemurs.

    PubMed

    Gudde, Renske; Venditti, Chris

    2016-12-01

    Conservation planning is important to protect species from going extinct now that natural habitats are decreasing owing to human activity and climate change. However, there is considerable controversy in choosing appropriate metrics to weigh the value of species and geographic regions. For example, the added value of phylogenetic conservation-selection criteria remains disputed because high correlations between them and the nonphylogenetic criteria of species richness have been reported. We evaluated the commonly used conservation metrics species richness, endemism, phylogenetic diversity (PD), and phylogenetic endemism (PE) in a case study on lemurs of Madagascar. This enabled us to identify the conservation target of each metric and consider how they may be used in future conservation planning. We also devised a novel metric that uses a phylogeny scaled according to the rate of phenotypic evolution as a proxy for a species' ability to adapt to change. High rates of evolution may indicate generalization or specialization. Both specialization and low rates of evolution may result in an inability to adapt to changing environments. We examined conservation priorities by using the inverse of the rate of body mass evolution to account for species with low rates of evolution. In line with previous work, we found high correlations among species richness and PD (r = 0.96), and endemism and PE (r = 0.82) in Malagasy lemurs. Phylogenetic endemism in combination with rates of evolution and their inverse prioritized grid cells containing highly endemic and specialized lemurs at risk of extinction, such as Avahi occidentalis and Lepilemur edwardsi, 2 endangered lemurs with high rates of phenotypic evolution and low-quality diets, and Hapalemur aureus, a critically endangered species with a low rate of body mass evolution and a diet consisting of very high doses of cyanide. © 2016 Society for Conservation Biology.

  15. Gene expression meta-analysis identifies chromosomal regions and candidate genes involved in breast cancer metastasis.

    PubMed

    Thomassen, Mads; Tan, Qihua; Kruse, Torben A

    2009-01-01

    Breast cancer cells exhibit complex karyotypic alterations causing deregulation of numerous genes. Some of these genes are probably causal for cancer formation and local growth whereas others are causal for the various steps of metastasis. In a fraction of tumors deregulation of the same genes might be caused by epigenetic modulations, point mutations or the influence of other genes. We have investigated the relation of gene expression and chromosomal position, using eight datasets including more than 1200 breast tumors, to identify chromosomal regions and candidate genes possibly causal for breast cancer metastasis. By use of "Gene Set Enrichment Analysis" we have ranked chromosomal regions according to their relation to metastasis. Overrepresentation analysis identified regions with increased expression for chromosome 1q41-42, 8q24, 12q14, 16q22, 16q24, 17q12-21.2, 17q21-23, 17q25, 20q11, and 20q13 among metastasizing tumors and reduced gene expression at 1p31-21, 8p22-21, and 14q24. By analysis of genes with extremely imbalanced expression in these regions we identified DIRAS3 at 1p31, PSD3, LPL, EPHX2 at 8p21-22, and FOS at 14q24 as candidate metastasis suppressor genes. Potential metastasis promoting genes includes RECQL4 at 8q24, PRMT7 at 16q22, GINS2 at 16q24, and AURKA at 20q13.

  16. Protein Sectors: Statistical Coupling Analysis versus Conservation

    PubMed Central

    Teşileanu, Tiberiu; Colwell, Lucy J.; Leibler, Stanislas

    2015-01-01

    Statistical coupling analysis (SCA) is a method for analyzing multiple sequence alignments that was used to identify groups of coevolving residues termed “sectors”. The method applies spectral analysis to a matrix obtained by combining correlation information with sequence conservation. It has been asserted that the protein sectors identified by SCA are functionally significant, with different sectors controlling different biochemical properties of the protein. Here we reconsider the available experimental data and note that it involves almost exclusively proteins with a single sector. We show that in this case sequence conservation is the dominating factor in SCA, and can alone be used to make statistically equivalent functional predictions. Therefore, we suggest shifting the experimental focus to proteins for which SCA identifies several sectors. Correlations in protein alignments, which have been shown to be informative in a number of independent studies, would then be less dominated by sequence conservation. PMID:25723535

  17. Impending conservation crisis for Southeast Asian amphibians.

    PubMed

    Rowley, Jodi; Brown, Rafe; Bain, Raoul; Kusrini, Mirza; Inger, Robert; Stuart, Bryan; Wogan, Guin; Thy, Neang; Chan-Ard, Tanya; Trung, Cao Tien; Diesmos, Arvin; Iskandar, Djoko T; Lau, Michael; Ming, Leong Tzi; Makchai, Sunchai; Truong, Nguyen Quang; Phimmachak, Somphouthone

    2010-06-23

    With an understudied amphibian fauna, the highest deforestation rate on the planet and high harvesting pressures, Southeast Asian amphibians are facing a conservation crisis. Owing to the overriding threat of habitat loss, the most critical conservation action required is the identification and strict protection of habitat assessed as having high amphibian species diversity and/or representing distinctive regional amphibian faunas. Long-term population monitoring, enhanced survey efforts, collection of basic biological and ecological information, continued taxonomic research and evaluation of the impact of commercial trade for food, medicine and pets are also needed. Strong involvement of regional stakeholders, students and professionals is essential to accomplish these actions.

  18. Impending conservation crisis for Southeast Asian amphibians

    PubMed Central

    Rowley, Jodi; Brown, Rafe; Bain, Raoul; Kusrini, Mirza; Inger, Robert; Stuart, Bryan; Wogan, Guin; Thy, Neang; Chan-ard, Tanya; Trung, Cao Tien; Diesmos, Arvin; Iskandar, Djoko T.; Lau, Michael; Ming, Leong Tzi; Makchai, Sunchai; Truong, Nguyen Quang; Phimmachak, Somphouthone

    2010-01-01

    With an understudied amphibian fauna, the highest deforestation rate on the planet and high harvesting pressures, Southeast Asian amphibians are facing a conservation crisis. Owing to the overriding threat of habitat loss, the most critical conservation action required is the identification and strict protection of habitat assessed as having high amphibian species diversity and/or representing distinctive regional amphibian faunas. Long-term population monitoring, enhanced survey efforts, collection of basic biological and ecological information, continued taxonomic research and evaluation of the impact of commercial trade for food, medicine and pets are also needed. Strong involvement of regional stakeholders, students and professionals is essential to accomplish these actions. PMID:20007165

  19. A biodiversity hotspot losing its top predator: The challenge of jaguar conservation in the Atlantic Forest of South America.

    PubMed

    Paviolo, Agustin; De Angelo, Carlos; Ferraz, Katia M P M B; Morato, Ronaldo G; Martinez Pardo, Julia; Srbek-Araujo, Ana C; Beisiegel, Beatriz de Mello; Lima, Fernando; Sana, Denis; Xavier da Silva, Marina; Velázquez, Myriam C; Cullen, Laury; Crawshaw, Peter; Jorge, María Luisa S P; Galetti, Pedro M; Di Bitetti, Mario S; de Paula, Rogerio Cunha; Eizirik, Eduardo; Aide, T Mitchell; Cruz, Paula; Perilli, Miriam L L; Souza, Andiara S M C; Quiroga, Verónica; Nakano, Eduardo; Ramírez Pinto, Fredy; Fernández, Sixto; Costa, Sebastian; Moraes, Edsel A; Azevedo, Fernando

    2016-11-16

    The jaguar is the top predator of the Atlantic Forest (AF), which is a highly threatened biodiversity hotspot that occurs in Brazil, Paraguay and Argentina. By combining data sets from 14 research groups across the region, we determine the population status of the jaguar and propose a spatial prioritization for conservation actions. About 85% of the jaguar's habitat in the AF has been lost and only 7% remains in good condition. Jaguars persist in around 2.8% of the region, and live in very low densities in most of the areas. The population of jaguars in the AF is probably lower than 300 individuals scattered in small sub-populations. We identified seven Jaguar Conservation Units (JCUs) and seven potential JCUs, and only three of these areas may have ≥50 individuals. A connectivity analysis shows that most of the JCUs are isolated. Habitat loss and fragmentation were the major causes for jaguar decline, but human induced mortality is the main threat for the remaining population. We classified areas according to their contribution to jaguar conservation and we recommend management actions for each of them. The methodology in this study could be used for conservation planning of other carnivore species.

  20. Toward a Conceptual Framework for Blending Social and Biophysical Attributes in Conservation Planning: A Case-Study of Privately-Conserved Lands

    NASA Astrophysics Data System (ADS)

    Pasquini, Lorena; Twyman, Chasca; Wainwright, John

    2010-11-01

    There has been increasing recognition within systematic conservation planning of the need to include social data alongside biophysical assessments. However, in the approaches to identify potential conservation sites, there remains much room for improvement in the treatment of social data. In particular, few rigorous methods to account for the diversity of less-easily quantifiable social attributes that influence the implementation success of conservation sites (such as willingness to conserve) have been developed. We use a case-study analysis of private conservation areas within the Little Karoo, South Africa, as a practical example of the importance of incorporating social data into the process of selecting potential conservation sites to improve their implementation likelihood. We draw on extensive data on the social attributes of our case study obtained from a combination of survey questionnaires and semi-structured interviews. We discuss the need to determine the social attributes that are important for achieving the chosen implementation strategy by offering four tested examples of important social attributes in the Little Karoo: the willingness of landowners to take part in a stewardship arrangement, their willingness to conserve, their capacity to conserve, and the social capital among private conservation area owners. We then discuss the process of using an implementation likelihood ratio (derived from a combined measure of the social attributes) to assist the choice of potential conservation sites. We conclude by summarizing our discussion into a simple conceptual framework for identifying biophysically-valuable sites which possess a high likelihood that the desired implementation strategy will be realized on them.