ABCE1 Is a Highly Conserved RNA Silencing Suppressor

PubMed Central

Kärblane, Kairi; Gerassimenko, Jelena; Nigul, Lenne; Piirsoo, Alla; Smialowska, Agata; Vinkel, Kadri; Kylsten, Per; Ekwall, Karl; Swoboda, Peter; Truve, Erkki; Sarmiento, Cecilia

2015-01-01

ATP-binding cassette sub-family E member 1 (ABCE1) is a highly conserved protein among eukaryotes and archaea. Recent studies have identified ABCE1 as a ribosome-recycling factor important for translation termination in mammalian cells, yeast and also archaea. Here we report another conserved function of ABCE1. We have previously described AtRLI2, the homolog of ABCE1 in the plant Arabidopsis thaliana, as an endogenous suppressor of RNA silencing. In this study we show that this function is conserved: human ABCE1 is able to suppress RNA silencing in Nicotiana benthamiana plants, in mammalian HEK293 cells and in the worm Caenorhabditis elegans. Using co-immunoprecipitation and mass spectrometry, we found a number of potential ABCE1-interacting proteins that might support its function as an endogenous suppressor of RNA interference. The interactor candidates are associated with epigenetic regulation, transcription, RNA processing and mRNA surveillance. In addition, one of the identified proteins is translin, which together with its binding partner TRAX supports RNA interference. PMID:25659154

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.

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

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

ERIC Educational Resources Information Center

Ensminger, Jack

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

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.

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

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.

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.

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.

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

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

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.

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

Multi-species comparative analysis of the equine ACE gene identifies a highly conserved potential transcription factor binding site in intron 16.

PubMed

Hamilton, Natasha A; Tammen, Imke; Raadsma, Herman W

2013-01-01

Angiotensin converting enzyme (ACE) is essential for control of blood pressure. The human ACE gene contains an intronic Alu indel (I/D) polymorphism that has been associated with variation in serum enzyme levels, although the functional mechanism has not been identified. The polymorphism has also been associated with cardiovascular disease, type II diabetes, renal disease and elite athleticism. We have characterized the ACE gene in horses of breeds selected for differing physical abilities. The equine gene has a similar structure to that of all known mammalian ACE genes. Nine common single nucleotide polymorphisms (SNPs) discovered in pooled DNA were found to be inherited in nine haplotypes. Three of these SNPs were located in intron 16, homologous to that containing the Alu polymorphism in the human. A highly conserved 18 bp sequence, also within that intron, was identified as being a potential binding site for the transcription factors Oct-1, HFH-1 and HNF-3β, and lies within a larger area of higher than normal homology. This putative regulatory element may contribute to regulation of the documented inter-individual variation in human circulating enzyme levels, for which a functional mechanism is yet to be defined. Two equine SNPs occurred within the conserved area in intron 16, although neither of them disrupted the putative binding site. We propose a possible regulatory mechanism of the ACE gene in mammalian species which was previously unknown. This advance will allow further analysis leading to a better understanding of the mechanisms underpinning the associations seen between the human Alu polymorphism and enzyme levels, cardiovascular disease states and elite athleticism.

Multi-Species Comparative Analysis of the Equine ACE Gene Identifies a Highly Conserved Potential Transcription Factor Binding Site in Intron 16

PubMed Central

Hamilton, Natasha A.; Tammen, Imke; Raadsma, Herman W.

2013-01-01

Angiotensin converting enzyme (ACE) is essential for control of blood pressure. The human ACE gene contains an intronic Alu indel (I/D) polymorphism that has been associated with variation in serum enzyme levels, although the functional mechanism has not been identified. The polymorphism has also been associated with cardiovascular disease, type II diabetes, renal disease and elite athleticism. We have characterized the ACE gene in horses of breeds selected for differing physical abilities. The equine gene has a similar structure to that of all known mammalian ACE genes. Nine common single nucleotide polymorphisms (SNPs) discovered in pooled DNA were found to be inherited in nine haplotypes. Three of these SNPs were located in intron 16, homologous to that containing the Alu polymorphism in the human. A highly conserved 18 bp sequence, also within that intron, was identified as being a potential binding site for the transcription factors Oct-1, HFH-1 and HNF-3β, and lies within a larger area of higher than normal homology. This putative regulatory element may contribute to regulation of the documented inter-individual variation in human circulating enzyme levels, for which a functional mechanism is yet to be defined. Two equine SNPs occurred within the conserved area in intron 16, although neither of them disrupted the putative binding site. We propose a possible regulatory mechanism of the ACE gene in mammalian species which was previously unknown. This advance will allow further analysis leading to a better understanding of the mechanisms underpinning the associations seen between the human Alu polymorphism and enzyme levels, cardiovascular disease states and elite athleticism. PMID:23408978

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

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

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

Freshwater habitats and species living in freshwater are generally more prone to extinction than terrestrial or marine ones. Immediate conservation measures for world-wide freshwater resources are thus of eminent importance. This is particularly true for so called ancient lakes. While these lakes are famous for being evolutionary theatres, often displaying an extraordinarily high degree of biodiversity and endemism, in many cases these biota are also experiencing extreme anthropogenic impact. Lake Ohrid, the European biodiversity hotspot, is a prime example for a lake with a magnitude of narrow range endemic taxa that are under increasing anthropogenic pressure. Unfortunately, evidence for a "creeping biodiversity crisis" has accumulated over the last decades, and major socio-political changes have gone along with human-mediated environmental changes. Based on field surveys, monitoring data, published records, and expert interviews, we aimed to (1) assess threats to Lake Ohrids' (endemic) biodiversity, (2) summarize existing conservation activities and strategies, and (3) outline future conservation needs for Lake Ohrid. We compiled threats to both specific taxa (and in cases to particular species) as well as to the lake ecosystems itself. Major conservation concerns identified for Lake Ohrid are: (1) watershed impacts, (2) agriculture and forestry, (3) tourism and population growth, (4) non-indigenous species, (5) habitat alteration or loss, (6) unsustainable exploitation of fisheries, and (7) global climate change. Of the 11 IUCN (International Union for Conservation of Nature and Natural Resources) threat classes scored, seven have moderate and three severe impacts. These latter threat classes are energy production and mining, biological resource use, and pollution. We review and discuss institutional responsibilities, environmental monitoring and ecosystem management, existing parks and reserves, biodiversity and species measures, international conservation

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.

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.

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.

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

PubMed

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

2014-01-01

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

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

A framework for addressing bird conservation priorities in high-elevation vegetation communities of the Appalachian Mountains

Treesearch

Brian W. Smith; Dean Demarest; Ed. Laurent

2010-01-01

The Appalachian Mountains Joint Venture (AMJV) is a self-directed, nonregulatory bird conservation partnership with the mission of restoring and sustaining native bird populations and their habitats throughout Appalachia. In 2008, the AMJV formed an ad hoc "high-elevation" technical working group to identify and address conservation priorities of bird species...

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.

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.

Antibody Recognition of a Highly Conserved Influenza Virus Epitope

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

Ekiert, Damian C.; Bhabha, Gira; Elsliger, Marc-André

2009-05-21

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

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/.

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

The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains.

PubMed

Ren, Siyuan; Yang, Guang; He, Youyu; Wang, Yiguo; Li, Yixue; Chen, Zhengjun

2008-10-01

Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs). Accurate prediction of SLiMs has been difficult because they are short (often < 10 amino acids) and highly degenerate. In this study, we combined scoring matrixes derived from peptide library and conservation analysis to identify protein classes enriched of functional SLiMs recognized by SH2, SH3, PDZ and S/T kinase domains. Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains.

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

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.

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

The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains

PubMed Central

Ren, Siyuan; Yang, Guang; He, Youyu; Wang, Yiguo; Li, Yixue; Chen, Zhengjun

2008-01-01

Background Many well-represented domains recognize primary sequences usually less than 10 amino acids in length, called Short Linear Motifs (SLiMs). Accurate prediction of SLiMs has been difficult because they are short (often < 10 amino acids) and highly degenerate. In this study, we combined scoring matrixes derived from peptide library and conservation analysis to identify protein classes enriched of functional SLiMs recognized by SH2, SH3, PDZ and S/T kinase domains. Results Our combined approach revealed that SLiMs are highly conserved in proteins from functional classes that are known to interact with a specific domain, but that they are not conserved in most other protein groups. We found that SLiMs recognized by SH2 domains were highly conserved in receptor kinases/phosphatases, adaptor molecules, and tyrosine kinases/phosphatases, that SLiMs recognized by SH3 domains were highly conserved in cytoskeletal and cytoskeletal-associated proteins, that SLiMs recognized by PDZ domains were highly conserved in membrane proteins such as channels and receptors, and that SLiMs recognized by S/T kinase domains were highly conserved in adaptor molecules, S/T kinases/phosphatases, and proteins involved in transcription or cell cycle control. We studied Tyr-SLiMs recognized by SH2 domains in more detail, and found that SH2-recognized Tyr-SLiMs on the cytoplasmic side of membrane proteins are more highly conserved than those on the extra-cellular side. Also, we found that SH2-recognized Tyr-SLiMs that are associated with SH3 motifs and a tyrosine kinase phosphorylation motif are more highly conserved. Conclusion The interactome of protein domains is reflected by the evolutionary conservation of SLiMs recognized by these domains. Combining scoring matrixes derived from peptide libraries and conservation analysis, we would be able to find those protein groups that are more likely to interact with specific domains. PMID:18828911

Conservation genetics of high elevation five-needle white pines

Treesearch

Andrew D. Bower; Sierra C. McLane; Andrew Eckert; Stacy Jorgensen; Anna Schoettle; Sally Aitken

2011-01-01

Conservation genetics examines the biophysical factors influencing genetic processes and uses that information to conserve and maintain the evolutionary potential of species and populations. Here we review published and unpublished literature on the conservation genetics of seven North American high-elevation five-needle pines. Although these species are widely...

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

PubMed

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

2016-10-01

Preserving intraspecific genetic diversity is essential for long-term forest sustainability in a climate change scenario. Despite that, genetic information is largely neglected in conservation planning, and how conservation units should be defined is still heatedly debated. Here, we use maritime pine (Pinus pinaster Ait.), an outcrossing long-lived tree with a highly fragmented distribution in the Mediterranean biodiversity hotspot, to prove the importance of accounting for genetic variation, of both neutral molecular markers and quantitative traits, to define useful conservation units. Six gene pools associated to distinct evolutionary histories were identified within the species using 12 microsatellites and 266 single nucleotide polymorphisms (SNPs). In addition, height and survival standing variation, their genetic control, and plasticity were assessed in a multisite clonal common garden experiment (16 544 trees). We found high levels of quantitative genetic differentiation within previously defined neutral gene pools. Subsequent cluster analysis and post hoc trait distribution comparisons allowed us to define 10 genetically homogeneous population groups with high evolutionary potential. They constitute the minimum number of units to be represented in a maritime pine dynamic conservation program. Our results uphold that the identification of conservation units below the species level should account for key neutral and adaptive components of genetic diversity, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be largely improved by gradually integrating molecular and quantitative trait information, as data become available. © 2016 by the Ecological Society of America.

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

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

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.

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

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

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

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.

Energy Conservation Featured in Illinois High School

ERIC Educational Resources Information Center

Modern Schools, 1976

1976-01-01

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

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

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.

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

PubMed

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

2017-05-15

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

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

High-resolution schemes for hyperbolic conservation laws

NASA Technical Reports Server (NTRS)

Harten, A.

1982-01-01

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

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

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

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.

Tilapia and human CLIC2 structures are highly conserved.

PubMed

Zeng, Jiao; Li, Zhengjun; Lui, Eei Yin; Lam, Siew Hong; Swaminathan, Kunchithapadam

2018-01-08

Chloride intracellular channels (CLICs) exist in soluble and membrane bound forms. We have determined the crystal structure of soluble Clic2 from the euryhaline teleost fish Oreochromis mossambicus. Structural comparison of tilapia and human CLIC2 with other CLICs shows that these proteins are highly conserved. We have also compared the expression levels of clic2 in selected osmoregulatory organs of tilapia, acclimated to freshwater, seawater and hypersaline water. Structural conservation of vertebrate CLICs implies that they might play conserved roles. Also, tissue-specific responsiveness of clic2 suggests that it might be involved in iono-osmoregulation under extreme conditions in tilapia. Copyright © 2017 Elsevier Inc. All rights reserved.

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

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.

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.

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...

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

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-05

... Conservation Program: Availability of the Interim Technical Support Document for High-Intensity Discharge Lamps... high-intensity discharge (HID) lamps energy conservation standards in the Federal Register. This... interim analysis for high- intensity discharge lamps energy conservation standards. The notice provided...

Dipeptide frequency/bias analysis identifies conserved sites of nonrandomness shared by cysteine-rich motifs.

PubMed

Campion, S R; Ameen, A S; Lai, L; King, J M; Munzenmaier, T N

2001-08-15

This report describes the application of a simple computational tool, AAPAIR.TAB, for the systematic analysis of the cysteine-rich EGF, Sushi, and Laminin motif/sequence families at the two-amino acid level. Automated dipeptide frequency/bias analysis detects preferences in the distribution of amino acids in established protein families, by determining which "ordered dipeptides" occur most frequently in comprehensive motif-specific sequence data sets. Graphic display of the dipeptide frequency/bias data revealed family-specific preferences for certain dipeptides, but more importantly detected a shared preference for employment of the ordered dipeptides Gly-Tyr (GY) and Gly-Phe (GF) in all three protein families. The dipeptide Asn-Gly (NG) also exhibited high-frequency and bias in the EGF and Sushi motif families, whereas Asn-Thr (NT) was distinguished in the Laminin family. Evaluation of the distribution of dipeptides identified by frequency/bias analysis subsequently revealed the highly restricted localization of the G(F/Y) and N(G/T) sequence elements at two separate sites of extreme conservation in the consensus sequence of all three sequence families. The similar employment of the high-frequency/bias dipeptides in three distinct protein sequence families was further correlated with the concurrence of these shared molecular determinants at similar positions within the distinctive scaffolds of three structurally divergent, but similarly employed, motif modules.

The yan gene is highly conserved in Drosophila and its expression suggests a complex role throughout development.

PubMed

Price, M D; Lai, Z

1999-04-01

Competence for cell fate determination and cellular differentiation is under tight control of regulatory genes. Yan, a nuclear target of receptor tyrosine kinase (RTK) signaling, is an E twenty six (ETS) DNA-binding protein that functions as a negative regulator of cell differentiation and proliferation in Drosophila. Most members of RTK signaling pathways are highly conserved through evolution, yet no yan orthologues have been identified to date in vertebrates. To investigate the degree of yan conservation during evolution, we have characterized a yan homologue from a sibling species of D. melanogaster, D. virilis. Our results show that the organization, primary structure and expression pattern of yan are highly conserved. Both genes span over 20 kb and contain four exons with introns at identical positions. The areas with highest amino acid similarity include the Pointed and ETS domain but there are other discrete regions with a high degree of similarity. Phylogenetic analysis reveals that yan's closest relative is the human tel gene, a negative regulator of differentiation in hematopoetic precursors. In both species, Yan is dynamically expressed beginning as early as stage 4/5 and persisting throughout embryogenesis. In third instar larvae, Yan is expressed in and behind the morphogenetic furrow of the eye imaginal disc as well as in the laminar precursor cells of the brain. Ovarian follicle cells also contain Yan protein. Conservation of the structure and expression patterns of yan genes strongly suggests that regulatory mechanisms for their expression are also conserved in these two species.

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.

Areas of high conservation value at risk by plant invaders in Georgia under climate change.

PubMed

Slodowicz, Daniel; Descombes, Patrice; Kikodze, David; Broennimann, Olivier; Müller-Schärer, Heinz

2018-05-01

Invasive alien plants (IAP) are a threat to biodiversity worldwide. Understanding and anticipating invasions allow for more efficient management. In this regard, predicting potential invasion risks by IAPs is essential to support conservation planning into areas of high conservation value (AHCV) such as sites exhibiting exceptional botanical richness, assemblage of rare, and threatened and/or endemic plant species. Here, we identified AHCV in Georgia, a country showing high plant richness, and assessed the susceptibility of these areas to colonization by IAPs under present and future climatic conditions. We used actual protected areas and areas of high plant endemism (identified using occurrences of 114 Georgian endemic plant species) as proxies for AHCV. Then, we assessed present and future potential distribution of 27 IAPs using species distribution models under four climate change scenarios and stacked single-species potential distribution into a consensus map representing IAPs richness. We evaluated present and future invasion risks in AHCV using IAPs richness as a metric of susceptibility. We show that the actual protected areas cover only 9.4% of the areas of high plant endemism in Georgia. IAPs are presently located at lower elevations around the large urban centers and in western Georgia. We predict a shift of IAPs toward eastern Georgia and higher altitudes and an increased susceptibility of AHCV to IAPs under future climate change. Our study provides a good baseline for decision makers and stakeholders on where and how resources should be invested in the most efficient way to protect Georgia's high plant richness from IAPs.

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

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

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

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

High-Throughput Sequencing and Characterization of the Small RNA Transcriptome Reveal Features of Novel and Conserved MicroRNAs in Panax ginseng

PubMed Central

Ma, Yimian; Yuan, Lichai; Lu, Shanfa

2012-01-01

microRNAs (miRNAs) play vital regulatory roles in many organisms through direct cleavage of transcripts, translational repression, or chromatin modification. Identification of miRNAs has been carried out in various plant species. However, no information is available for miRNAs from Panax ginseng, an economically significant medicinal plant species. Using the next generation high-throughput sequencing technology, we obtained 13,326,328 small RNA reads from the roots, stems, leaves and flowers of P. ginseng. Analysis of these small RNAs revealed the existence of a large, diverse and highly complicated small RNA population in P. ginseng. We identified 73 conserved miRNAs, which could be grouped into 33 families, and 28 non-conserved ones belonging to 9 families. Characterization of P. ginseng miRNA precursors revealed many features, such as production of two miRNAs from distinct regions of a precursor, clusters of two precursors in a transcript, and generation of miRNAs from both sense and antisense transcripts. It suggests the complexity of miRNA production in P. gingseng. Using a computational approach, we predicted for the conserved and non-conserved miRNA families 99 and 31 target genes, respectively, of which eight were experimentally validated. Among all predicted targets, only about 20% are conserved among various plant species, whereas the others appear to be non-conserved, indicating the diversity of miRNA functions. Consistently, many miRNAs exhibited tissue-specific expression patterns. Moreover, we identified five dehydration- and ten heat-responsive miRNAs and found the existence of a crosstalk among some of the stress-responsive miRNAs. Our results provide the first clue to the elucidation of miRNA functions in P. ginseng. PMID:22962612

Conservative Management of Urinary Incontinence in Women

PubMed Central

Faiena, Izak; Patel, Neal; Parihar, Jaspreet S; Calabrese, Marc; Tunuguntla, Hari

2015-01-01

Urinary incontinence in women has a high prevalence and causes significant morbidity. Given that urinary incontinence is not generally a progressive disease, conservative therapies play an integral part in the management of these patients. We conducted a nonsystematic review of the literature to identify high-quality studies that evaluated the different components of conservative management of stress urinary incontinence, including behavioral therapy, bladder training, pelvic floor muscle training, lifestyle changes, mechanical devices, vaginal cones, and electrical stimulation. Urinary incontinence can have a severe impact on our healthcare system and patients’ quality of life. There are currently a wide variety of treatment options for these patients, ranging from conservative treatment to surgical treatment. Although further research is required in the area of conservative therapies, nonsurgical treatments are effective and are preferred by some patients. PMID:26543427

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

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.

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…

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

Community Markets for Conservation (COMACO) links biodiversity conservation with sustainable improvements in livelihoods and food production

PubMed Central

Lewis, Dale; Bell, Samuel D.; Fay, John; Bothi, Kim L.; Gatere, Lydiah; Kabila, Makando; Mukamba, Mwangala; Matokwani, Edwin; Mushimbalume, Matthews; Moraru, Carmen I.; Lehmann, Johannes; Lassoie, James; Wolfe, David; Lee, David R.; Buck, Louise; Travis, Alexander J.

2011-01-01

In the Luangwa Valley, Zambia, persistent poverty and hunger present linked challenges to rural development and biodiversity conservation. Both household coping strategies and larger-scale economic development efforts have caused severe natural resource degradation that limits future economic opportunities and endangers ecosystem services. A model based on a business infrastructure has been developed to promote and maintain sustainable agricultural and natural resource management practices, leading to direct and indirect conservation outcomes. The Community Markets for Conservation (COMACO) model operates primarily with communities surrounding national parks, strengthening conservation benefits produced by these protected areas. COMACO first identifies the least food-secure households and trains them in sustainable agricultural practices that minimize threats to natural resources while meeting household needs. In addition, COMACO identifies people responsible for severe natural resource depletion and trains them to generate alternative income sources. In an effort to maintain compliance with these practices, COMACO provides extension support and access to high-value markets that would otherwise be inaccessible to participants. Because the model is continually evolving via adaptive management, success or failure of the model as a whole is difficult to quantify at this early stage. We therefore test specific hypotheses and present data documenting the stabilization of previously declining wildlife populations; the meeting of thresholds of productivity that give COMACO access to stable, high-value markets and progress toward economic self-sufficiency; and the adoption of sustainable agricultural practices by participants and other community members. Together, these findings describe a unique, business-oriented model for poverty alleviation, food production, and biodiversity conservation. PMID:21873184

Community Markets for Conservation (COMACO) links biodiversity conservation with sustainable improvements in livelihoods and food production.

PubMed

Lewis, Dale; Bell, Samuel D; Fay, John; Bothi, Kim L; Gatere, Lydiah; Kabila, Makando; Mukamba, Mwangala; Matokwani, Edwin; Mushimbalume, Matthews; Moraru, Carmen I; Lehmann, Johannes; Lassoie, James; Wolfe, David; Lee, David R; Buck, Louise; Travis, Alexander J

2011-08-23

In the Luangwa Valley, Zambia, persistent poverty and hunger present linked challenges to rural development and biodiversity conservation. Both household coping strategies and larger-scale economic development efforts have caused severe natural resource degradation that limits future economic opportunities and endangers ecosystem services. A model based on a business infrastructure has been developed to promote and maintain sustainable agricultural and natural resource management practices, leading to direct and indirect conservation outcomes. The Community Markets for Conservation (COMACO) model operates primarily with communities surrounding national parks, strengthening conservation benefits produced by these protected areas. COMACO first identifies the least food-secure households and trains them in sustainable agricultural practices that minimize threats to natural resources while meeting household needs. In addition, COMACO identifies people responsible for severe natural resource depletion and trains them to generate alternative income sources. In an effort to maintain compliance with these practices, COMACO provides extension support and access to high-value markets that would otherwise be inaccessible to participants. Because the model is continually evolving via adaptive management, success or failure of the model as a whole is difficult to quantify at this early stage. We therefore test specific hypotheses and present data documenting the stabilization of previously declining wildlife populations; the meeting of thresholds of productivity that give COMACO access to stable, high-value markets and progress toward economic self-sufficiency; and the adoption of sustainable agricultural practices by participants and other community members. Together, these findings describe a unique, business-oriented model for poverty alleviation, food production, and biodiversity conservation.

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/.

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.

Targeted carbon conservation at national scales with high-resolution monitoring

PubMed Central

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

2014-01-01

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

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

PubMed

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

2014-11-25

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

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.

A stewardship approach to grassland bird habitat conservation in Saskatchewan, Canada

Treesearch

Stephen K. Davis; Bob Springer; Jennifer Lohmeyer; Lesley Hall; Tom Harrison

2005-01-01

Saskatchewan provides habitat for a number of grassland specialists that are of high conservation concern. For example, 10 of 12 “primary endemic,” and 17 of 25 “secondary endemic” species of the Great Plains identified by Mengel (1970) regularly breed in Saskatchewan. In addition, each of the 30 species of high conservation...

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,...

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.

Threats from urban expansion, agricultural transformation and forest loss on global conservation priority areas.

PubMed

Veach, Victoria; Moilanen, Atte; Di Minin, Enrico

2017-01-01

Including threats in spatial conservation prioritization helps identify areas for conservation actions where biodiversity is at imminent risk of extinction. At the global level, an important limitation when identifying spatial priorities for conservation actions is the lack of information on the spatial distribution of threats. Here, we identify spatial conservation priorities under three prominent threats to biodiversity (residential and commercial development, agricultural expansion, and forest loss), which are primary drivers of habitat loss and threaten the persistence of the highest number of species in the International Union for the Conservation of Nature (IUCN) Red List, and for which spatial data is available. We first explore how global priority areas for the conservation of vertebrate (mammals, birds, and amphibians) species coded in the Red List as vulnerable to each threat differ spatially. We then identify spatial conservation priorities for all species vulnerable to all threats. Finally, we identify the potentially most threatened areas by overlapping the identified priority areas for conservation with maps for each threat. We repeat the same with four other well-known global conservation priority area schemes, namely Key Biodiversity Areas, Biodiversity Hotspots, the global Protected Area Network, and Wilderness Areas. We find that residential and commercial development directly threatens only about 4% of the global top 17% priority areas for species vulnerable under this threat. However, 50% of the high priority areas for species vulnerable to forest loss overlap with areas that have already experienced some forest loss. Agricultural expansion overlapped with ~20% of high priority areas. Biodiversity Hotspots had the greatest proportion of their total area under direct threat from all threats, while expansion of low intensity agriculture was found to pose an imminent threat to Wilderness Areas under future agricultural expansion. Our results

Threats from urban expansion, agricultural transformation and forest loss on global conservation priority areas

PubMed Central

Moilanen, Atte; Di Minin, Enrico

2017-01-01

Including threats in spatial conservation prioritization helps identify areas for conservation actions where biodiversity is at imminent risk of extinction. At the global level, an important limitation when identifying spatial priorities for conservation actions is the lack of information on the spatial distribution of threats. Here, we identify spatial conservation priorities under three prominent threats to biodiversity (residential and commercial development, agricultural expansion, and forest loss), which are primary drivers of habitat loss and threaten the persistence of the highest number of species in the International Union for the Conservation of Nature (IUCN) Red List, and for which spatial data is available. We first explore how global priority areas for the conservation of vertebrate (mammals, birds, and amphibians) species coded in the Red List as vulnerable to each threat differ spatially. We then identify spatial conservation priorities for all species vulnerable to all threats. Finally, we identify the potentially most threatened areas by overlapping the identified priority areas for conservation with maps for each threat. We repeat the same with four other well-known global conservation priority area schemes, namely Key Biodiversity Areas, Biodiversity Hotspots, the global Protected Area Network, and Wilderness Areas. We find that residential and commercial development directly threatens only about 4% of the global top 17% priority areas for species vulnerable under this threat. However, 50% of the high priority areas for species vulnerable to forest loss overlap with areas that have already experienced some forest loss. Agricultural expansion overlapped with ~20% of high priority areas. Biodiversity Hotspots had the greatest proportion of their total area under direct threat from all threats, while expansion of low intensity agriculture was found to pose an imminent threat to Wilderness Areas under future agricultural expansion. Our results

An effective approach for annotation of protein families with low sequence similarity and conserved motifs: identifying GDSL hydrolases across the plant kingdom.

PubMed

Vujaklija, Ivan; Bielen, Ana; Paradžik, Tina; Biđin, Siniša; Goldstein, Pavle; Vujaklija, Dušica

2016-02-18

The massive accumulation of protein sequences arising from the rapid development of high-throughput sequencing, coupled with automatic annotation, results in high levels of incorrect annotations. In this study, we describe an approach to decrease annotation errors of protein families characterized by low overall sequence similarity. The GDSL lipolytic family comprises proteins with multifunctional properties and high potential for pharmaceutical and industrial applications. The number of proteins assigned to this family has increased rapidly over the last few years. In particular, the natural abundance of GDSL enzymes reported recently in plants indicates that they could be a good source of novel GDSL enzymes. We noticed that a significant proportion of annotated sequences lack specific GDSL motif(s) or catalytic residue(s). Here, we applied motif-based sequence analyses to identify enzymes possessing conserved GDSL motifs in selected proteomes across the plant kingdom. Motif-based HMM scanning (Viterbi decoding-VD and posterior decoding-PD) and the here described PD/VD protocol were successfully applied on 12 selected plant proteomes to identify sequences with GDSL motifs. A significant number of identified GDSL sequences were novel. Moreover, our scanning approach successfully detected protein sequences lacking at least one of the essential motifs (171/820) annotated by Pfam profile search (PfamA) as GDSL. Based on these analyses we provide a curated list of GDSL enzymes from the selected plants. CLANS clustering and phylogenetic analysis helped us to gain a better insight into the evolutionary relationship of all identified GDSL sequences. Three novel GDSL subfamilies as well as unreported variations in GDSL motifs were discovered in this study. In addition, analyses of selected proteomes showed a remarkable expansion of GDSL enzymes in the lycophyte, Selaginella moellendorffii. Finally, we provide a general motif-HMM scanner which is easily accessible through

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.

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

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.

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...

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

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

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...

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

Comparative interactomics: analysis of arabidopsis 14-3-3 complexes reveals highly conserved 14-3-3 interactions between humans and plants.

PubMed

Paul, Anna-Lisa; Liu, Li; McClung, Scott; Laughner, Beth; Chen, Sixue; Ferl, Robert J

2009-04-01

As a first step in the broad characterization of plant 14-3-3 multiprotein complexes in vivo, stringent and specific antibody affinity purification was used to capture 14-3-3s together with their interacting proteins from extracts of Arabidopsis cell suspension cultures. Approximately 120 proteins were identified as potential in vivo 14-3-3 interacting proteins by mass spectrometry of the recovered complexes. Comparison of the proteins in this data set with the 14-3-3 interacting proteins from a similar study in human embryonic kidney cell cultures revealed eight interacting proteins that likely represent reasonably abundant, fundamental 14-3-3 interaction complexes that are highly conserved across all eukaryotes. The Arabidopsis 14-3-3 interaction data set was also compared to a yeast in vivo 14-3-3 interaction data set. Four 14-3-3 interacting proteins are conserved in yeast, humans, and Arabidopsis. Comparisons of the data sets based on biochemical function revealed many additional similarities in the human and Arabidopsis data sets that represent conserved functional interactions, while also leaving many proteins uniquely identified in either Arabidopsis or human cells. In particular, the Arabidopsis interaction data set is enriched for proteins involved in metabolism.

Equity trade-offs in conservation decision making.

PubMed

Law, Elizabeth A; Bennett, Nathan J; Ives, Christopher D; Friedman, Rachel; Davis, Katrina J; Archibald, Carla; Wilson, Kerrie A

2018-04-01

Conservation decisions increasingly involve multiple environmental and social objectives, which result in complex decision contexts with high potential for trade-offs. Improving social equity is one such objective that is often considered an enabler of successful outcomes and a virtuous ideal in itself. Despite its idealized importance in conservation policy, social equity is often highly simplified or ill-defined and is applied uncritically. What constitutes equitable outcomes and processes is highly normative and subject to ethical deliberation. Different ethical frameworks may lead to different conceptions of equity through alternative perspectives of what is good or right. This can lead to different and potentially conflicting equity objectives in practice. We promote a more transparent, nuanced, and pluralistic conceptualization of equity in conservation decision making that particularly recognizes where multidimensional equity objectives may conflict. To help identify and mitigate ethical conflicts and avoid cases of good intentions producing bad outcomes, we encourage a more analytical incorporation of equity into conservation decision making particularly during mechanistic integration of equity objectives. We recommend that in conservation planning motivations and objectives for equity be made explicit within the problem context, methods used to incorporate equity objectives be applied with respect to stated objectives, and, should objectives dictate, evaluation of equity outcomes and adaptation of strategies be employed during policy implementation. © 2017 Society for Conservation Biology.

Enhancing Conservation with High Resolution Productivity Datasets for the Conterminous United States

NASA Astrophysics Data System (ADS)

Robinson, Nathaniel Paul

Human driven alteration of the earth's terrestrial surface is accelerating through land use changes, intensification of human activity, climate change, and other anthropogenic pressures. These changes occur at broad spatio-temporal scales, challenging our ability to effectively monitor and assess the impacts and subsequent conservation strategies. While satellite remote sensing (SRS) products enable monitoring of the earth's terrestrial surface continuously across space and time, the practical applications for conservation and management of these products are limited. Often the processes driving ecological change occur at fine spatial resolutions and are undetectable given the resolution of available datasets. Additionally, the links between SRS data and ecologically meaningful metrics are weak. Recent advances in cloud computing technology along with the growing record of high resolution SRS data enable the development of SRS products that quantify ecologically meaningful variables at relevant scales applicable for conservation and management. The focus of my dissertation is to improve the applicability of terrestrial gross and net primary productivity (GPP/NPP) datasets for the conterminous United States (CONUS). In chapter one, I develop a framework for creating high resolution datasets of vegetation dynamics. I use the entire archive of Landsat 5, 7, and 8 surface reflectance data and a novel gap filling approach to create spatially continuous 30 m, 16-day composites of the normalized difference vegetation index (NDVI) from 1986 to 2016. In chapter two, I integrate this with other high resolution datasets and the MOD17 algorithm to create the first high resolution GPP and NPP datasets for CONUS. I demonstrate the applicability of these products for conservation and management, showing the improvements beyond currently available products. In chapter three, I utilize this dataset to evaluate the relationships between land ownership and terrestrial production

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.

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.

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

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

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

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...

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.

Genetic diversity and genetic structure of an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified agricultural landscape: implications for conservation.

PubMed

Sunny, Armando; Monroy-Vilchis, Octavio; Zarco-González, Martha M; Mendoza-Martínez, Germán David; Martínez-Gómez, Daniel

2015-12-01

It is necessary to determine genetic diversity of fragmented populations in highly modified landscapes to understand how populations respond to land-use change. This information will help guide future conservation and management strategies. We conducted a population genetic study on an endemic Mexican Dusky Rattlesnake (Crotalus triseriatus) in a highly modified landscape near the Toluca metropolitan area, in order to provide crucial information for the conservation of this species. There was medium levels of genetic diversity, with a few alleles and genotypes. We identified three genetically differentiated clusters, likely as a result of different habitat cover type. We also found evidence of an ancestral genetic bottleneck and medium values of effective population size. Inbreeding coefficients were low and there was a moderate gene flow. Our results can be used as a basis for future research and C. triseriatus conservation efforts, particularly considering that the Trans-Mexican Volcanic Belt is heavily impacted by destructive land-use practices.

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.

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

Conservative Management for Stable High Ankle Injuries in Professional Football Players.

PubMed

Knapik, Derrick M; Trem, Anthony; Sheehan, Joseph; Salata, Michael J; Voos, James E

High ankle "syndesmosis" injuries are common in American football players relative to the general population. At the professional level, syndesmotic sprains represent a challenging and unique injury lacking a standardized rehabilitation protocol during conservative management. PubMed, Biosis Preview, SPORTDiscus, PEDro, and EMBASE databases were searched using the terms syndesmotic injuries, American football, conservative management, and rehabilitation. Clinical review. Level 3. When compared with lateral ankle sprains, syndesmosis injuries result in significantly prolonged recovery times and games lost. For stable syndesmotic injuries, conservative management features a brief period of immobilization and protected weightbearing followed by progressive strengthening exercises and running, and athletes can expect to return to competition in 2 to 6 weeks. Further research investigating the efficacy of dry needling and blood flow restriction therapy is necessary to evaluate the benefit of these techniques in the rehabilitation process. Successful conservative management of stable syndesmotic injuries in professional American football athletes requires a thorough understanding of the anatomy, injury mechanisms, diagnosis, and rehabilitation strategies utilized in elite athletes.

Conservation agriculture in high tunnels: soil health and profit enhancement

USDA-ARS?s Scientific Manuscript database

In 2013, through the USDA’s Evans-Allen capacity grant, the high tunnel became an on-farm research laboratory for conservation agriculture. Dr. Manuel R. Reyes, Professor and his research team from the North Carolina Agriculture and Technology State University (NCATSU), Greensboro, North Carolina (1...

Proteomic Analysis of Pathogenic Fungi Reveals Highly Expressed Conserved Cell Wall Proteins

PubMed Central

Champer, Jackson; Ito, James I.; Clemons, Karl V.; Stevens, David A.; Kalkum, Markus

2016-01-01

We are presenting a quantitative proteomics tally of the most commonly expressed conserved fungal proteins of the cytosol, the cell wall, and the secretome. It was our goal to identify fungi-typical proteins that do not share significant homology with human proteins. Such fungal proteins are of interest to the development of vaccines or drug targets. Protein samples were derived from 13 fungal species, cultured in rich or in minimal media; these included clinical isolates of Aspergillus, Candida, Mucor, Cryptococcus, and Coccidioides species. Proteomes were analyzed by quantitative MSE (Mass Spectrometry—Elevated Collision Energy). Several thousand proteins were identified and quantified in total across all fractions and culture conditions. The 42 most abundant proteins identified in fungal cell walls or supernatants shared no to very little homology with human proteins. In contrast, all but five of the 50 most abundant cytosolic proteins had human homologs with sequence identity averaging 59%. Proteomic comparisons of the secreted or surface localized fungal proteins highlighted conserved homologs of the Aspergillus fumigatus proteins 1,3-β-glucanosyltransferases (Bgt1, Gel1-4), Crf1, Ecm33, EglC, and others. The fact that Crf1 and Gel1 were previously shown to be promising vaccine candidates, underlines the value of the proteomics data presented here. PMID:26878023

Identifying missing dictionary entries with frequency-conserving context models.

PubMed

Williams, Jake Ryland; Clark, Eric M; Bagrow, James P; Danforth, Christopher M; Dodds, Peter Sheridan

2015-10-01

In an effort to better understand meaning from natural language texts, we explore methods aimed at organizing lexical objects into contexts. A number of these methods for organization fall into a family defined by word ordering. Unlike demographic or spatial partitions of data, these collocation models are of special importance for their universal applicability. While we are interested here in text and have framed our treatment appropriately, our work is potentially applicable to other areas of research (e.g., speech, genomics, and mobility patterns) where one has ordered categorical data (e.g., sounds, genes, and locations). Our approach focuses on the phrase (whether word or larger) as the primary meaning-bearing lexical unit and object of study. To do so, we employ our previously developed framework for generating word-conserving phrase-frequency data. Upon training our model with the Wiktionary, an extensive, online, collaborative, and open-source dictionary that contains over 100000 phrasal definitions, we develop highly effective filters for the identification of meaningful, missing phrase entries. With our predictions we then engage the editorial community of the Wiktionary and propose short lists of potential missing entries for definition, developing a breakthrough, lexical extraction technique and expanding our knowledge of the defined English lexicon of phrases.

Identifying missing dictionary entries with frequency-conserving context models

NASA Astrophysics Data System (ADS)

Williams, Jake Ryland; Clark, Eric M.; Bagrow, James P.; Danforth, Christopher M.; Dodds, Peter Sheridan

2015-10-01

In an effort to better understand meaning from natural language texts, we explore methods aimed at organizing lexical objects into contexts. A number of these methods for organization fall into a family defined by word ordering. Unlike demographic or spatial partitions of data, these collocation models are of special importance for their universal applicability. While we are interested here in text and have framed our treatment appropriately, our work is potentially applicable to other areas of research (e.g., speech, genomics, and mobility patterns) where one has ordered categorical data (e.g., sounds, genes, and locations). Our approach focuses on the phrase (whether word or larger) as the primary meaning-bearing lexical unit and object of study. To do so, we employ our previously developed framework for generating word-conserving phrase-frequency data. Upon training our model with the Wiktionary, an extensive, online, collaborative, and open-source dictionary that contains over 100 000 phrasal definitions, we develop highly effective filters for the identification of meaningful, missing phrase entries. With our predictions we then engage the editorial community of the Wiktionary and propose short lists of potential missing entries for definition, developing a breakthrough, lexical extraction technique and expanding our knowledge of the defined English lexicon of phrases.

High order entropy conservative central schemes for wide ranges of compressible gas dynamics and MHD flows

NASA Astrophysics Data System (ADS)

Sjögreen, Björn; Yee, H. C.

2018-07-01

The Sjogreen and Yee [31] high order entropy conservative numerical method for compressible gas dynamics is extended to include discontinuities and also extended to equations of ideal magnetohydrodynamics (MHD). The basic idea is based on Tadmor's [40] original work for inviscid perfect gas flows. For the MHD four formulations of the MHD are considered: (a) the conservative MHD, (b) the Godunov [14] non-conservative form, (c) the Janhunen [19] - MHD with magnetic field source terms, and (d) a MHD with source terms by Brackbill and Barnes [5]. Three forms of the high order entropy numerical fluxes for the MHD in the finite difference framework are constructed. They are based on the extension of the low order form of Chandrashekar and Klingenberg [9], and two forms with modifications of the Winters and Gassner [49] numerical fluxes. For flows containing discontinuities and multiscale turbulence fluctuations the high order entropy conservative numerical fluxes as the new base scheme under the Yee and Sjogreen [31] and Kotov et al. [21,22] high order nonlinear filter approach is developed. The added nonlinear filter step on the high order centered entropy conservative spatial base scheme is only utilized at isolated computational regions, while maintaining high accuracy almost everywhere for long time integration of unsteady flows and DNS and LES of turbulence computations. Representative test cases for both smooth flows and problems containing discontinuities for the gas dynamics and the ideal MHD are included. The results illustrate the improved stability by using the high order entropy conservative numerical flux as the base scheme instead of the pure high order central scheme.

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

NASA Technical Reports Server (NTRS)

Fisher, Travis C.; Carpenter, Mark H.

2013-01-01

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

Cross-cohort analysis identifies a TEAD4 ↔ MYCN positive-feedback loop as the core regulatory element of high-risk neuroblastoma. | Office of Cancer Genomics

Cancer.gov

High-risk neuroblastomas show a paucity of recurrent somatic mutations at diagnosis. As a result, the molecular basis for this aggressive phenotype remains elusive. Recent progress in regulatory network analysis helped us elucidate disease-driving mechanisms downstream of genomic alterations, including recurrent chromosomal alterations. Our analysis identified three molecular subtypes of high-risk neuroblastomas, consistent with chromosomal alterations, and identified subtype-specific master regulator (MR) proteins that were conserved across independent cohorts.

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

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

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.

77 FR 11785 - Energy Conservation Program: Public Meeting and Availability of the Framework Document for High...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-28

... Conservation Program: Public Meeting and Availability of the Framework Document for High-Intensity Discharge...) is initiating the rulemaking and data collection process to consider establishing energy conservation... Policy and Conservation Act (EPCA) (42 U.S.C. 6291, et seq.; EPCA or ``the Act'') sets forth a variety of...

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

NASA Technical Reports Server (NTRS)

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

1999-01-01

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

Evolutionary growth process of highly conserved sequences in vertebrate genomes.

PubMed

Ishibashi, Minaka; Noda, Akiko Ogura; Sakate, Ryuichi; Imanishi, Tadashi

2012-08-01

Genome sequence comparison between evolutionarily distant species revealed ultraconserved elements (UCEs) among mammals under strong purifying selection. Most of them were also conserved among vertebrates. Because they tend to be located in the flanking regions of developmental genes, they would have fundamental roles in creating vertebrate body plans. However, the evolutionary origin and selection mechanism of these UCEs remain unclear. Here we report that UCEs arose in primitive vertebrates, and gradually grew in vertebrate evolution. We searched for UCEs in two teleost fishes, Tetraodon nigroviridis and Oryzias latipes, and found 554 UCEs with 100% identity over 100 bps. Comparison of teleost and mammalian UCEs revealed 43 pairs of common, jawed-vertebrate UCEs (jUCE) with high sequence identities, ranging from 83.1% to 99.2%. Ten of them retain lower similarities to the Petromyzon marinus genome, and the substitution rates of four non-exonic jUCEs were reduced after the teleost-mammal divergence, suggesting that robust conservation had been acquired in the jawed vertebrate lineage. Our results indicate that prototypical UCEs originated before the divergence of jawed and jawless vertebrates and have been frozen as perfect conserved sequences in the jawed vertebrate lineage. In addition, our comparative sequence analyses of UCEs and neighboring regions resulted in a discovery of lineage-specific conserved sequences. They were added progressively to prototypical UCEs, suggesting step-wise acquisition of novel regulatory roles. Our results indicate that conserved non-coding elements (CNEs) consist of blocks with distinct evolutionary history, each having been frozen since different evolutionary era along the vertebrate lineage. Copyright © 2012 Elsevier B.V. All rights reserved.

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

Genome-wide identification of conserved intronic non-coding sequences using a Bayesian segmentation approach.

PubMed

Algama, Manjula; Tasker, Edward; Williams, Caitlin; Parslow, Adam C; Bryson-Richardson, Robert J; Keith, Jonathan M

2017-03-27

Computational identification of non-coding RNAs (ncRNAs) is a challenging problem. We describe a genome-wide analysis using Bayesian segmentation to identify intronic elements highly conserved between three evolutionarily distant vertebrate species: human, mouse and zebrafish. We investigate the extent to which these elements include ncRNAs (or conserved domains of ncRNAs) and regulatory sequences. We identified 655 deeply conserved intronic sequences in a genome-wide analysis. We also performed a pathway-focussed analysis on genes involved in muscle development, detecting 27 intronic elements, of which 22 were not detected in the genome-wide analysis. At least 87% of the genome-wide and 70% of the pathway-focussed elements have existing annotations indicative of conserved RNA secondary structure. The expression of 26 of the pathway-focused elements was examined using RT-PCR, providing confirmation that they include expressed ncRNAs. Consistent with previous studies, these elements are significantly over-represented in the introns of transcription factors. This study demonstrates a novel, highly effective, Bayesian approach to identifying conserved non-coding sequences. Our results complement previous findings that these sequences are enriched in transcription factors. However, in contrast to previous studies which suggest the majority of conserved sequences are regulatory factor binding sites, the majority of conserved sequences identified using our approach contain evidence of conserved RNA secondary structures, and our laboratory results suggest most are expressed. Functional roles at DNA and RNA levels are not mutually exclusive, and many of our elements possess evidence of both. Moreover, ncRNAs play roles in transcriptional and post-transcriptional regulation, and this may contribute to the over-representation of these elements in introns of transcription factors. We attribute the higher sensitivity of the pathway-focussed analysis compared to the genome

Highly conserved small subunit residues influence rubisco large subunit catalysis.

PubMed

Genkov, Todor; Spreitzer, Robert J

2009-10-30

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

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

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.

Genome-Wide Identification of Evolutionarily Conserved Alternative Splicing Events in Flowering Plants

PubMed Central

Chamala, Srikar; Feng, Guanqiao; Chavarro, Carolina; Barbazuk, W. Brad

2015-01-01

Alternative splicing (AS) plays important roles in many plant functions, but its conservation across the plant kingdom is not known. We describe a methodology to identify AS events and identify conserved AS events across large phylogenetic distances using RNA-Seq datasets. We applied this methodology to transcriptome data from nine angiosperms including Amborella, the single sister species to all other extant flowering plants. AS events within 40–70% of the expressed multi-exonic genes per species were found, 27,120 of which are conserved among two or more of the taxa studied. While many events are species specific, many others are shared across long evolutionary distances suggesting they have functional significance. Conservation of AS event data provides an estimate of the number of ancestral AS events present at each node of the tree representing the nine species studied. Furthermore, the presence or absence of AS isoforms between species with different whole genome duplication (WGD) histories provides the opportunity to examine the impact of WDG on AS potential. Examining AS in gene families identifies those with high rates of AS, and conservation can distinguish ancient events vs. recent or species specific adaptations. The MADS-box and SR protein families are found to represent families with low and high occurrences of AS, respectively, yet their AS events were likely present in the MRCA of angiosperms. PMID:25859541

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...

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.

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

Constraints of philanthropy on determining the distribution of biodiversity conservation funding.

PubMed

Larson, Eric R; Howell, Stephen; Kareiva, Peter; Armsworth, Paul R

2016-02-01

Caught between ongoing habitat destruction and funding shortfalls, conservation organizations are using systematic planning approaches to identify places that offer the highest biodiversity return per dollar invested. However, available tools do not account for the landscape of funding for conservation or quantify the constraints this landscape imposes on conservation outcomes. Using state-level data on philanthropic giving to and investments in land conservation by a large nonprofit organization, we applied linear regression to evaluate whether the spatial distribution of conservation philanthropy better explained expenditures on conservation than maps of biodiversity priorities, which were derived from a planning process internal to the organization and return on investment (ROI) analyses based on data on species richness, land costs, and existing protected areas. Philanthropic fund raising accounted for considerably more spatial variation in conservation spending (r(2) = 0.64) than either of the 2 systematic conservation planning approaches (r(2) = 0.08-0.21). We used results of one of the ROI analyses to evaluate whether increases in flexibility to reallocate funding across space provides conservation gains. Small but plausible "tax" increments of 1-10% on states redistributed to the optimal funding allocation from the ROI analysis could result in gains in endemic species protected of 8.5-80.2%. When such increases in spatial flexibility are not possible, conservation organizations should seek to cultivate increased support for conservation in priority locations. We used lagged correlations of giving to and spending by the organization to evaluate whether investments in habitat protection stimulate future giving to conservation. The most common outcome at the state level was that conservation spending quarters correlated significantly and positively with lagged fund raising quarters. In effect, periods of high fund raising for biodiversity followed (rather than

A strategy for detecting the conservation of folding-nucleus residues in protein superfamilies.

PubMed

Michnick, S W; Shakhnovich, E

1998-01-01

Nucleation-growth theory predicts that fast-folding peptide sequences fold to their native structure via structures in a transition-state ensemble that share a small number of native contacts (the folding nucleus). Experimental and theoretical studies of proteins suggest that residues participating in folding nuclei are conserved among homologs. We attempted to determine if this is true in proteins with highly diverged sequences but identical folds (superfamilies). We describe a strategy based on comparisons of residue conservation in natural superfamily sequences with simulated sequences (generated with a Monte-Carlo sequence design strategy) for the same proteins. The basic assumptions of the strategy were that natural sequences will conserve residues needed for folding and stability plus function, the simulated sequences contain no functional conservation, and nucleus residues make native contacts with each other. Based on these assumptions, we identified seven potential nucleus residues in ubiquitin superfamily members. Non-nucleus conserved residues were also identified; these are proposed to be involved in stabilizing native interactions. We found that all superfamily members conserved the same potential nucleus residue positions, except those for which the structural topology is significantly different. Our results suggest that the conservation of the nucleus of a specific fold can be predicted by comparing designed simulated sequences with natural highly diverged sequences that fold to the same structure. We suggest that such a strategy could be used to help plan protein folding and design experiments, to identify new superfamily members, and to subdivide superfamilies further into classes having a similar folding mechanism.

Improving effectiveness of systematic conservation planning with density data.

PubMed

Veloz, Samuel; Salas, Leonardo; Altman, Bob; Alexander, John; Jongsomjit, Dennis; Elliott, Nathan; Ballard, Grant

2015-08-01

Systematic conservation planning aims to design networks of protected areas that meet conservation goals across large landscapes. The optimal design of these conservation networks is most frequently based on the modeled habitat suitability or probability of occurrence of species, despite evidence that model predictions may not be highly correlated with species density. We hypothesized that conservation networks designed using species density distributions more efficiently conserve populations of all species considered than networks designed using probability of occurrence models. To test this hypothesis, we used the Zonation conservation prioritization algorithm to evaluate conservation network designs based on probability of occurrence versus density models for 26 land bird species in the U.S. Pacific Northwest. We assessed the efficacy of each conservation network based on predicted species densities and predicted species diversity. High-density model Zonation rankings protected more individuals per species when networks protected the highest priority 10-40% of the landscape. Compared with density-based models, the occurrence-based models protected more individuals in the lowest 50% priority areas of the landscape. The 2 approaches conserved species diversity in similar ways: predicted diversity was higher in higher priority locations in both conservation networks. We conclude that both density and probability of occurrence models can be useful for setting conservation priorities but that density-based models are best suited for identifying the highest priority areas. Developing methods to aggregate species count data from unrelated monitoring efforts and making these data widely available through ecoinformatics portals such as the Avian Knowledge Network will enable species count data to be more widely incorporated into systematic conservation planning efforts. © 2015, Society for Conservation Biology.

Dynamic conservation of forest genetic resources in 33 European countries.

PubMed

Lefèvre, François; Koskela, Jarkko; Hubert, Jason; Kraigher, Hojka; Longauer, Roman; Olrik, Ditte C; Schüler, Silvio; Bozzano, Michele; Alizoti, Paraskevi; Bakys, Remigijus; Baldwin, Cathleen; Ballian, Dalibor; Black-Samuelsson, Sanna; Bednarova, Dagmar; Bordács, Sándor; Collin, Eric; de Cuyper, Bart; de Vries, Sven M G; Eysteinsson, Thröstur; Frýdl, Josef; Haverkamp, Michaela; Ivankovic, Mladen; Konrad, Heino; Koziol, Czesław; Maaten, Tiit; Notivol Paino, Eduardo; Oztürk, Hikmet; Pandeva, Ivanova Denitsa; Parnuta, Gheorghe; Pilipovič, Andrej; Postolache, Dragos; Ryan, Cathal; Steffenrem, Arne; Varela, Maria Carolina; Vessella, Federico; Volosyanchuk, Roman T; Westergren, Marjana; Wolter, Frank; Yrjänä, Leena; Zariŋa, Inga

2013-04-01

Dynamic conservation of forest genetic resources (FGR) means maintaining the genetic diversity of trees within an evolutionary process and allowing generation turnover in the forest. We assessed the network of forests areas managed for the dynamic conservation of FGR (conservation units) across Europe (33 countries). On the basis of information available in the European Information System on FGR (EUFGIS Portal), species distribution maps, and environmental stratification of the continent, we developed ecogeographic indicators, a marginality index, and demographic indicators to assess and monitor forest conservation efforts. The pan-European network has 1967 conservation units, 2737 populations of target trees, and 86 species of target trees. We detected a poor coincidence between FGR conservation and other biodiversity conservation objectives within this network. We identified 2 complementary strategies: a species-oriented strategy in which national conservation networks are specifically designed for key target species and a site-oriented strategy in which multiple-target units include so-called secondary species conserved within a few sites. The network is highly unbalanced in terms of species representation, and 7 key target species are conserved in 60% of the conservation units. We performed specific gap analyses for 11 tree species, including assessment of ecogeographic, demographic, and genetic criteria. For each species, we identified gaps, particularly in the marginal parts of their distribution range, and found multiple redundant conservation units in other areas. The Mediterranean forests and to a lesser extent the boreal forests are underrepresented. Monitoring the conservation efficiency of each unit remains challenging; however, <2% of the conserved populations seem to be at risk of extinction. On the basis of our results, we recommend combining species-oriented and site-oriented strategies. © 2012 Society for Conservation Biology.

Targeting global conservation funding to limit immediate biodiversity declines

PubMed Central

Waldron, Anthony; Mooers, Arne O.; Miller, Daniel C.; Nibbelink, Nate; Redding, David; Kuhn, Tyler S.; Roberts, J. Timmons; Gittleman, John L.

2013-01-01

Inadequate funding levels are a major impediment to effective global biodiversity conservation and are likely associated with recent failures to meet United Nations biodiversity targets. Some countries are more severely underfunded than others and therefore represent urgent financial priorities. However, attempts to identify these highly underfunded countries have been hampered for decades by poor and incomplete data on actual spending, coupled with uncertainty and lack of consensus over the relative size of spending gaps. Here, we assemble a global database of annual conservation spending. We then develop a statistical model that explains 86% of variation in conservation expenditures, and use this to identify countries where funding is robustly below expected levels. The 40 most severely underfunded countries contain 32% of all threatened mammalian diversity and include neighbors in some of the world’s most biodiversity-rich areas (Sundaland, Wallacea, and Near Oceania). However, very modest increases in international assistance would achieve a large improvement in the relative adequacy of global conservation finance. Our results could therefore be quickly applied to limit immediate biodiversity losses at relatively little cost. PMID:23818619

Targeting global conservation funding to limit immediate biodiversity declines.

PubMed

Waldron, Anthony; Mooers, Arne O; Miller, Daniel C; Nibbelink, Nate; Redding, David; Kuhn, Tyler S; Roberts, J Timmons; Gittleman, John L

2013-07-16

Inadequate funding levels are a major impediment to effective global biodiversity conservation and are likely associated with recent failures to meet United Nations biodiversity targets. Some countries are more severely underfunded than others and therefore represent urgent financial priorities. However, attempts to identify these highly underfunded countries have been hampered for decades by poor and incomplete data on actual spending, coupled with uncertainty and lack of consensus over the relative size of spending gaps. Here, we assemble a global database of annual conservation spending. We then develop a statistical model that explains 86% of variation in conservation expenditures, and use this to identify countries where funding is robustly below expected levels. The 40 most severely underfunded countries contain 32% of all threatened mammalian diversity and include neighbors in some of the world's most biodiversity-rich areas (Sundaland, Wallacea, and Near Oceania). However, very modest increases in international assistance would achieve a large improvement in the relative adequacy of global conservation finance. Our results could therefore be quickly applied to limit immediate biodiversity losses at relatively little cost.

Determining the drivers of population structure in a highly urbanized landscape to inform conservation planning.

PubMed

Thomassen, Henri A; Harrigan, Ryan J; Semple Delaney, Kathleen; Riley, Seth P D; Serieys, Laurel E K; Pease, Katherine; Wayne, Robert K; Smith, Thomas B

2018-02-01

Understanding the environmental contributors to population structure is of paramount importance for conservation in urbanized environments. We used spatially explicit models to determine genetic population structure under current and future environmental conditions across a highly fragmented, human-dominated environment in Southern California to assess the effects of natural ecological variation and urbanization. We focused on 7 common species with diverse habitat requirements, home-range sizes, and dispersal abilities. We quantified the relative roles of potential barriers, including natural environmental characteristics and an anthropogenic barrier created by a major highway, in shaping genetic variation. The ability to predict genetic variation in our models differed among species: 11-81% of intraspecific genetic variation was explained by environmental variables. Although an anthropogenically induced barrier (a major highway) severely restricted gene flow and movement at broad scales for some species, genetic variation seemed to be primarily driven by natural environmental heterogeneity at a local level. Our results show how assessing environmentally associated variation for multiple species under current and future climate conditions can help identify priority regions for maximizing population persistence under environmental change in urbanized regions. © 2017 Society for Conservation Biology.

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.

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.

Identification of areas in Brazil that optimize conservation of forest carbon, jaguars, and biodiversity.

PubMed

De Barros, Alan E; MacDonald, Ewan A; Matsumoto, Marcelo H; Paula, Rogério C; Nijhawan, Sahil; Malhi, Y; MacDonald, David W

2014-04-01

A major question in global environmental policy is whether schemes to reduce carbon pollution through forest management, such as Reducing Emissions from Deforestation and Degradation (REDD+), can also benefit biodiversity conservation in tropical countries. We identified municipalities in Brazil that are priorities for reducing rates of deforestation and thus preserving carbon stocks that are also conservation targets for the endangered jaguar (Panthera onca) and biodiversity in general. Preliminary statistical analysis showed that municipalities with high biodiversity were positively associated with high forest carbon stocks. We used a multicriteria decision analysis to identify municipalities that offered the best opportunities for the conservation of forest carbon stocks and biodiversity conservation under a range of scenarios with different rates of deforestation and carbon values. We further categorized these areas by their representativeness of the entire country (through measures such as percent forest cover) and an indirect measure of cost (number of municipalities). The municipalities that offered optimal co-benefits for forest carbon stocks and conservation were termed REDDspots (n = 159), and their spatial distribution was compared with the distribution of current and proposed REDD projects (n = 135). We defined REDDspots as the municipalities that offer the best opportunities for co-benefits between the conservation of forest carbon stocks, jaguars, and other wildlife. These areas coincided in 25% (n = 40) of municipalities. We identified a further 95 municipalities that may have the greatest potential to develop additional REDD+ projects while also targeting biodiversity conservation. We concluded that REDD+ strategies could be an efficient tool for biodiversity conservation in key locations, especially in Amazonian and Atlantic Forest biomes. ©2013 Society for Conservation Biology.

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

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.

Carbon payments and low-cost conservation.

PubMed

Crossman, Neville D; Bryan, Brett A; Summers, David M

2011-08-01

A price on carbon is expected to generate demand for carbon offset schemes. This demand could drive investment in tree-based monocultures that provide higher carbon yields than diverse plantings of native tree and shrub species, which sequester less carbon but provide greater variation in vegetation structure and composition. Economic instruments such as species conservation banking, the creation and trading of credits that represent biological-diversity values on private land, could close the financial gap between monocultures and more diverse plantings by providing payments to individuals who plant diverse species in locations that contribute to conservation and restoration goals. We studied a highly modified agricultural system in southern Australia that is typical of many temperate agriculture zones globally (i.e., has a high proportion of endangered species, high levels of habitat fragmentation, and presence of non-native species). We quantified the economic returns from agriculture and from carbon plantings (monoculture and mixed tree and shrubs) under six carbon-price scenarios. We also identified high-priority locations for restoration of cleared landscapes with mixed tree and shrub carbon plantings. Depending on the price of carbon, direct annual payments to landowners of AU$7/ha/year to $125/ha/year (US$6-120/ha/year) may be sufficient to augment economic returns from a carbon market and encourage tree plantings that contribute more to the restoration of natural systems and endangered species habitats than monocultures. Thus, areas of high priority for conservation and restoration may be restored relatively cheaply in the presence of a carbon market. Overall, however, less carbon is sequestered by mixed native tree and shrub plantings. © 2011 Society for Conservation Biology.

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

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

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.

Silencing Effect of Hominoid Highly Conserved Noncoding Sequences on Embryonic Brain Development

PubMed Central

Mahmoudi Saber, Morteza

2017-01-01

Abstract Superfamily Hominoidea, which consists of Hominidae (humans and great apes) and Hylobatidae (gibbons), is well-known for sharing human-like characteristics, however, the genomic origins of these shared unique phenotypes have mainly remained elusive. To decipher the underlying genomic basis of Hominoidea-restricted phenotypes, we identified and characterized Hominoidea-restricted highly conserved noncoding sequences (HCNSs) that are a class of potential regulatory elements which may be involved in evolution of lineage-specific phenotypes. We discovered 679 such HCNSs from human, chimpanzee, gorilla, orangutan and gibbon genomes. These HCNSs were demonstrated to be under purifying selection but with lineage-restricted characteristics different from old CNSs. A significant proportion of their ancestral sequences had accelerated rates of nucleotide substitutions, insertions and deletions during the evolution of common ancestor of Hominoidea, suggesting the intervention of positive Darwinian selection for creating those HCNSs. In contrary to enhancer elements and similar to silencer sequences, these Hominoidea-restricted HCNSs are located in close proximity of transcription start sites. Their target genes are enriched in the nervous system, development and transcription, and they tend to be remotely located from the nearest coding gene. Chip-seq signals and gene expression patterns suggest that Hominoidea-restricted HCNSs are likely to be functional regulatory elements by imposing silencing effects on their target genes in a tissue-restricted manner during fetal brain development. These HCNSs, emerged through adaptive evolution and conserved through purifying selection, represent a set of promising targets for future functional studies of the evolution of Hominoidea-restricted phenotypes. PMID:28633494

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants.

PubMed

Li, Xinguo; Wu, Harry X; Southerton, Simon G

2010-06-21

Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution.

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

Integrating environmental gap analysis with spatial conservation prioritization: a case study from Victoria, Australia.

PubMed

Sharafi, Seyedeh Mahdieh; Moilanen, Atte; White, Matt; Burgman, Mark

2012-12-15

Gap analysis is used to analyse reserve networks and their coverage of biodiversity, thus identifying gaps in biodiversity representation that may be filled by additional conservation measures. Gap analysis has been used to identify priorities for species and habitat types. When it is applied to identify gaps in the coverage of environmental variables, it embodies the assumption that combinations of environmental variables are effective surrogates for biodiversity attributes. The question remains of how to fill gaps in conservation systems efficiently. Conservation prioritization software can identify those areas outside existing conservation areas that contribute to the efficient covering of gaps in biodiversity features. We show how environmental gap analysis can be implemented using high-resolution information about environmental variables and ecosystem condition with the publicly available conservation prioritization software, Zonation. Our method is based on the conversion of combinations of environmental variables into biodiversity features. We also replicated the analysis by using Species Distribution Models (SDMs) as biodiversity features to evaluate the robustness and utility of our environment-based analysis. We apply the technique to a planning case study of the state of Victoria, Australia. Copyright © 2012 Elsevier Ltd. All rights reserved.

Factors influencing property selection for conservation revolving funds.

PubMed

Hardy, Mathew J; Fitzsimons, James A; Bekessy, Sarah A; Gordon, Ascelin

2018-04-01

Finding sustainable ways to increase the amount of private land protected for biodiversity is challenging for many conservation organizations. In some countries, organizations use revolving-fund programs, whereby land is purchased and then sold to conservation-minded owners under condition they enter into a conservation covenant or easement. The sale proceeds are used to purchase, protect, and sell additional properties, incrementally increasing the amount of protected private land. Because the effectiveness of this approach relies on selecting appropriate properties, we explored factors currently considered by practitioners and how these are integrated into decision making. We conducted exploratory, semistructured interviews with managers from each of the 5 major revolving funds in Australia. Responses indicated although conservation factors are important, financial and social factors are also highly influential. A major determinant was whether the property could be resold within a reasonable period at a price that replenishes the fund. To facilitate resale, often selected properties include the potential for the construction of a dwelling. Practitioners face with clear trade-offs between conservation, financial, amenity, and other factors in selecting properties and 3 main challenges: recovering the costs of acquisition, protection, and resale; reselling the property; and meeting conservation goals. Our findings suggest the complexity of these decisions may constrain revolving-fund effectiveness. Drawing from participant responses, we identified potential strategies to mitigate these risks, such as providing adequate recreational space without jeopardizing ecological assets. We suggest managers could benefit from a shared-learning and adaptive approach to property selection given the commonalities between programs. Understanding how practitioners deal with complex decisions in the implementation of revolving funds helps identify future research to improve the

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.

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

Identifying Preservation and Restoration Priority Areas for Desert Fishes in an Increasingly Invaded World

NASA Astrophysics Data System (ADS)

Pool, Thomas K.; Strecker, Angela L.; Olden, Julian D.

2013-03-01

A commonly overlooked aspect of conservation planning assessments is that wildlife managers are increasingly focused on habitats that contain non-native species. We examine this management challenge in the Gila River basin (150,730 km2), and present a new planning strategy for fish conservation. By applying a hierarchical prioritization algorithm to >850,000 fish records in 27,181 sub-watersheds we first identified high priority areas (PAs) termed "preservation PAs" with high native fish richness and low non-native richness; these represent traditional conservation targets. Second, we identified "restoration PAs" with high native fish richness that also contained high numbers of non-native species; these represent less traditional conservation targets. The top 10 % of preservation and restoration PAs contained common native species (e.g., Catostomus clarkii, desert sucker; Catostomus insignis, Sonora sucker) in addition to native species with limited distributions (i.e., Xyrauchen texanus, razorback sucker; Oncorhynchus gilae apache, Apache trout). The top preservation and restoration PAs overlapped by 42 %, indicating areas with high native fish richness range from minimally to highly invaded. Areas exclusively identified as restoration PAs also encompassed a greater percentage of native species ranges than would be expected by the random addition of an equivalent basin area. Restoration PAs identified an additional 19.0 and 26.6 % of the total ranges of two federally endangered species— Meda fulgida (spikedace) and Gila intermedia (Gila chub), respectively, compared to top preservation PAs alone—despite adding only 5.8 % of basin area. We contend that in addition to preservation PAs, restoration PAs are well suited for complementary management activities benefiting native fishes.

Identifying preservation and restoration priority areas for desert fishes in an increasingly invaded world.

PubMed

Pool, Thomas K; Strecker, Angela L; Olden, Julian D

2013-03-01

A commonly overlooked aspect of conservation planning assessments is that wildlife managers are increasingly focused on habitats that contain non-native species. We examine this management challenge in the Gila River basin (150,730 km(2)), and present a new planning strategy for fish conservation. By applying a hierarchical prioritization algorithm to >850,000 fish records in 27,181 sub-watersheds we first identified high priority areas (PAs) termed "preservation PAs" with high native fish richness and low non-native richness; these represent traditional conservation targets. Second, we identified "restoration PAs" with high native fish richness that also contained high numbers of non-native species; these represent less traditional conservation targets. The top 10 % of preservation and restoration PAs contained common native species (e.g., Catostomus clarkii, desert sucker; Catostomus insignis, Sonora sucker) in addition to native species with limited distributions (i.e., Xyrauchen texanus, razorback sucker; Oncorhynchus gilae apache, Apache trout). The top preservation and restoration PAs overlapped by 42 %, indicating areas with high native fish richness range from minimally to highly invaded. Areas exclusively identified as restoration PAs also encompassed a greater percentage of native species ranges than would be expected by the random addition of an equivalent basin area. Restoration PAs identified an additional 19.0 and 26.6 % of the total ranges of two federally endangered species-Meda fulgida (spikedace) and Gila intermedia (Gila chub), respectively, compared to top preservation PAs alone-despite adding only 5.8 % of basin area. We contend that in addition to preservation PAs, restoration PAs are well suited for complementary management activities benefiting native fishes.

7 CFR 12.23 - Conservation plans and conservation systems.

Code of Federal Regulations, 2010 CFR

2010-01-01

... to produce agricultural commodities prior to December 23, 1985, the applicable conservation systems... available conservation technology; cost-effective; and shall not cause undue economic hardship on the person... containing highly erodible cropland which was used to produce an agricultural commodity prior to December 23...

Effects of attitudes and demography on public support for endangered species conservation.

PubMed

Liordos, Vasilios; Kontsiotis, Vasileios J; Anastasiadou, Magdalini; Karavasias, Efstathios

2017-10-01

It is critical for managers to understand how attitudes and demography affect public's preferences for species protection for designing successful conservation projects. 1080 adults in Greece were asked to rate pictures of 12 endangered species on aesthetic and negativistic attitudes, and intention to support their conservation. Factor analysis identified a group of animals for which respondents indicated high levels of support for their conservation (red deer, loggerhead sea turtle, brown bear, common pheasant, European ground squirrel, glossy ibis) and a group of animals for which respondents indicated low levels of support (black vulture, great white shark, fire-bellied toad, western barbastelle, Cretan tube web spider, Milos viper). The species that received the highest support were also rated as the most attractive and safest, excluding the fearsome brown bear. Structural models revealed that aesthetic, moralistic and negativistic attitudes were the stronger predictors of support. Aesthetic and moralistic attitudes were positively, and negativistic attitudes negatively, correlated with support for conservation in both groups. Consumptive users scored lower in aesthetics and were less supportive of protection in the high support group, while nonconsumptive users showed the opposite trend. Respondents residing in urban areas deemed animals of high support more attractive and less fearsome and were more supportive of conservation than rural residents in both groups. Females of higher education viewed animals of low support as fearsome, however they supported their conservation. Our study identified popular species that can be used as flagship species to facilitate the implementation of conservation projects. The results of this study could also be used to design a communication and outreach campaign to raise awareness about the ecosystem value of less attractive species. Copyright © 2017 Elsevier B.V. All rights reserved.

Antigenic potential of a highly conserved Neisseria meningitidis lipopolysaccharide inner core structure defined by chemical synthesis.

PubMed

Reinhardt, Anika; Yang, You; Claus, Heike; Pereira, Claney L; Cox, Andrew D; Vogel, Ulrich; Anish, Chakkumkal; Seeberger, Peter H

2015-01-22

Neisseria meningitidis is a leading cause of bacterial meningitis worldwide. We studied the potential of synthetic lipopolysaccharide (LPS) inner core structures as broadly protective antigens against N. meningitidis. Based on the specific reactivity of human serum antibodies to synthetic LPS cores, we selected a highly conserved LPS core tetrasaccharide as a promising antigen. This LPS inner core tetrasaccharide induced a robust IgG response in mice when formulated as an immunogenic glycoconjugate. Binding of raised mouse serum to a broad collection of N. meningitidis strains demonstrated the accessibility of the LPS core on viable bacteria. The distal trisaccharide was identified as the crucial epitope, whereas the proximal Kdo moiety was immunodominant and induced mainly nonprotective antibodies that are responsible for lack of functional protection in polyclonal serum. Our results identified key antigenic determinants of LPS core glycan and, hence, may aid the design of a broadly protective immunization against N. meningitidis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Global priorities for national carnivore conservation under land use change

PubMed Central

Di Minin, Enrico; Slotow, Rob; Hunter, Luke T. B.; Montesino Pouzols, Federico; Toivonen, Tuuli; Verburg, Peter H.; Leader-Williams, Nigel; Petracca, Lisanne; Moilanen, Atte

2016-01-01

Mammalian carnivores have suffered the biggest range contraction among all biodiversity and are particularly vulnerable to habitat loss and fragmentation. Therefore, we identified priority areas for the conservation of mammalian carnivores, while accounting for species-specific requirements for connectivity and expected agricultural and urban expansion. While prioritizing for carnivores only, we were also able to test their effectiveness as surrogates for 23,110 species of amphibians, birds, mammals and reptiles and 867 terrestrial ecoregions. We then assessed the risks to carnivore conservation within each country that makes a contribution to global carnivore conservation. We found that land use change will potentially lead to important range losses, particularly amongst already threatened carnivore species. In addition, the 17% of land targeted for protection under the Aichi Target 11 was found to be inadequate to conserve carnivores under expected land use change. Our results also highlight that land use change will decrease the effectiveness of carnivores to protect other threatened species, especially threatened amphibians. In addition, the risk of human-carnivore conflict is potentially high in countries where we identified spatial priorities for their conservation. As meeting the global biodiversity target will be inadequate for carnivore protection, innovative interventions are needed to conserve carnivores outside protected areas to compliment any proposed expansion of the protected area network. PMID:27034197

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

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....

Comparative genomics reveals conservative evolution of the xylem transcriptome in vascular plants

PubMed Central

2010-01-01

Background Wood is a valuable natural resource and a major carbon sink. Wood formation is an important developmental process in vascular plants which played a crucial role in plant evolution. Although genes involved in xylem formation have been investigated, the molecular mechanisms of xylem evolution are not well understood. We use comparative genomics to examine evolution of the xylem transcriptome to gain insights into xylem evolution. Results The xylem transcriptome is highly conserved in conifers, but considerably divergent in angiosperms. The functional domains of genes in the xylem transcriptome are moderately to highly conserved in vascular plants, suggesting the existence of a common ancestral xylem transcriptome. Compared to the total transcriptome derived from a range of tissues, the xylem transcriptome is relatively conserved in vascular plants. Of the xylem transcriptome, cell wall genes, ancestral xylem genes, known proteins and transcription factors are relatively more conserved in vascular plants. A total of 527 putative xylem orthologs were identified, which are unevenly distributed across the Arabidopsis chromosomes with eight hot spots observed. Phylogenetic analysis revealed that evolution of the xylem transcriptome has paralleled plant evolution. We also identified 274 conifer-specific xylem unigenes, all of which are of unknown function. These xylem orthologs and conifer-specific unigenes are likely to have played a crucial role in xylem evolution. Conclusions Conifers have highly conserved xylem transcriptomes, while angiosperm xylem transcriptomes are relatively diversified. Vascular plants share a common ancestral xylem transcriptome. The xylem transcriptomes of vascular plants are more conserved than the total transcriptomes. Evolution of the xylem transcriptome has largely followed the trend of plant evolution. PMID:20565927

Ten-year assessment of the 100 priority questions for global biodiversity conservation.

PubMed

Jucker, Tommaso; Wintle, Bonnie; Shackelford, Gorm; Bocquillon, Pierre; Geffert, Jan Laurens; Kasoar, Tim; Kovacs, Eszter; Mumby, Hannah S; Orland, Chloé; Schleicher, Judith; Tew, Eleanor R; Zabala, Aiora; Amano, Tatsuya; Bell, Alexandra; Bongalov, Boris; Chambers, Josephine M; Corrigan, Colleen; Durán, América P; Duvic-Paoli, Leslie-Anne; Emilson, Caroline; da Silva, Jéssica Fonseca; Garnett, Emma E; Green, Elizabeth J; Guth, Miriam K; Hacket-Pain, Andrew; Hinsley, Amy; Igea, Javier; Kunz, Martina; Luke, Sarah H; Lynam, William; Martin, Philip A; Nunes, Matheus H; Ockendon, Nancy; Pavitt, Aly; Payne, Charlotte L R; Plutshack, Victoria; Rademacher, Tim T; Robertson, Rebecca J; Rose, David C; Serban, Anca; Simmons, Benno I; Emilson, Erik J S; Tayleur, Catherine; Wordley, Claire F R; Mukherjee, Nibedita

2018-06-20

In 2008, a group of conservation scientists compiled a list of 100 priority questions for the conservation of the world's biodiversity [Sutherland et al. (2009) Conservation Biology, 23, 557-567]. However, now almost a decade later, no one has yet published a study gauging how much progress has been made in addressing these 100 high-priority questions in the peer-reviewed literature. Here we take a first step toward re-examining the 100 questions and identify key knowledge gaps that still remain. Through a combination of a questionnaire and a literature review, we evaluated each of the 100 questions on the basis of two criteria: relevance and effort. We defined highly-relevant questions as those which - if answered - would have the greatest impact on global biodiversity conservation, while effort was quantified based on the number of review publications addressing a particular question, which we used as a proxy for research effort. Using this approach we identified a set of questions that, despite being perceived as highly relevant, have been the focus of relatively few review publications over the past ten years. These questions covered a broad range of topics but predominantly tackled three major themes: the conservation and management of freshwater ecosystems, the role of societal structures in shaping interactions between people and the environment, and the impacts of conservation interventions. We see these questions as important knowledge gaps that have so far received insufficient attention and may need to be prioritised in future research. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Understanding conservationists' perspectives on the new-conservation debate.

PubMed

Holmes, George; Sandbrook, Chris; Fisher, Janet A

2017-04-01

A vibrant debate about the future direction of biodiversity conservation centers on the merits of the so-called new conservation. Proponents of the new conservation advocate a series of positions on key conservation ideas, such as the importance of human-dominated landscapes and conservation's engagement with capitalism. These have been fiercely contested in a debate dominated by a few high-profile individuals, and so far there has been no empirical exploration of existing perspectives on these issues among a wider community of conservationists. We used Q methodology to examine empirically perspectives on the new conservation held by attendees at the 2015 International Congress for Conservation Biology (ICCB). Although we identified a consensus on several key issues, 3 distinct positions emerged: in favor of conservation to benefit people but opposed to links with capitalism and corporations, in favor of biocentric approaches but with less emphasis on wilderness protection than prominent opponents of new conservation, and in favor of the published new conservation perspective but with less emphasis on increasing human well-being as a goal of conservation. Our results revealed differences between the debate on the new conservation in the literature and views held within a wider, but still limited, conservation community and demonstrated the existence of at least one viewpoint (in favor of conservation to benefit people but opposed to links with capitalism and corporations) that is almost absent from the published debate. We hope the fuller understanding we present of the variety of views that exist but have not yet been heard, will improve the quality and tone of debates on the subject. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

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.

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

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.

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...

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.

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.

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

The Universally Conserved Prokaryotic GTPases

PubMed Central

Verstraeten, Natalie; Fauvart, Maarten; Versées, Wim; Michiels, Jan

2011-01-01

Summary: Members of the large superclass of P-loop GTPases share a core domain with a conserved three-dimensional structure. In eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. As targets of mutation and toxins, GTPases are involved in the pathogenesis of cancer and infectious diseases. In prokaryotes also, it is hard to overestimate the importance of GTPases in cell physiology. Numerous papers have shed new light on the role of bacterial GTPases in cell cycle regulation, ribosome assembly, the stress response, and other cellular processes. Moreover, bacterial GTPases have been identified as high-potential drug targets. A key paper published over 2 decades ago stated that, “It may never again be possible to capture [GTPases] in a family portrait” (H. R. Bourne, D. A. Sanders, and F. McCormick, Nature 348:125-132, 1990) and indeed, the last 20 years have seen a tremendous increase in publications on the subject. Sequence analysis identified 13 bacterial GTPases that are conserved in at least 75% of all bacterial species. We here provide an overview of these 13 protein subfamilies, covering their cellular functions as well as cellular localization and expression levels, three-dimensional structures, biochemical properties, and gene organization. Conserved roles in eukaryotic homologs will be discussed as well. A comprehensive overview summarizing current knowledge on prokaryotic GTPases will aid in further elucidating the function of these important proteins. PMID:21885683

How to Identify High-Growth Schools

ERIC Educational Resources Information Center

Pfeiffer, Linda E.

2015-01-01

When researching school options, parents may want to look for schools with high-growth scores which, according to research, may be indicators of other characteristics such as programming, leadership, culture, and size. This quick guide offers parents tips on how to identify high-growth schools and what to ask when evaluating school options. An…

Highly conserved elements discovered in vertebrates are present in non-syntenic loci of tunicates, act as enhancers and can be transcribed during development

PubMed Central

Sanges, Remo; Hadzhiev, Yavor; Gueroult-Bellone, Marion; Roure, Agnes; Ferg, Marco; Meola, Nicola; Amore, Gabriele; Basu, Swaraj; Brown, Euan R.; De Simone, Marco; Petrera, Francesca; Licastro, Danilo; Strähle, Uwe; Banfi, Sandro; Lemaire, Patrick; Birney, Ewan; Müller, Ferenc; Stupka, Elia

2013-01-01

Co-option of cis-regulatory modules has been suggested as a mechanism for the evolution of expression sites during development. However, the extent and mechanisms involved in mobilization of cis-regulatory modules remains elusive. To trace the history of non-coding elements, which may represent candidate ancestral cis-regulatory modules affirmed during chordate evolution, we have searched for conserved elements in tunicate and vertebrate (Olfactores) genomes. We identified, for the first time, 183 non-coding sequences that are highly conserved between the two groups. Our results show that all but one element are conserved in non-syntenic regions between vertebrate and tunicate genomes, while being syntenic among vertebrates. Nevertheless, in all the groups, they are significantly associated with transcription factors showing specific functions fundamental to animal development, such as multicellular organism development and sequence-specific DNA binding. The majority of these regions map onto ultraconserved elements and we demonstrate that they can act as functional enhancers within the organism of origin, as well as in cross-transgenesis experiments, and that they are transcribed in extant species of Olfactores. We refer to the elements as ‘Olfactores conserved non-coding elements’. PMID:23393190

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

Identifying Greater Sage-Grouse source and sink habitats for conservation planning in an energy development landscape.

PubMed

Kirol, Christopher P; Beck, Jeffrey L; Huzurbazar, Snehalata V; Holloran, Matthew J; Miller, Scott N

2015-06-01

Conserving a declining species that is facing many threats, including overlap of its habitats with energy extraction activities, depends upon identifying and prioritizing the value of the habitats that remain. In addition, habitat quality is often compromised when source habitats are lost or fragmented due to anthropogenic development. Our objective was to build an ecological model to classify and map habitat quality in terms of source or sink dynamics for Greater Sage-Grouse (Centrocercus urophasianus) in the Atlantic Rim Project Area (ARPA), a developing coalbed natural gas field in south-central Wyoming, USA. We used occurrence and survival modeling to evaluate relationships between environmental and anthropogenic variables at multiple spatial scales and for all female summer life stages, including nesting, brood-rearing, and non-brooding females. For each life stage, we created resource selection functions (RSFs). We weighted the RSFs and combined them to form a female summer occurrence map. We modeled survival also as a function of spatial variables for nest, brood, and adult female summer survival. Our survival-models were mapped as survival probability functions individually and then combined with fixed vital rates in a fitness metric model that, when mapped, predicted habitat productivity (productivity map). Our results demonstrate a suite of environmental and anthropogenic variables at multiple scales that were predictive of occurrence and survival. We created a source-sink map by overlaying our female summer occurrence map and productivity map to predict habitats contributing to population surpluses (source habitats) or deficits (sink habitat) and low-occurrence habitats on the landscape. The source-sink map predicted that of the Sage-Grouse habitat within the ARPA, 30% was primary source, 29% was secondary source, 4% was primary sink, 6% was secondary sink, and 31% was low occurrence. Our results provide evidence that energy development and avoidance of

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

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.

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.

Crystal structure of AFV3-109, a highly conserved protein from crenarchaeal viruses

PubMed Central

Keller, Jenny; Leulliot, Nicolas; Cambillau, Christian; Campanacci, Valérie; Porciero, Stéphanie; Prangishvili, David; Forterre, Patrick; Cortez, Diego; Quevillon-Cheruel, Sophie; van Tilbeurgh, Herman

2007-01-01

The extraordinary morphologies of viruses infecting hyperthermophilic archaea clearly distinguish them from bacterial and eukaryotic viruses. Moreover, their genomes code for proteins that to a large extend have no related sequences in the extent databases. However, a small pool of genes is shared by overlapping subsets of these viruses, and the most conserved gene, exemplified by the ORF109 of the Acidianus Filamentous Virus 3, AFV3, is present on genomes of members of three viral familes, the Lipothrixviridae, Rudiviridae, and "Bicaudaviridae", as well as of the unclassified Sulfolobus Turreted Icosahedral Virus, STIV. We present here the crystal structure of the protein (Mr = 13.1 kD, 109 residues) encoded by the AFV3 ORF 109 in two different crystal forms at 1.5 and 1.3 Å resolution. The structure of AFV3-109 is a five stranded β-sheet with loops on one side and three helices on the other. It forms a dimer adopting the shape of a cradle that encompasses the best conserved regions of the sequence. No protein with a related fold could be identified except for the ortholog from STIV1, whose structure was deposited at the Protein Data Bank. We could clearly identify a well bound glycerol inside the cradle, contacting exclusively totally conserved residues. This interaction was confirmed in solution by fluorescence titration. Although the function of AFV3-109 cannot be deduced directly from its structure, structural homology with the STIV1 protein, and the size and charge distribution of the cavity suggested it could interact with nucleic acids. Fluorescence quenching titrations also showed that AFV3-109 interacts with dsDNA. Genomic sequence analysis revealed bacterial homologs of AFV3-109 as a part of a putative previously unidentified prophage sequences in some Firmicutes. PMID:17241456

High order filtering methods for approximating hyperbolic systems of conservation laws

NASA Technical Reports Server (NTRS)

Lafon, F.; Osher, S.

1991-01-01

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

Climate change adaptation benefits of potential conservation partnerships.

PubMed

Monahan, William B; Theobald, David M

2018-01-01

We evaluate the world terrestrial network of protected areas (PAs) for its partnership potential in responding to climate change. That is, if a PA engaged in collaborative, trans-boundary management of species, by investing in conservation partnerships with neighboring areas, what climate change adaptation benefits might accrue? We consider core tenets of conservation biology related to protecting large areas with high environmental heterogeneity and low climate change velocity and ask how a series of biodiversity adaptation indicators change across spatial scales encompassing potential PA and non-PA partners. Less than 1% of current world terrestrial PAs equal or exceed the size of established and successful conservation partnerships. Partnering at this scale would increase the biodiversity adaptation indicators by factors up to two orders of magnitude, compared to a null model in which each PA is isolated. Most partnership area surrounding PAs is comprised of non-PAs (70%), indicating the importance of looking beyond the current network of PAs when promoting climate change adaptation. Given monumental challenges with PA-based species conservation in the face of climate change, partnerships provide a logical and achievable strategy for helping areas adapt. Our findings identify where strategic partnering efforts in highly vulnerable areas of the world may prove critical in safeguarding biodiversity.

Landscape Suitability in Botswana for the Conservation of Its Six Large African Carnivores

PubMed Central

Winterbach, Hanlie E. K.; Winterbach, Christiaan W.; Somers, Michael J.

2014-01-01

Wide-ranging large carnivores often range beyond the boundaries of protected areas into human-dominated areas. Mapping out potentially suitable habitats on a country-wide scale and identifying areas with potentially high levels of threats to large carnivore survival is necessary to develop national conservation action plans. We used a novel approach to map and identify these areas in Botswana for its large carnivore guild consisting of lion (Panthera leo), leopard (Panthera pardus), spotted hyaena (Crocuta crocuta), brown hyaena (Hyaena brunnea), cheetah (Acinonyx jubatus) and African wild dog (Lycaon pictus). The habitat suitability for large carnivores depends primarily on prey availability, interspecific competition, and conflict with humans. Prey availability is most likely the strongest natural determinant. We used the distribution of biomass of typical wild ungulate species occurring in Botswana which is preyed upon by the six large carnivores to evaluate the potential suitability of the different management zones in the country to sustain large carnivore populations. In areas where a high biomass of large prey species occurred, we assumed interspecific competition between dominant and subordinated competitors to be high. This reduced the suitability of these areas for conservation of subordinate competitors, and vice versa. We used the percentage of prey biomass of the total prey and livestock biomass to identify areas with potentially high levels of conflict in agricultural areas. High to medium biomass of large prey was mostly confined to conservation zones, while small prey biomass was more evenly spread across large parts of the country. This necessitates different conservation strategies for carnivores with a preference for large prey, and those that can persist in the agricultural areas. To ensure connectivity between populations inside Botswana and also with its neighbours, a number of critical areas for priority management actions exist in the

Landscape suitability in Botswana for the conservation of its six large African carnivores.

PubMed

Winterbach, Hanlie E K; Winterbach, Christiaan W; Somers, Michael J

2014-01-01

Wide-ranging large carnivores often range beyond the boundaries of protected areas into human-dominated areas. Mapping out potentially suitable habitats on a country-wide scale and identifying areas with potentially high levels of threats to large carnivore survival is necessary to develop national conservation action plans. We used a novel approach to map and identify these areas in Botswana for its large carnivore guild consisting of lion (Panthera leo), leopard (Panthera pardus), spotted hyaena (Crocuta crocuta), brown hyaena (Hyaena brunnea), cheetah (Acinonyx jubatus) and African wild dog (Lycaon pictus). The habitat suitability for large carnivores depends primarily on prey availability, interspecific competition, and conflict with humans. Prey availability is most likely the strongest natural determinant. We used the distribution of biomass of typical wild ungulate species occurring in Botswana which is preyed upon by the six large carnivores to evaluate the potential suitability of the different management zones in the country to sustain large carnivore populations. In areas where a high biomass of large prey species occurred, we assumed interspecific competition between dominant and subordinated competitors to be high. This reduced the suitability of these areas for conservation of subordinate competitors, and vice versa. We used the percentage of prey biomass of the total prey and livestock biomass to identify areas with potentially high levels of conflict in agricultural areas. High to medium biomass of large prey was mostly confined to conservation zones, while small prey biomass was more evenly spread across large parts of the country. This necessitates different conservation strategies for carnivores with a preference for large prey, and those that can persist in the agricultural areas. To ensure connectivity between populations inside Botswana and also with its neighbours, a number of critical areas for priority management actions exist in the

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.

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.

High spatial resolution mapping of the Cerrado's land cover and land use types in the priority area for conservation Chapada da Contagem, Brazil.

NASA Astrophysics Data System (ADS)

Ribeiro, F.; Roberts, D. A.; Davis, F. W.; Antunes Daldegan, G.; Nackoney, J.; Hess, L. L.

2016-12-01

The Brazilian savanna, Cerrado, is the second largest biome over South America and the most floristically diverse savanna in the world. This biome is considered a conservation hotspot in respect to its biodiversity importance and rapid transformation of its landscape. The Cerrado's natural vegetation has been severely transformed by agriculture and pasture activities. Currently it is the main agricultural frontier in Brazil and one of the most threatened Brazilian biomes. This scenario results in environmental impacts such as ecosystems fragmentation as well as losses in connectivity, biodiversity and gene flow, changes in the microclimate and energy, carbon and nutrients cycles, among others. The Priority Areas for Conservation is a governmental program from Brazil that identifies areas with high conservation priority. One of this program's recommendation is a natural vegetation map including their major ecosystem classes. This study aims to generate more precise information for the Cerrado's vegetation. The main objective of this study is to identify which ecosystems are being prioritized and/or threatened by land use, refining information for further protection. In order to test methods, the priority area for conservation Chapada da Contagem was selected as the study site. This area is ranked as "extremely high priority" by the government and is located in the Federal District and Goias State, Brazil. Satellites with finer spatial resolution may improve the classification of the Cerrado's vegetation. Remote sensing methods and two criteria were tested using RapidEye 3A imagery (5m spatial resolution) collected in 2014 in order to classify the Cerrado's major land cover types of this area, as well as its land use. One criterion considers the Cerrado's major terrestrial ecosystems, which are divided into forest, savanna and grassland. The other involves scaling it down to the major physiognomic groups of each ecosystem. Other sources of environmental dataset such

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

PubMed Central

Shuey, John A.

2013-01-01

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

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

PubMed

Shuey, John A

2013-12-05

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

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...

Identifying key conservation threats to Alpine birds through expert knowledge

PubMed Central

Pedrini, Paolo; Brambilla, Mattia; Rolando, Antonio; Girardello, Marco

2016-01-01

Alpine biodiversity is subject to a range of increasing threats, but the scarcity of data for many taxa means that it is difficult to assess the level and likely future impact of a given threat. Expert opinion can be a useful tool to address knowledge gaps in the absence of adequate data. Experts with experience in Alpine ecology were approached to rank threat levels for 69 Alpine bird species over the next 50 years for the whole European Alps in relation to ten categories: land abandonment, climate change, renewable energy, fire, forestry practices, grazing practices, hunting, leisure, mining and urbanization. There was a high degree of concordance in ranking of perceived threats among experts for most threat categories. The major overall perceived threats to Alpine birds identified through expert knowledge were land abandonment, urbanization, leisure and forestry, although other perceived threats were ranked highly for particular species groups (renewable energy and hunting for raptors, hunting for gamebirds). For groups of species defined according to their breeding habitat, open habitat species and treeline species were perceived as the most threatened. A spatial risk assessment tool based on summed scores for the whole community showed threat levels were highest for bird communities of the northern and western Alps. Development of the approaches given in this paper, including addressing biases in the selection of experts and adopting a more detailed ranking procedure, could prove useful in the future in identifying future threats, and in carrying out risk assessments based on levels of threat to the whole bird community. PMID:26966659

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.

Identifying and Prioritizing Greater Sage-Grouse Nesting and Brood-Rearing Habitat for Conservation in Human-Modified Landscapes

PubMed Central

Dzialak, Matthew R.; Olson, Chad V.; Harju, Seth M.; Webb, Stephen L.; Mudd, James P.; Winstead, Jeffrey B.; Hayden-Wing, L.D.

2011-01-01

Background Balancing animal conservation and human use of the landscape is an ongoing scientific and practical challenge throughout the world. We investigated reproductive success in female greater sage-grouse (Centrocercus urophasianus) relative to seasonal patterns of resource selection, with the larger goal of developing a spatially-explicit framework for managing human activity and sage-grouse conservation at the landscape level. Methodology/Principal Findings We integrated field-observation, Global Positioning Systems telemetry, and statistical modeling to quantify the spatial pattern of occurrence and risk during nesting and brood-rearing. We linked occurrence and risk models to provide spatially-explicit indices of habitat-performance relationships. As part of the analysis, we offer novel biological information on resource selection during egg-laying, incubation, and night. The spatial pattern of occurrence during all reproductive phases was driven largely by selection or avoidance of terrain features and vegetation, with little variation explained by anthropogenic features. Specifically, sage-grouse consistently avoided rough terrain, selected for moderate shrub cover at the patch level (within 90 m2), and selected for mesic habitat in mid and late brood-rearing phases. In contrast, risk of nest and brood failure was structured by proximity to anthropogenic features including natural gas wells and human-created mesic areas, as well as vegetation features such as shrub cover. Conclusions/Significance Risk in this and perhaps other human-modified landscapes is a top-down (i.e., human-mediated) process that would most effectively be minimized by developing a better understanding of specific mechanisms (e.g., predator subsidization) driving observed patterns, and using habitat-performance indices such as those developed herein for spatially-explicit guidance of conservation intervention. Working under the hypothesis that industrial activity structures risk by

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.…

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

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

High-Throughput Sequencing Reveals Diverse Sets of Conserved, Nonconserved, and Species-Specific miRNAs in Jute

PubMed Central

Islam, Md. Tariqul; Ferdous, Ahlan Sabah; Najnin, Rifat Ara; Sarker, Suprovath Kumar; Khan, Haseena

2015-01-01

MicroRNAs play a pivotal role in regulating a broad range of biological processes, acting by cleaving mRNAs or by translational repression. A group of plant microRNAs are evolutionarily conserved; however, others are expressed in a species-specific manner. Jute is an agroeconomically important fibre crop; nonetheless, no practical information is available for microRNAs in jute to date. In this study, Illumina sequencing revealed a total of 227 known microRNAs and 17 potential novel microRNA candidates in jute, of which 164 belong to 23 conserved families and the remaining 63 belong to 58 nonconserved families. Among a total of 81 identified microRNA families, 116 potential target genes were predicted for 39 families and 11 targets were predicted for 4 among the 17 identified novel microRNAs. For understanding better the functions of microRNAs, target genes were analyzed by Gene Ontology and their pathways illustrated by KEGG pathway analyses. The presence of microRNAs identified in jute was validated by stem-loop RT-PCR followed by end point PCR and qPCR for randomly selected 20 known and novel microRNAs. This study exhaustively identifies microRNAs and their target genes in jute which will ultimately pave the way for understanding their role in this crop and other crops. PMID:25861616

A Highly Conserved Bacterial D-Serine Uptake System Links Host Metabolism and Virulence

PubMed Central

Connolly, James P. R.; Gabrielsen, Mads; Goldstone, Robert J.; Grinter, Rhys; Wang, Dai; Cogdell, Richard J.; Walker, Daniel; Smith, David G. E.; Roe, Andrew J.

2016-01-01

The ability of any organism to sense and respond to challenges presented in the environment is critically important for promoting or restricting colonization of specific sites. Recent work has demonstrated that the host metabolite D-serine has the ability to markedly influence the outcome of infection by repressing the type III secretion system of enterohaemorrhagic Escherichia coli (EHEC) in a concentration-dependent manner. However, exactly how EHEC monitors environmental D-serine is not understood. In this work, we have identified two highly conserved members of the E. coli core genome, encoding an inner membrane transporter and a transcriptional regulator, which collectively help to “sense” levels of D-serine by regulating its uptake from the environment and in turn influencing global gene expression. Both proteins are required for full expression of the type III secretion system and diversely regulated prophage-encoded effector proteins demonstrating an important infection-relevant adaptation of the core genome. We propose that this system acts as a key safety net, sampling the environment for this metabolite, thereby promoting colonization of EHEC to favorable sites within the host. PMID:26727373

Integrating economic costs and biological traits into global conservation priorities for carnivores.

PubMed

Loyola, Rafael Dias; Oliveira-Santos, Luiz Gustavo Rodrigues; Almeida-Neto, Mário; Nogueira, Denise Martins; Kubota, Umberto; Diniz-Filho, José Alexandre Felizola; Lewinsohn, Thomas Michael

2009-08-27

Prioritization schemes usually highlight species-rich areas, where many species are at imminent risk of extinction. To be ecologically relevant these schemes should also include species biological traits into area-setting methods. Furthermore, in a world of limited funds for conservation, conservation action is constrained by land acquisition costs. Hence, including economic costs into conservation priorities can substantially improve their conservation cost-effectiveness. We examined four global conservation scenarios for carnivores based on the joint mapping of economic costs and species biological traits. These scenarios identify the most cost-effective priority sets of ecoregions, indicating best investment opportunities for safeguarding every carnivore species, and also establish priority sets that can maximize species representation in areas harboring highly vulnerable species. We compared these results with a scenario that minimizes the total number of ecoregions required for conserving all species, irrespective of other factors. We found that cost-effective conservation investments should focus on 41 ecoregions highlighted in the scenario that consider simultaneously both ecoregion vulnerability and economic costs of land acquisition. Ecoregions included in priority sets under these criteria should yield best returns of investments since they harbor species with high extinction risk and have lower mean land cost. Our study highlights ecoregions of particular importance for the conservation of the world's carnivores defining global conservation priorities in analyses that encompass socioeconomic and life-history factors. We consider the identification of a comprehensive priority-set of areas as a first step towards an in-situ biodiversity maintenance strategy.

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.

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

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

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-29

... the Framework Document for High-Intensity Discharge Lamps AGENCY: Office of Energy Efficiency and... availability of framework document for high-intensity discharge (HID) lamps, initiating the rulemaking and data... Availability of Framework Document Regarding Energy Conservation Standards for High-Intensity Discharge (HID...

Tiered High-Throughput Screening Approach to Identify ...

EPA Pesticide Factsheets

High-throughput screening (HTS) for potential thyroid–disrupting chemicals requires a system of assays to capture multiple molecular-initiating events (MIEs) that converge on perturbed thyroid hormone (TH) homeostasis. Screening for MIEs specific to TH-disrupting pathways is limited in the US EPA ToxCast screening assay portfolio. To fill one critical screening gap, the Amplex UltraRed-thyroperoxidase (AUR-TPO) assay was developed to identify chemicals that inhibit TPO, as decreased TPO activity reduces TH synthesis. The ToxCast Phase I and II chemical libraries, comprised of 1,074 unique chemicals, were initially screened using a single, high concentration to identify potential TPO inhibitors. Chemicals positive in the single concentration screen were retested in concentration-response. Due to high false positive rates typically observed with loss-of-signal assays such as AUR-TPO, we also employed two additional assays in parallel to identify possible sources of nonspecific assay signal loss, enabling stratification of roughly 300 putative TPO inhibitors based upon selective AUR-TPO activity. A cell-free luciferase inhibition assay was used to identify nonspecific enzyme inhibition among the putative TPO inhibitors, and a cytotoxicity assay using a human cell line was used to estimate the cellular tolerance limit. Additionally, the TPO inhibition activities of 150 chemicals were compared between the AUR-TPO and an orthogonal peroxidase oxidation assay using

A comparison of global conservation prioritization models with spatial spending patterns of conservation nongovernmental organizations.

PubMed

Holmes, George; Scholfield, Katherine; Brockington, Dan

2012-08-01

In recent decades, various conservation organizations have developed models to prioritize locations for conservation. Through a survey of the spending patterns of 281 conservation nongovernmental organizations (NGOs), we examined the relation between 2 such models and spatial patterns of spending by conservation NGOs in 44 countries in sub-Saharan Africa. We tested whether, at the country level, the proportion of a country designated as a conservation priority was correlated with where NGOs spent money. For one model (the combination of Conservation International's hotspots and High Biodiversity Wilderness Areas, which are areas of high endemism with high or low levels of vegetation loss respectively), there was no relation between the proportion of a country designated as a priority and levels of NGO spending, including by the NGO associated with the model. In the second model (Global 200), the proportion of a country designated as a priority and the amount of money spent by NGOs were significantly and positively related. Less money was spent in countries in northern and western sub-Saharan Africa than countries in southern and eastern Africa, relative to the proportion of the country designated as a conservation priority. We suggest that on the basis of our results some NGOs consider increasing their spending on the areas designated as of conservation priority which are currently relatively underfunded, although there are economic, political, cultural, historical, biological, and practical reasons why current spending patterns may not align with priority sites. ©2012 Society for Conservation Biology.

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

ERIC Educational Resources Information Center

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

2012-01-01

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

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

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.

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

Usherin expression is highly conserved in mouse and human tissues.

PubMed

Pearsall, Nicole; Bhattacharya, Gautam; Wisecarver, Jim; Adams, Joe; Cosgrove, Dominic; Kimberling, William

2002-12-01

Usher syndrome is an autosomal recessive disease that results in varying degrees of hearing loss and retinitis pigmentosa. Three types of Usher syndrome (I, II, and III) have been identified clinically with Usher type II being the most common of the three types. Usher type II has been localized to three different chromosomes 1q41, 3p, and 5q, corresponding to Usher type 2A, 2B, and 2C respectively. Usherin is a basement membrane protein encoded by the USH2A gene. Expression of usherin has been localized in the basement membrane of several tissues, however it is not ubiquitous. Immunohistochemistry detected usherin in the following human tissues: retina, cochlea, small and large intestine, pancreas, bladder, prostate, esophagus, trachea, thymus, salivary glands, placenta, ovary, fallopian tube, uterus, and testis. Usherin was absent in many other tissues such as heart, lung, liver, kidney, and brain. This distribution is consistent with the usherin distribution seen in the mouse. Conservation of usherin is also seen at the nucleotide and amino acid level when comparing the mouse and human gene sequences. Evolutionary conservation of usherin expression at the molecular level and in tissues unaffected by Usher 2a supports the important structural and functional role this protein plays in the human. In addition, we believe that these results could lead to a diagnostic procedure for the detection of Usher syndrome and those who carry an USH2A mutation.

A case study of assigning conservation value to dispersed habitat units for conservation planning

USGS Publications Warehouse

Rohweder, Jason J.; Sara C. Vacek,; Crimmins, Shawn M.; Thogmartin, Wayne E.

2015-01-01

Resource managers are increasingly tasked with developing habitat conservation plans in the face of numerous, sometimes competing, objectives. These plans must often be implemented across dispersed habitat conservation units that may contribute unequally to overall conservation objectives. Using U.S. Fish and Wildlife Service waterfowl production areas (WPA) in western Minnesota as our conservation landscape, we develop a landscape-scale approach for evaluating the conservation value of dispersed habitat conservation units with multiple conservation priorities. We evaluated conservation value based on a suite of variables directly applicable to conservation management practices, thus providing a direct link between conservation actions and outcomes. We developed spatial models specific to each of these conservation objectives and also developed two freely available prioritization tools to implement these analyses. We found that some WPAs provided high conservation value across a range of conservation objectives, suggesting that managing these specific areas would achieve multiple conservation goals. Conversely, other WPAs provided low conservation value for some objectives, suggesting they would be most effectively managed for a distinct set of specific conservation goals. Approaches such as ours provide a direct means of assessing the conservation value of dispersed habitat conservation units and could be useful in the development of habitat management plans, particularly when faced with multiple conservation objectives.

Conserved domains and SINE diversity during animal evolution.

PubMed

Luchetti, Andrea; Mantovani, Barbara

2013-10-01

Eukaryotic genomes harbour a number of mobile genetic elements (MGEs); moving from one genomic location to another, they are known to impact on the host genome. Short interspersed elements (SINEs) are well-represented, non-autonomous retroelements and they are likely the most diversified MGEs. In some instances, sequence domains conserved across unrelated SINEs have been identified; remarkably, one of these, called Nin, has been conserved since the Radiata-Bilateria splitting. Here we report on two new domains: Inv, derived from Nin, identified in insects and in deuterostomes, and Pln, restricted to polyneopteran insects. The identification of Inv and Pln sequences allowed us to retrieve new SINEs, two in insects and one in a hemichordate. The diverse structural combination of the different domains in different SINE families, during metazoan evolution, offers a clearer view of SINE diversity and their frequent de novo emergence through module exchange, possibly underlying the high evolutionary success of SINEs. © 2013 Elsevier Inc. All rights reserved.

Genome-wide identification of conserved microRNA and their response to drought stress in Dongxiang wild rice (Oryza rufipogon Griff.).

PubMed

Zhang, Fantao; Luo, Xiangdong; Zhou, Yi; Xie, Jiankun

2016-04-01

To identify drought stress-responsive conserved microRNA (miRNA) from Dongxiang wild rice (Oryza rufipogon Griff., DXWR) on a genome-wide scale, high-throughput sequencing technology was used to sequence libraries of DXWR samples, treated with and without drought stress. 505 conserved miRNAs corresponding to 215 families were identified. 17 were significantly down-regulated and 16 were up-regulated under drought stress. Stem-loop qRT-PCR revealed the same expression patterns as high-throughput sequencing, suggesting the accuracy of the sequencing result was high. Potential target genes of the drought-responsive miRNA were predicted to be involved in diverse biological processes. Furthermore, 16 miRNA families were first identified to be involved in drought stress response from plants. These results present a comprehensive view of the conserved miRNA and their expression patterns under drought stress for DXWR, which will provide valuable information and sequence resources for future basis studies.

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

USDA-ARS?s Scientific Manuscript database

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

Reef sharks: recent advances in ecological understanding to inform conservation.

PubMed

Osgood, G J; Baum, J K

2015-12-01

Sharks are increasingly being recognized as important members of coral-reef communities, but their overall conservation status remains uncertain. Nine of the 29 reef-shark species are designated as data deficient in the IUCN Red List, and three-fourths of reef sharks had unknown population trends at the time of their assessment. Fortunately, reef-shark research is on the rise. This new body of research demonstrates reef sharks' high site restriction, fidelity and residency on coral reefs, their broad trophic roles connecting reef communities and their high population genetic structure, all information that should be useful for their management and conservation. Importantly, recent studies on the abundance and population trends of the three classic carcharhinid reef sharks (grey reef shark Carcharhinus amblyrhynchos, blacktip reef shark Carcharhinus melanopterus and whitetip reef shark Triaenodon obesus) may contribute to reassessments identifying them as more vulnerable than currently realized. Because over half of the research effort has focused on only these three reef sharks and the nurse shark Ginglymostoma cirratum in only a few locales, there remain large taxonomic and geographic gaps in reef-shark knowledge. As such, a large portion of reef-shark biodiversity remains uncharacterized despite needs for targeted research identified in their red list assessments. A research agenda for the future should integrate abundance, life history, trophic ecology, genetics, habitat use and movement studies, and expand the breadth of such research to understudied species and localities, in order to better understand the conservation requirements of these species and to motivate effective conservation solutions. © 2015 The Fisheries Society of the British Isles.

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.

A Sensitive in Vitro High-Throughput Screen To Identify Pan-filoviral Replication Inhibitors Targeting the VP35–NP Interface

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

Liu, Gai; Nash, Peter J.; Johnson, Britney

The 2014 Ebola outbreak in West Africa, the largest outbreak on record, highlighted the need for novel approaches to therapeutics targeting Ebola virus (EBOV). Within the EBOV replication complex, the interaction between polymerase cofactor, viral protein 35 (VP35), and nucleoprotein (NP) is critical for viral RNA synthesis. We recently identified a peptide at the N-terminus of VP35 (termed NPBP) that is sufficient for interaction with NP and suppresses EBOV replication, suggesting that the NPBP binding pocket can serve as a potential drug target. Here we describe the development and validation of a sensitive high-throughput screen (HTS) using a fluorescence polarizationmore » assay. Initial hits from this HTS include the FDA-approved compound tolcapone, whose potency against EBOV infection was validated in a nonfluorescent secondary assay. High conservation of the NP–VP35 interface among filoviruses suggests that this assay has the capacity to identify pan-filoviral inhibitors for development as antivirals.« less

A modified reverse one-hybrid screen identifies transcriptional activation in Phyochrome-Interacting Factor 3

USDA-ARS?s Scientific Manuscript database

Transcriptional activation domains (TAD) are difficult to predict and identify, since they are not conserved and have little consensus. Here, we describe a yeast-based screening method that is able to identify individual amino acid residues involved in transcriptional activation in a high throughput...

Prioritizing landscapes for longleaf pine conservation

USGS Publications Warehouse

Grand, James B.; Kleiner, Kevin J.

2016-01-01

We developed a spatially explicit model and map, as a decision support tool (DST), to aid conservation agencies creating or maintaining open pine ecosystems. The tool identified areas that are likely to provide the greatest benefit to focal bird populations based on a comprehensive landscape analysis. We used NLCD 2011, SSURGO, and SEGAP data to map the density of desired resources for open pine ecosystems and six focal species of birds and 2 reptiles within the historic range of longleaf pine east of the Mississippi River. Binary rasters were created of sites with desired characteristics such as land form, hydrology, land use and land cover, soils, potential habitat for focal species, and putative source populations of focal species. Each raster was smoothed using a kernel density estimator. Rasters were combined and scaled to map priority locations for the management of each focal species. Species’ rasters were combined and scaled to provide maps of overall priority for birds and for birds and reptiles. The spatial data can be used to identify high priority areas for conservation or to compare areas under consideration for maintenance or creation of open pine ecosystems.

Synthesis of the conservation value of the early-successional stage in forests of eastern North America

Treesearch

David I. King; Scott Schlossberg

2014-01-01

As a result of changes in natural and anthropogenic disturbance regimes, the extent of early-successional forest across much of eastern North American is near historic lows, and continues to decline. This has caused many scientists to identify the conservation of early-successional species as a high priority. In this synthesis, we discuss the conservation implications...

High order filtering methods for approximating hyberbolic systems of conservation laws

NASA Technical Reports Server (NTRS)

Lafon, F.; Osher, S.

1990-01-01

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

Novel high-molecular weight fucosylated milk oligosaccharides identified in dairy streams.

PubMed

Mehra, Raj; Barile, Daniela; Marotta, Mariarosaria; Lebrilla, Carlito B; Chu, Caroline; German, J Bruce

2014-01-01

Oligosaccharides are the third largest component in human milk. This abundance is remarkable because oligosaccharides are not digestible by the newborn, and yet they have been conserved and amplified during evolution. In addition to encouraging the growth of a protective microbiota dominated by bifidobacteria, oligosaccharides have anti-infective activity, preventing pathogens from binding to intestinal cells. Although it would be advantageous adding these valuable molecules to infant milk formula, the technologies to reproduce the variety and complexity of human milk oligosaccharides by enzymatic/organic synthesis are not yet mature. Consequently, there is an enormous interest in alternative sources of these valuable oligosaccharides. Recent research has demonstrated that bovine milk and whey permeate also contain oligosaccharides. Thus, a thorough characterization of oligosaccharides in bovine dairy streams is an important step towards fully assessing their specific functionalities. In this study, bovine milk oligosaccharides (BMOs) were concentrated by membrane filtration from a readily available dairy stream called "mother liquor", and analyzed by high accuracy MALDI FT-ICR mass spectrometry. The combination of HPLC and accurate mass spectrometry allowed the identification of ideal processing conditions leading to the production of Kg amount of BMO enriched powders. Among the BMOs identified, 18 have high-molecular weight and corresponded in size to the most abundant oligosaccharides present in human milk. Notably 6 oligosaccharides contained fucose, a sugar monomer that is highly abundant in human milk, but is rarely observed in bovine milk. This work shows that dairy streams represent a potential source of complex milk oligosaccharides for commercial development of unique dairy ingredients in functional foods that reproduce the benefits of human milk.

Novel High-Molecular Weight Fucosylated Milk Oligosaccharides Identified in Dairy Streams

PubMed Central

Mehra, Raj; Barile, Daniela; Marotta, Mariarosaria; Lebrilla, Carlito B.; Chu, Caroline; German, J. Bruce

2014-01-01

Oligosaccharides are the third largest component in human milk. This abundance is remarkable because oligosaccharides are not digestible by the newborn, and yet they have been conserved and amplified during evolution. In addition to encouraging the growth of a protective microbiota dominated by bifidobacteria, oligosaccharides have anti-infective activity, preventing pathogens from binding to intestinal cells. Although it would be advantageous adding these valuable molecules to infant milk formula, the technologies to reproduce the variety and complexity of human milk oligosaccharides by enzymatic/organic synthesis are not yet mature. Consequently, there is an enormous interest in alternative sources of these valuable oligosaccharides. Recent research has demonstrated that bovine milk and whey permeate also contain oligosaccharides. Thus, a thorough characterization of oligosaccharides in bovine dairy streams is an important step towards fully assessing their specific functionalities. In this study, bovine milk oligosaccharides (BMOs) were concentrated by membrane filtration from a readily available dairy stream called “mother liquor”, and analyzed by high accuracy MALDI FT-ICR mass spectrometry. The combination of HPLC and accurate mass spectrometry allowed the identification of ideal processing conditions leading to the production of Kg amount of BMO enriched powders. Among the BMOs identified, 18 have high-molecular weight and corresponded in size to the most abundant oligosaccharides present in human milk. Notably 6 oligosaccharides contained fucose, a sugar monomer that is highly abundant in human milk, but is rarely observed in bovine milk. This work shows that dairy streams represent a potential source of complex milk oligosaccharides for commercial development of unique dairy ingredients in functional foods that reproduce the benefits of human milk. PMID:24810963

Minimizing species extinctions through strategic planning for conservation fencing.

PubMed

Ringma, Jeremy L; Wintle, Brendan; Fuller, Richard A; Fisher, Diana; Bode, Michael

2017-10-01

Conservation fences are an increasingly common management action, particularly for species threatened by invasive predators. However, unlike many conservation actions, fence networks are expanding in an unsystematic manner, generally as a reaction to local funding opportunities or threats. We conducted a gap analysis of Australia's large predator-exclusion fence network by examining translocation of Australian mammals relative to their extinction risk. To address gaps identified in species representation, we devised a systematic prioritization method for expanding the conservation fence network that explicitly incorporated population viability analysis and minimized expected species' extinctions. The approach was applied to New South Wales, Australia, where the state government intends to expand the existing conservation fence network. Existing protection of species in fenced areas was highly uneven; 67% of predator-sensitive species were unrepresented in the fence network. Our systematic prioritization yielded substantial efficiencies in that it reduced expected number of species extinctions up to 17 times more effectively than ad hoc approaches. The outcome illustrates the importance of governance in coordinating management action when multiple projects have similar objectives and rely on systematic methods rather than expanding networks opportunistically. © 2017 Society for Conservation Biology.

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.

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

USGS Publications Warehouse

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

2011-01-01

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

Identifying High-Rate Flows Based on Sequential Sampling

NASA Astrophysics Data System (ADS)

Zhang, Yu; Fang, Binxing; Luo, Hao

We consider the problem of fast identification of high-rate flows in backbone links with possibly millions of flows. Accurate identification of high-rate flows is important for active queue management, traffic measurement and network security such as detection of distributed denial of service attacks. It is difficult to directly identify high-rate flows in backbone links because tracking the possible millions of flows needs correspondingly large high speed memories. To reduce the measurement overhead, the deterministic 1-out-of-k sampling technique is adopted which is also implemented in Cisco routers (NetFlow). Ideally, a high-rate flow identification method should have short identification time, low memory cost and processing cost. Most importantly, it should be able to specify the identification accuracy. We develop two such methods. The first method is based on fixed sample size test (FSST) which is able to identify high-rate flows with user-specified identification accuracy. However, since FSST has to record every sampled flow during the measurement period, it is not memory efficient. Therefore the second novel method based on truncated sequential probability ratio test (TSPRT) is proposed. Through sequential sampling, TSPRT is able to remove the low-rate flows and identify the high-rate flows at the early stage which can reduce the memory cost and identification time respectively. According to the way to determine the parameters in TSPRT, two versions of TSPRT are proposed: TSPRT-M which is suitable when low memory cost is preferred and TSPRT-T which is suitable when short identification time is preferred. The experimental results show that TSPRT requires less memory and identification time in identifying high-rate flows while satisfying the accuracy requirement as compared to previously proposed methods.

Ramachandran analysis of conserved glycyl residues in homologous proteins of known structure.

PubMed

Lakshmi, Balasubramanian; Sinduja, Chandrasekaran; Archunan, Govind; Srinivasan, Narayanaswamy

2014-06-01

High conservation of glycyl residues in homologous proteins is fairly frequent. It is commonly understood that glycine tends to be highly conserved either because of its unique Ramachandran angles or to avoid steric clash that would arise with a larger side chain. Using a database of aligned 3D structures of homologous proteins we identified conserved Gly in 288 alignment positions from 85 families. Ninety-six of these alignment positions correspond to conserved Gly residue with (φ, ψ) values allowed for non-glycyl residues. Reasons for this observation were investigated by in-silico mutation of these glycyl residues to Ala. We found in 94% of the cases a short contact exists between the C(β) atom of the introduced Ala with the atoms which are often distant in the primary structure. This suggests the lack of space even for a short side chain thereby explaining high conservation of glycyl residues even when they adopt (φ, ψ) values allowed for Ala. In 189 alignment positions, the conserved glycyl residues adopt (φ, ψ) values which are disallowed for Ala. In-silico mutation of these Gly residues to Ala almost always results in steric hindrance involving C(β) atom of Ala as one would expect by comparing Ramachandran maps for Ala and Gly. Rare occurrence of the disallowed glycyl conformations even in ultrahigh resolution protein structures are accompanied by short contacts in the crystal structures and such disallowed conformations are not conserved in the homologues. These observations raise the doubt on the accuracy of such glycyl conformations in proteins. © 2014 The Protein Society.

Cultivating creativity in conservation science.

PubMed

Aslan, Clare E; Pinsky, Malin L; Ryan, Maureen E; Souther, Sara; Terrell, Kimberly A

2014-04-01

Conservation practitioners and scientists are often faced with seemingly intractable problems in which traditional approaches fail. While other sectors (e.g., business) frequently emphasize creative thinking to overcome complex challenges, creativity is rarely identified as an essential skill for conservationists. Yet more creative approaches are urgently needed in the effort to sustain Earth's biodiversity. We identified 4 strategies to develop skills in creative thinking and discuss underlying research and examples supporting each strategy. First, by breaking down barriers between disciplines and surrounding oneself with unfamiliar people, concepts, and perspectives, one can expand base knowledge and experiences and increase the potential for new combinations of ideas. Second, by meeting people where they are (both literally and figuratively), one exposes oneself to new environments and perspectives, which again broadens experiences and increases ability to communicate effectively with stakeholders. Third, by embracing risk responsibly, one is more likely to develop new, nontraditional solutions and be open to high-impact outcomes. Finally, by following a cycle of learning, struggle, and reflection, one can trigger neurophysiological changes that allow the brain to become more creative. Creativity is a learned trait, rather than an innate skill. It can be actively developed at both the individual and institutional levels, and learning to navigate the relevant social and practical barriers is key to the process. To maximize the success of conservation in the face of escalating challenges, one must take advantage of what has been learned from other disciplines and foster creativity as both a professional skill and an essential component of career training and individual development. © 2013 Society for Conservation Biology.

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.

Evaluation of 19,460 Wheat Accessions Conserved in the Indian National Genebank to Identify New Sources of Resistance to Rust and Spot Blotch Diseases.

PubMed

Kumar, Sundeep; Archak, Sunil; Tyagi, R K; Kumar, Jagdish; Vk, Vikas; Jacob, Sherry R; Srinivasan, Kalyani; Radhamani, J; Parimalan, R; Sivaswamy, M; Tyagi, Sandhya; Yadav, Mamata; Kumari, Jyotisna; Deepali; Sharma, Sandeep; Bhagat, Indoo; Meeta, Madhu; Bains, N S; Chowdhury, A K; Saha, B C; Bhattacharya, P M; Kumari, Jyoti; Singh, M C; Gangwar, O P; Prasad, P; Bharadwaj, S C; Gogoi, Robin; Sharma, J B; Gm, Sandeep Kumar; Saharan, M S; Bag, Manas; Roy, Anirban; Prasad, T V; Sharma, R K; Dutta, M; Sharma, Indu; Bansal, K C

2016-01-01

A comprehensive germplasm evaluation study of wheat accessions conserved in the Indian National Genebank was conducted to identify sources of rust and spot blotch resistance. Genebank accessions comprising three species of wheat-Triticum aestivum, T. durum and T. dicoccum were screened sequentially at multiple disease hotspots, during the 2011-14 crop seasons, carrying only resistant accessions to the next step of evaluation. Wheat accessions which were found to be resistant in the field were then assayed for seedling resistance and profiled using molecular markers. In the primary evaluation, 19,460 accessions were screened at Wellington (Tamil Nadu), a hotspot for wheat rusts. We identified 4925 accessions to be resistant and these were further evaluated at Gurdaspur (Punjab), a hotspot for stripe rust and at Cooch Behar (West Bengal), a hotspot for spot blotch. The second round evaluation identified 498 accessions potentially resistant to multiple rusts and 868 accessions potentially resistant to spot blotch. Evaluation of rust resistant accessions for seedling resistance against seven virulent pathotypes of three rusts under artificial epiphytotic conditions identified 137 accessions potentially resistant to multiple rusts. Molecular analysis to identify different combinations of genetic loci imparting resistance to leaf rust, stem rust, stripe rust and spot blotch using linked molecular markers, identified 45 wheat accessions containing known resistance genes against all three rusts as well as a QTL for spot blotch resistance. The resistant germplasm accessions, particularly against stripe rust, identified in this study can be excellent potential candidates to be employed for breeding resistance into the background of high yielding wheat cultivars through conventional or molecular breeding approaches, and are expected to contribute toward food security at national and global levels.

Evaluation of 19,460 Wheat Accessions Conserved in the Indian National Genebank to Identify New Sources of Resistance to Rust and Spot Blotch Diseases

PubMed Central

Jacob, Sherry R.; Srinivasan, Kalyani; Radhamani, J.; Parimalan, R.; Sivaswamy, M.; Tyagi, Sandhya; Yadav, Mamata; Kumari, Jyotisna; Deepali; Sharma, Sandeep; Bhagat, Indoo; Meeta, Madhu; Bains, N. S.; Chowdhury, A. K.; Saha, B. C.; Bhattacharya, P. M.; Kumari, Jyoti; Singh, M. C.; Gangwar, O. P.; Prasad, P.; Bharadwaj, S. C.; Gogoi, Robin; Sharma, J. B.; GM, Sandeep Kumar; Saharan, M. S.; Bag, Manas; Roy, Anirban; Prasad, T. V.; Sharma, R. K.; Dutta, M.; Sharma, Indu; Bansal, K. C.

2016-01-01

A comprehensive germplasm evaluation study of wheat accessions conserved in the Indian National Genebank was conducted to identify sources of rust and spot blotch resistance. Genebank accessions comprising three species of wheat–Triticum aestivum, T. durum and T. dicoccum were screened sequentially at multiple disease hotspots, during the 2011–14 crop seasons, carrying only resistant accessions to the next step of evaluation. Wheat accessions which were found to be resistant in the field were then assayed for seedling resistance and profiled using molecular markers. In the primary evaluation, 19,460 accessions were screened at Wellington (Tamil Nadu), a hotspot for wheat rusts. We identified 4925 accessions to be resistant and these were further evaluated at Gurdaspur (Punjab), a hotspot for stripe rust and at Cooch Behar (West Bengal), a hotspot for spot blotch. The second round evaluation identified 498 accessions potentially resistant to multiple rusts and 868 accessions potentially resistant to spot blotch. Evaluation of rust resistant accessions for seedling resistance against seven virulent pathotypes of three rusts under artificial epiphytotic conditions identified 137 accessions potentially resistant to multiple rusts. Molecular analysis to identify different combinations of genetic loci imparting resistance to leaf rust, stem rust, stripe rust and spot blotch using linked molecular markers, identified 45 wheat accessions containing known resistance genes against all three rusts as well as a QTL for spot blotch resistance. The resistant germplasm accessions, particularly against stripe rust, identified in this study can be excellent potential candidates to be employed for breeding resistance into the background of high yielding wheat cultivars through conventional or molecular breeding approaches, and are expected to contribute toward food security at national and global levels. PMID:27942031

Integrating Economic Costs and Biological Traits into Global Conservation Priorities for Carnivores

PubMed Central

Loyola, Rafael Dias; Oliveira-Santos, Luiz Gustavo Rodrigues; Almeida-Neto, Mário; Nogueira, Denise Martins; Kubota, Umberto; Diniz-Filho, José Alexandre Felizola; Lewinsohn, Thomas Michael

2009-01-01

Background Prioritization schemes usually highlight species-rich areas, where many species are at imminent risk of extinction. To be ecologically relevant these schemes should also include species biological traits into area-setting methods. Furthermore, in a world of limited funds for conservation, conservation action is constrained by land acquisition costs. Hence, including economic costs into conservation priorities can substantially improve their conservation cost-effectiveness. Methodology/Principal Findings We examined four global conservation scenarios for carnivores based on the joint mapping of economic costs and species biological traits. These scenarios identify the most cost-effective priority sets of ecoregions, indicating best investment opportunities for safeguarding every carnivore species, and also establish priority sets that can maximize species representation in areas harboring highly vulnerable species. We compared these results with a scenario that minimizes the total number of ecoregions required for conserving all species, irrespective of other factors. We found that cost-effective conservation investments should focus on 41 ecoregions highlighted in the scenario that consider simultaneously both ecoregion vulnerability and economic costs of land acquisition. Ecoregions included in priority sets under these criteria should yield best returns of investments since they harbor species with high extinction risk and have lower mean land cost. Conclusions/Significance Our study highlights ecoregions of particular importance for the conservation of the world's carnivores defining global conservation priorities in analyses that encompass socioeconomic and life-history factors. We consider the identification of a comprehensive priority-set of areas as a first step towards an in-situ biodiversity maintenance strategy. PMID:19710911

Growth/differentiation factor-11: an evolutionary conserved growth factor in vertebrates.

PubMed

Funkenstein, Bruria; Olekh, Elena

2010-11-01

Growth and differentiation factor-11 (GDF-11) is a member of the transforming growth factor-β superfamily and is thought to be derived together with myostatin (known also as GDF-8) from an ancestral gene. In the present study, we report the isolation and characterization of GDF-11 homolog from a marine teleost, the gilthead sea bream Sparus aurata, and show that this growth factor is highly conserved throughout vertebrates. Using bioinformatics, we identified GDF-11 in Tetraodon, Takifugu, medaka, and stickleback and found that they are highly conserved at the amino acid sequence as well as gene organization. Moreover, we found conservation of syntenic relationships among vertebrates in the GDF-11 locus. Transcripts for GDF-11 can be found in eggs and early embryos, albeit at low levels, while in post-hatching larvae expression levels are high and decreases as development progresses, suggesting that GDF-11 might have a role during early development of fish as found in tetrapods and zebrafish. Finally, GDF-11 is expressed in various tissues in the adult fish including muscle, brain, and eye.

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.

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

PubMed

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

2017-04-01

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

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

PubMed Central

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

2017-01-01

Poor dispersal species represent conservative benchmarks for biodiversity management because they provide insights into ecological processes influenced by habitat fragmentation that are less evident in more dispersive organisms. Here we used the poorly dispersive and threatened river blackfish (Gadopsis marmoratus) as a surrogate indicator system for assessing the effects of fragmentation in highly modified river basins and for prioritizing basin-wide management strategies. We combined individual, population and landscape-based approaches to analyze genetic variation in samples spanning the distribution of the species in Australia's Murray–Darling Basin, one of the world's most degraded freshwater systems. Our results indicate that G. marmoratus displays the hallmark of severe habitat fragmentation with notably scattered, small and demographically isolated populations with very low genetic diversity—a pattern found not only between regions and catchments but also between streams within catchments. By using hierarchically nested population sampling and assessing relationships between genetic uniqueness and genetic diversity across populations, we developed a spatial management framework that includes the selection of populations in need of genetic rescue. Landscape genetics provided an environmental criterion to identify associations between landscape features and ecological processes. Our results further our understanding of the impact that habitat quality and quantity has on habitat specialists with similarly low dispersal. They should also have practical applications for prioritizing both large- and small-scale conservation management actions for organisms inhabiting highly fragmented ecosystems. PMID:27876805

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

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.

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.

Conserved expression of transposon-derived non-coding transcripts in primate stem cells.

PubMed

Ramsay, LeeAnn; Marchetto, Maria C; Caron, Maxime; Chen, Shu-Huang; Busche, Stephan; Kwan, Tony; Pastinen, Tomi; Gage, Fred H; Bourque, Guillaume

2017-02-28

A significant portion of expressed non-coding RNAs in human cells is derived from transposable elements (TEs). Moreover, it has been shown that various long non-coding RNAs (lncRNAs), which come from the human endogenous retrovirus subfamily H (HERVH), are not only expressed but required for pluripotency in human embryonic stem cells (hESCs). To identify additional TE-derived functional non-coding transcripts, we generated RNA-seq data from induced pluripotent stem cells (iPSCs) of four primate species (human, chimpanzee, gorilla, and rhesus) and searched for transcripts whose expression was conserved. We observed that about 30% of TE instances expressed in human iPSCs had orthologous TE instances that were also expressed in chimpanzee and gorilla. Notably, our analysis revealed a number of repeat families with highly conserved expression profiles including HERVH but also MER53, which is known to be the source of a placental-specific family of microRNAs (miRNAs). We also identified a number of repeat families from all classes of TEs, including MLT1-type and Tigger families, that contributed a significant amount of sequence to primate lncRNAs whose expression was conserved. Together, these results describe TE families and TE-derived lncRNAs whose conserved expression patterns can be used to identify what are likely functional TE-derived non-coding transcripts in primate iPSCs.

Traveling waves and conservation laws for highly nonlinear wave equations modeling Hertz chains

NASA Astrophysics Data System (ADS)

Przedborski, Michelle; Anco, Stephen C.

2017-09-01

A highly nonlinear, fourth-order wave equation that models the continuum theory of long wavelength pulses in weakly compressed, homogeneous, discrete chains with a general power-law contact interaction is studied. For this wave equation, all solitary wave solutions and all nonlinear periodic wave solutions, along with all conservation laws, are derived. The solutions are explicitly parameterized in terms of the asymptotic value of the wave amplitude in the case of solitary waves and the peak of the wave amplitude in the case of nonlinear periodic waves. All cases in which the solution expressions can be stated in an explicit analytic form using elementary functions are worked out. In these cases, explicit expressions for the total energy and total momentum for all solutions are obtained as well. The derivation of the solutions uses the conservation laws combined with an energy analysis argument to reduce the wave equation directly to a separable first-order differential equation that determines the wave amplitude in terms of the traveling wave variable. This method can be applied more generally to other highly nonlinear wave equations.

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.

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

Backcasting the decline of a vulnerable Great Plains reproductive ecotype: identifying threats and conservation priorities.

PubMed

Worthington, Thomas A; Brewer, Shannon K; Grabowski, Timothy B; Mueller, Julia

2014-01-01

Conservation efforts for threatened or endangered species are challenging because the multi-scale factors that relate to their decline or inhibit their recovery are often unknown. To further exacerbate matters, the perceptions associated with the mechanisms of species decline are often viewed myopically rather than across the entire species range. We used over 80 years of fish presence data collected from the Great Plains and associated ecoregions of the United States, to investigate the relative influence of changing environmental factors on the historic and current truncated distributions of the Arkansas River shiner Notropis girardi. Arkansas River shiner represent a threatened reproductive ecotype considered especially well adapted to the harsh environmental extremes of the Great Plains. Historic (n = 163 records) and current (n = 47 records) species distribution models were constructed using a vector-based approach in MaxEnt by splitting the available data at a time when Arkansas River shiner dramatically declined. Discharge and stream order were significant predictors in both models; however, the shape of the relationship between the predictors and species presence varied between time periods. Drift distance (river fragment length available for ichthyoplankton downstream drift before meeting a barrier) was a more important predictor in the current model and indicated river segments 375-780 km had the highest probability of species presence. Performance for the historic and current models was high (area under the curve; AUC > 0.95); however, forecasting and backcasting to alternative time periods suggested less predictive power. Our results identify fragments that could be considered refuges for endemic plains fish species and we highlight significant environmental factors (e.g., discharge) that could be manipulated to aid recovery. Published 2013. This article is a U.S. Government work and is in the public domain in the U.S.A.

Backcasting the decline of a vulnerable Great Plains reproductive ecotype: identifying threats and conservation priorities

USGS Publications Warehouse

Worthington, Thomas A.; Brewer, Shannon K.; Grabowski, Timothy B.; Mueller, Julia

2014-01-01

Conservation efforts for threatened or endangered species are challenging because the multi-scale factors that relate to their decline or inhibit their recovery are often unknown. To further exacerbate matters, the perceptions associated with the mechanisms of species decline are often viewed myopically rather than across the entire species range. We used over 80 years of fish presence data collected from the Great Plains and associated ecoregions of the United States, to investigate the relative influence of changing environmental factors on the historic and current truncated distributions of the Arkansas River shiner Notropis girardi. Arkansas River shiner represent a threatened reproductive ecotype considered especially well adapted to the harsh environmental extremes of the Great Plains. Historic (n = 163 records) and current (n = 47 records) species distribution models were constructed using a vector-based approach in MaxEnt by splitting the available data at a time when Arkansas River shiner dramatically declined. Discharge and stream order were significant predictors in both models; however, the shape of the relationship between the predictors and species presence varied between time periods. Drift distance (river fragment length available for ichthyoplankton downstream drift before meeting a barrier) was a more important predictor in the current model and indicated river segments 375–780 km had the highest probability of species presence. Performance for the historic and current models was high (area under the curve; AUC > 0.95); however, forecasting and backcasting to alternative time periods suggested less predictive power. Our results identify fragments that could be considered refuges for endemic plains fish species and we highlight significant environmental factors (e.g., discharge) that could be manipulated to aid recovery.

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.

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

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

Criterion for Identifying Vortices in High-Pressure Flows

NASA Technical Reports Server (NTRS)

Bellan, Josette; Okong'o, Nora

2007-01-01

A study of four previously published computational criteria for identifying vortices in high-pressure flows has led to the selection of one of them as the best. This development can be expected to contribute to understanding of high-pressure flows, which occur in diverse settings, including diesel, gas turbine, and rocket engines and the atmospheres of Jupiter and other large gaseous planets. Information on the atmospheres of gaseous planets consists mainly of visual and thermal images of the flows over the planets. Also, validation of recently proposed computational models of high-pressure flows entails comparison with measurements, which are mainly of visual nature. Heretofore, the interpretation of images of high-pressure flows to identify vortices has been based on experience with low-pressure flows. However, high-pressure flows have features distinct from those of low-pressure flows, particularly in regions of high pressure gradient magnitude caused by dynamic turbulent effects and by thermodynamic mixing of chemical species. Therefore, interpretations based on low-pressure behavior may lead to misidentification of vortices and other flow structures in high-pressure flows. The study reported here was performed in recognition of the need for one or more quantitative criteria for identifying coherent flow structures - especially vortices - from previously generated flow-field data, to complement or supersede the determination of flow structures by visual inspection of instantaneous fields or flow animations. The focus in the study was on correlating visible images of flow features with various quantities computed from flow-field data.

The selective conservative management of small traumatic pneumothoraces following stab injuries is safe: experience from a high-volume trauma service in South Africa.

PubMed

Kong, V Y; Oosthuizen, G V; Clarke, D L

2015-02-01

The selective conservative management of small pneumothoraces (PTXs) following stab injuries is controversial. We reviewed a cohort of patients managed conservatively in a high volume trauma service in South Africa. A retrospective review over a 2-year period identified 125 asymptomatic patients with small PTXs measuring <2 cm on chest radiograph who were managed conservatively. Of the 125 patients included in the study, 92% were male (115/125), and the median age for all patients was 21 years (19-24). Ninety-seven per cent (121/125) of the weapons involved were knives, and 3% (4/125) were screwdrivers. Sixty-one per cent of all injuries were on the left side. Eighty-two per cent (102/125) sustained a single stab, and 18% (23/125) had multiple stabs. Thirty-nine per cent (49/125) had a PTX <0.5 cm (Group A), 26% (32/125) were ≥ 0.5 to <1 cm (Group B), 19% (24/125) were ≥ 1 to <1.5 cm (Group C) and 15% (20/125) were ≥ 1.5 to <2 cm (Group D). Three per cent of all patients (4/125) eventually required ICDs (one in Group C, three in Group D). All four patients had ICDs in situ for 24 h. The remaining 97% (121/125) were all managed successfully by active clinical observation alone. There were no subsequent readmissions, morbidity or mortality as a direct result of our conservative approach. The selective conservative management of asymptomatic small PTXs from stab injuries is safe if undertaken in the appropriate setting.

A highly conserved metalloprotease effector enhances virulence in the maize anthracnose fungus Colletotrichum graminicola.

PubMed

Sanz-Martín, José M; Pacheco-Arjona, José Ramón; Bello-Rico, Víctor; Vargas, Walter A; Monod, Michel; Díaz-Mínguez, José M; Thon, Michael R; Sukno, Serenella A

2016-09-01

Colletotrichum graminicola causes maize anthracnose, an agronomically important disease with a worldwide distribution. We have identified a fungalysin metalloprotease (Cgfl) with a role in virulence. Transcriptional profiling experiments and live cell imaging show that Cgfl is specifically expressed during the biotrophic stage of infection. To determine whether Cgfl has a role in virulence, we obtained null mutants lacking Cgfl and performed pathogenicity and live microscopy assays. The appressorium morphology of the null mutants is normal, but they exhibit delayed development during the infection process on maize leaves and roots, showing that Cgfl has a role in virulence. In vitro chitinase activity assays of leaves infected with wild-type and null mutant strains show that, in the absence of Cgfl, maize leaves exhibit increased chitinase activity. Phylogenetic analyses show that Cgfl is highly conserved in fungi. Similarity searches, phylogenetic analysis and transcriptional profiling show that C. graminicola encodes two LysM domain-containing homologues of Ecp6, suggesting that this fungus employs both Cgfl-mediated and LysM protein-mediated strategies to control chitin signalling. © 2015 BSPP and John Wiley & Sons Ltd.

Landowner and practitioner perspectives on private land conservation programs

USGS Publications Warehouse

Lute, Michelle L.; Gillespie, Caitlyn R.; Fontaine, Joseph J.; Martin, Dustin R.

2018-01-01

Efforts to reverse declines in native grasslands benefit from agricultural policies that encourage private land conservation. The U.S. Department of Agriculture’s Conservation Reserve Program (CRP) improved conservation across landscapes but enrollment has declined. We used sequential exploratory mixed methods to compare landowner and conservation practitioners’ perceptions, evaluate perceived benefits, and identify potential improvements to CRP. Focus groups of practitioners informed a quantitative survey of landowners who had properties >160 total acres in Nebraska. Results suggest potential misalignment in perceptions between practitioners and landowners. Practitioners were concerned that conservation, especially of wildlife, was secondary to profit. But the majority of landowners valued CRP-related ecosystem services, including native pollinators. Practitioners posited that younger landowners were primarily profit motivated, but CRP enrollment did not differ by demographics. Practitioners and landowners identified rule complexity as a major challenge and practitioner–landowner relationships as critical to success. Findings suggest that practitioners may underestimate non-economic motivations and illuminate opportunities to encourage private land conservation.

Liberal or conservative? Gender, identity, and perception of historical religious positions.

PubMed

Bensko, N L; Canetto, S S; Sugar, J A; Viney, W

1995-11-01

Conservatism is often assumed to imply a continuity of values and positions between past and present. Previous research has demonstrated, however, that there are discontinuities between historical and contemporary political conservatism and that modern political conservatives endorse programs and legislation once regarded as liberal. Testing whether the same pattern may hold for religious conservatism was the purpose of this research. Perceptions of conservative positions in Christian history were assessed among young adults (N = 221). Results showed that individuals who identified themselves as conservatives were less likely to recognize past conservative positions on religious issues than individuals who identified themselves as liberals. These findings were not accounted for by lack of knowledge about religious history on the part of conservatives. Furthermore, women were more likely than men to accurately identify conservative and liberal positions of the past. The findings suggest that religious conservatism, like political conservatism, does not necessarily involve a continuity of positions between past and present.

Interactions between the Nse3 and Nse4 Components of the SMC5-6 Complex Identify Evolutionarily Conserved Interactions between MAGE and EID Families

PubMed Central

Kozakova, Lucie; Liao, Chunyan; Guerineau, Marc; Colnaghi, Rita; Vidot, Susanne; Marek, Jaromir; Bathula, Sreenivas R.; Lehmann, Alan R.; Palecek, Jan

2011-01-01

Background The SMC5-6 protein complex is involved in the cellular response to DNA damage. It is composed of 6–8 polypeptides, of which Nse1, Nse3 and Nse4 form a tight sub-complex. MAGEG1, the mammalian ortholog of Nse3, is the founding member of the MAGE (melanoma-associated antigen) protein family and Nse4 is related to the EID (E1A-like inhibitor of differentiation) family of transcriptional repressors. Methodology/Principal Findings Using site-directed mutagenesis, protein-protein interaction analyses and molecular modelling, we have identified a conserved hydrophobic surface on the C-terminal domain of Nse3 that interacts with Nse4 and identified residues in its N-terminal domain that are essential for interaction with Nse1. We show that these interactions are conserved in the human orthologs. Furthermore, interaction of MAGEG1, the mammalian ortholog of Nse3, with NSE4b, one of the mammalian orthologs of Nse4, results in transcriptional co-activation of the nuclear receptor, steroidogenic factor 1 (SF1). In an examination of the evolutionary conservation of the Nse3-Nse4 interactions, we find that several MAGE proteins can interact with at least one of the NSE4/EID proteins. Conclusions/Significance We have found that, despite the evolutionary diversification of the MAGE family, the characteristic hydrophobic surface shared by all MAGE proteins from yeast to humans mediates its binding to NSE4/EID proteins. Our work provides new insights into the interactions, evolution and functions of the enigmatic MAGE proteins. PMID:21364888

Planning for land use and conservation: Assessing GIS-based conservation software for land use planning

Treesearch

Rob Baldwin; Ryan Scherzinger; Don Lipscomb; Miranda Mockrin; Susan Stein

2014-01-01

Recent advances in planning and ecological software make it possible to conduct highly technical analyses to prioritize conservation investments and inform local land use planning. We review these tools, termed conservation planning tools, and assess the knowledge of a key set of potential users: the land use planning community. We grouped several conservation software...

Logic of energy conservation

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

Schipper, L.; Darmstadter, J.

1978-01-01

Energy conservation is seen as a complex mix of economic and moral considerations, which should be applied to specific strategies for changing waste handling, lifestyle, growth, etc., after meaningful payoffs have been researched and identified. The author recommends measuring energy conservation in terms of primary energy resources saved, and evaluating changes in consumption patterns on the basis of indirect as well as direct energy use. He feels consideration should be given to the intensity of energy use as well as to before-and-after comparisons. Human factors and wellbeing need to be included in shifts from energy-intensive to labor-intensive equipment. Curtailment ofmore » energy supplies as a conservation technique is seen as less effective than substitution, changes in habit and attitude, and changes in the types of goods and services demanded. While add-on investments have short-term value, new capital-equipment investments offer greater energy and economic savings in the long run. The author cautions against using strict rules to determine energy efficiency by relating energy to gross national product. Conservation is seen as an economic stimulus when compared to the costs of not conserving. 14 references. (DCK)« less

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.

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

High spatial resolution mapping of land cover types in a priority area for conservation in the Brazilian savanna

NASA Astrophysics Data System (ADS)

Ribeiro, F.; Roberts, D. A.; Hess, L. L.; Davis, F. W.; Caylor, K. K.; Nackoney, J.; Antunes Daldegan, G.

2017-12-01

Savannas are heterogeneous landscapes consisting of highly mixed land cover types that lack clear distinct boundaries. The Brazilian Cerrado is a Neotropical savanna considered a biodiversity hotspot for conservation due to its biodiversity richness and rapid transformation of its landscape by crop and pasture activities. The Cerrado is one of the most threatened Brazilian biomes and only 2.2% of its original extent is strictly protected. Accurate mapping and monitoring of its ecosystems and adjacent land use are important to select areas for conservation and to improve our understanding of the dynamics in this biome. Land cover mapping of savannas is difficult due to spectral similarity between land cover types resulting from similar vegetation structure, floristically similar components, generalization of land cover classes, and heterogeneity usually expressed as small patch sizes within the natural landscape. These factors are the major contributor to misclassification and low map accuracies among remote sensing studies in savannas. Specific challenges to map the Cerrado's land cover types are related to the spectral similarity between classes of land use and natural vegetation, such as natural grassland vs. cultivated pasture, and forest ecosystem vs. crops. This study seeks to classify and evaluate the land cover patterns across an area ranked as having extremely high priority for future conservation in the Cerrado. The main objective of this study is to identify the representativeness of each vegetation type across the landscape using high to moderate spatial resolution imagery using an automated scheme. A combination of pixel-based and object-based approaches were tested using RapidEye 3A imagery (5m spatial resolution) to classify the Cerrado's major land cover types. The random forest classifier was used to map the major ecosystems present across the area, and demonstrated to have an effective result with 68% of overall accuracy. Post

Conservation and diversification of Msx protein in metazoan evolution.

PubMed

Takahashi, Hirokazu; Kamiya, Akiko; Ishiguro, Akira; Suzuki, Atsushi C; Saitou, Naruya; Toyoda, Atsushi; Aruga, Jun

2008-01-01

Msx (/msh) family genes encode homeodomain (HD) proteins that control ontogeny in many animal species. We compared the structures of Msx genes from a wide range of Metazoa (Porifera, Cnidaria, Nematoda, Arthropoda, Tardigrada, Platyhelminthes, Mollusca, Brachiopoda, Annelida, Echiura, Echinodermata, Hemichordata, and Chordata) to gain an understanding of the role of these genes in phylogeny. Exon-intron boundary analysis suggested that the position of the intron located N-terminally to the HDs was widely conserved in all the genes examined, including those of cnidarians. Amino acid (aa) sequence comparison revealed 3 new evolutionarily conserved domains, as well as very strong conservation of the HDs. Two of the three domains were associated with Groucho-like protein binding in both a vertebrate and a cnidarian Msx homolog, suggesting that the interaction between Groucho-like proteins and Msx proteins was established in eumetazoan ancestors. Pairwise comparison among the collected HDs and their C-flanking aa sequences revealed that the degree of sequence conservation varied depending on the animal taxa from which the sequences were derived. Highly conserved Msx genes were identified in the Vertebrata, Cephalochordata, Hemichordata, Echinodermata, Mollusca, Brachiopoda, and Anthozoa. The wide distribution of the conserved sequences in the animal phylogenetic tree suggested that metazoan ancestors had already acquired a set of conserved domains of the current Msx family genes. Interestingly, although strongly conserved sequences were recovered from the Vertebrata, Cephalochordata, and Anthozoa, the sequences from the Urochordata and Hydrozoa showed weak conservation. Because the Vertebrata-Cephalochordata-Urochordata and Anthozoa-Hydrozoa represent sister groups in the Chordata and Cnidaria, respectively, Msx sequence diversification may have occurred differentially in the course of evolution. We speculate that selective loss of the conserved domains in Msx family

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

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

Delineating priority habitat areas for the conservation of Andean bears in northern Ecuador

USGS Publications Warehouse

Peralvo, M.F.; Cuesta, F.; Van Manen, F.

2005-01-01

We sought to identify priority areas for the conservation of Andean bear (Tremarctos ornatus) habitat in the northern portion of the eastern Andean cordillera in Ecuador. The study area included pa??ramo and montane forest habitats within the Antisana and Cayambe-Coca ecological reserves, and unprotected areas north of these reserves with elevations ranging from 1,800 to 4,300 m. We collected data on bear occurrence along 53 transects during 2000-01 in the Oyacachi River basin, an area of indigenous communities within the Cayambe-Coca Ecological Reserve. We used those data and a set of 7 environmental variables to predict suitability of Andean bear habitat using Mahalanobis distance, a multivariate measure of dissimilarity. The Mahalanobis distance values were classified into 5 classes of habitat suitability and generalized to a resolution of 1,650-m ?? 1,650-m grid cells. Clusters of grid cells with high suitability values were delineated from the generalized model and denned as important habitat areas (IHAs) for conservation. The IHAs were ranked using a weighted index that included factors of elevation range, influence from disturbed areas, and current conservation status. We identified 12 IHAs, which were mainly associated with pa??ramo and cloud forest habitats; 2 of these areas have high conservation priorities because they are outside existing reserves and close to areas of human pressure. The distribution of the IHAs highlighted the role of human land use as the main source of fragmentation of Andean bear habitat in this region, emphasizing the importance of preserving habitat connectivity to allow the seasonal movements among habitat types that we documented for this species. Furthermore, the existence of areas with high habitat suitability close to areas of intense human use indicates the importance of bear-human conflict management as a critical Andean bear conservation strategy. We suggest that a promising conservation opportunity for this species is

Energy conservation of the scattering from one-dimensional random rough surfaces in the high-frequency limit.

PubMed

Pinel, Nicolas; Bourlier, Christophe; Saillard, Joseph

2005-08-01

Energy conservation of the scattering from one-dimensional strongly rough dielectric surfaces is investigated using the Kirchhoff approximation with single reflection and by taking the shadowing phenomenon into account, both in reflection and transmission. In addition, because no shadowing function in transmission exists in the literature, this function is presented here in detail. The model is reduced to the high-frequency limit (or geometric optics). The energy conservation criterion is investigated versus the incidence angle, the permittivity of the lower medium, and the surface rms slope.

Optimum allocation of conservation funds and choice of conservation programs for a set of African cattle breeds

PubMed Central

Reist-Marti, Sabine B; Abdulai, Awudu; Simianer, Henner

2006-01-01

Although funds for livestock conservation are limited there is little known about the optimal allocation of conservation funds. A new algorithm was used to allocate Mio US$ 1, 2, 3, 5 or unlimited funds, discounted over 50 years, on 23 African cattle breeds conserved with four different possible conservation programs. Additionally, Mio US$ 1 was preferably allocated to breeds with special traits. The conceptional in situ conservation programs strongly involve breeders and give them part of the responsibility for the conservation of the breed. Therefore, the pure in situ conservation was more efficient than cryoconservation or combined in situ and cryoconservation. The average annual discounted conservation cost for a breed can be as low as US$ 1000 to US$ 4400 depending on the design of the conservation program and the economic situation of the country of conservation. The choice of the breeds and the optimal conservation program and the amount of money allocated to each breed depend on many factors such as the amount of funds available, the conservation potential of each breed, the effects of the conservation program as well as its cost. With Mio US$ 1, 64% of the present diversity could be maintained over 50 years, which is 13% more than would be maintained if no conservation measures were implemented. Special traits could be conserved with a rather small amount of the total funds. Diversity can not be conserved completely, not even with unlimited funds. A maximum of 92% of the present diversity could be conserved with Mio US$ 10, leaving 8% of the diversity to unpredictable happenings. The suggested algorithm proved to be useful for optimal allocation of conservation funds. It allocated the funds optimally among breeds by identifying the most suited conservation program for each breed, also accounting for differences in currency exchange rates between the different countries. PMID:16451794

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

NASA Technical Reports Server (NTRS)

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

1990-01-01

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

Rapid identifying high-influence nodes in complex networks

NASA Astrophysics Data System (ADS)

Song, Bo; Jiang, Guo-Ping; Song, Yu-Rong; Xia, Ling-Ling

2015-10-01

A tiny fraction of influential individuals play a critical role in the dynamics on complex systems. Identifying the influential nodes in complex networks has theoretical and practical significance. Considering the uncertainties of network scale and topology, and the timeliness of dynamic behaviors in real networks, we propose a rapid identifying method (RIM) to find the fraction of high-influential nodes. Instead of ranking all nodes, our method only aims at ranking a small number of nodes in network. We set the high-influential nodes as initial spreaders, and evaluate the performance of RIM by the susceptible-infected-recovered (SIR) model. The simulations show that in different networks, RIM performs well on rapid identifying high-influential nodes, which is verified by typical ranking methods, such as degree, closeness, betweenness, and eigenvector centrality methods. Project supported by the National Natural Science Foundation of China (Grant Nos. 61374180 and 61373136), the Ministry of Education Research in the Humanities and Social Sciences Planning Fund Project, China (Grant No. 12YJAZH120), and the Six Projects Sponsoring Talent Summits of Jiangsu Province, China (Grant No. RLD201212).

Genome-wide discovery of novel and conserved microRNAs in white shrimp (Litopenaeus vannamei).

PubMed

Xi, Qian-Yun; Xiong, Yuan-Yan; Wang, Yuan-Mei; Cheng, Xiao; Qi, Qi-En; Shu, Gang; Wang, Song-Bo; Wang, Li-Na; Gao, Ping; Zhu, Xiao-Tong; Jiang, Qing-Yan; Zhang, Yong-Liang; Liu, Li

2015-01-01

Of late years, a large amount of conserved and species-specific microRNAs (miRNAs) have been performed on identification from species which are economically important but lack a full genome sequence. In this study, Solexa deep sequencing and cross-species miRNA microarray were used to detect miRNAs in white shrimp. We identified 239 conserved miRNAs, 14 miRNA* sequences and 20 novel miRNAs by bioinformatics analysis from 7,561,406 high-quality reads representing 325,370 distinct sequences. The all 20 novel miRNAs were species-specific in white shrimp and not homologous in other species. Using the conserved miRNAs from the miRBase database as a query set to search for homologs from shrimp expressed sequence tags (ESTs), 32 conserved computationally predicted miRNAs were discovered in shrimp. In addition, using microarray analysis in the shrimp fed with Panax ginseng polysaccharide complex, 151 conserved miRNAs were identified, 18 of which were significant up-expression, while 49 miRNAs were significant down-expression. In particular, qRT-PCR analysis was also performed for nine miRNAs in three shrimp tissues such as muscle, gill and hepatopancreas. Results showed that these miRNAs expression are tissue specific. Combining results of the three methods, we detected 20 novel and 394 conserved miRNAs. Verification with quantitative reverse transcription (qRT-PCR) and Northern blot showed a high confidentiality of data. The study provides the first comprehensive specific miRNA profile of white shrimp, which includes useful information for future investigations into the function of miRNAs in regulation of shrimp development and immunology.

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

PubMed

Larue, Michelle A; Knight, Joseph

2014-12-01

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

Ten ways remote sensing can contribute to conservation.

PubMed

Rose, Robert A; Byler, Dirck; Eastman, J Ron; Fleishman, Erica; Geller, Gary; Goetz, Scott; Guild, Liane; Hamilton, Healy; Hansen, Matt; Headley, Rachel; Hewson, Jennifer; Horning, Ned; Kaplin, Beth A; Laporte, Nadine; Leidner, Allison; Leimgruber, Peter; Morisette, Jeffrey; Musinsky, John; Pintea, Lilian; Prados, Ana; Radeloff, Volker C; Rowen, Mary; Saatchi, Sassan; Schill, Steve; Tabor, Karyn; Turner, Woody; Vodacek, Anthony; Vogelmann, James; Wegmann, Martin; Wilkie, David; Wilson, Cara

2015-04-01

In an effort to increase conservation effectiveness through the use of Earth observation technologies, a group of remote sensing scientists affiliated with government and academic institutions and conservation organizations identified 10 questions in conservation for which the potential to be answered would be greatly increased by use of remotely sensed data and analyses of those data. Our goals were to increase conservation practitioners' use of remote sensing to support their work, increase collaboration between the conservation science and remote sensing communities, identify and develop new and innovative uses of remote sensing for advancing conservation science, provide guidance to space agencies on how future satellite missions can support conservation science, and generate support from the public and private sector in the use of remote sensing data to address the 10 conservation questions. We identified a broad initial list of questions on the basis of an email chain-referral survey. We then used a workshop-based iterative and collaborative approach to whittle the list down to these final questions (which represent 10 major themes in conservation): How can global Earth observation data be used to model species distributions and abundances? How can remote sensing improve the understanding of animal movements? How can remotely sensed ecosystem variables be used to understand, monitor, and predict ecosystem response and resilience to multiple stressors? How can remote sensing be used to monitor the effects of climate on ecosystems? How can near real-time ecosystem monitoring catalyze threat reduction, governance and regulation compliance, and resource management decisions? How can remote sensing inform configuration of protected area networks at spatial extents relevant to populations of target species and ecosystem services? How can remote sensing-derived products be used to value and monitor changes in ecosystem services? How can remote sensing be used to

Using risk-adjustment models to identify high-cost risks.

PubMed

Meenan, Richard T; Goodman, Michael J; Fishman, Paul A; Hornbrook, Mark C; O'Keeffe-Rosetti, Maureen C; Bachman, Donald J

2003-11-01

We examine the ability of various publicly available risk models to identify high-cost individuals and enrollee groups using multi-HMO administrative data. Five risk-adjustment models (the Global Risk-Adjustment Model [GRAM], Diagnostic Cost Groups [DCGs], Adjusted Clinical Groups [ACGs], RxRisk, and Prior-expense) were estimated on a multi-HMO administrative data set of 1.5 million individual-level observations for 1995-1996. Models produced distributions of individual-level annual expense forecasts for comparison to actual values. Prespecified "high-cost" thresholds were set within each distribution. The area under the receiver operating characteristic curve (AUC) for "high-cost" prevalences of 1% and 0.5% was calculated, as was the proportion of "high-cost" dollars correctly identified. Results are based on a separate 106,000-observation validation dataset. For "high-cost" prevalence targets of 1% and 0.5%, ACGs, DCGs, GRAM, and Prior-expense are very comparable in overall discrimination (AUCs, 0.83-0.86). Given a 0.5% prevalence target and a 0.5% prediction threshold, DCGs, GRAM, and Prior-expense captured $963,000 (approximately 3%) more "high-cost" sample dollars than other models. DCGs captured the most "high-cost" dollars among enrollees with asthma, diabetes, and depression; predictive performance among demographic groups (Medicaid members, members over 64, and children under 13) varied across models. Risk models can efficiently identify enrollees who are likely to generate future high costs and who could benefit from case management. The dollar value of improved prediction performance of the most accurate risk models should be meaningful to decision-makers and encourage their broader use for identifying high costs.

Conservation laws shape dissipation

NASA Astrophysics Data System (ADS)

Rao, Riccardo; Esposito, Massimiliano

2018-02-01

Starting from the most general formulation of stochastic thermodynamics—i.e. a thermodynamically consistent nonautonomous stochastic dynamics describing systems in contact with several reservoirs—we define a procedure to identify the conservative and the minimal set of nonconservative contributions in the entropy production. The former is expressed as the difference between changes caused by time-dependent drivings and a generalized potential difference. The latter is a sum over the minimal set of flux-force contributions controlling the dissipative flows across the system. When the system is initially prepared at equilibrium (e.g. by turning off drivings and forces), a finite-time detailed fluctuation theorem holds for the different contributions. Our approach relies on identifying the complete set of conserved quantities and can be viewed as the extension of the theory of generalized Gibbs ensembles to nonequilibrium situations.

7 CFR 766.110 - Conservation Contract.

Code of Federal Regulations, 2010 CFR

2010-01-01

... floodplains; (iii) Areas of high water quality or scenic value; (iv) Historic or cultural properties listed in..., or 50 years. (e) Conservation management plan. The Agency, through the recommendations of the Conservation Contract review team, is responsible for approving the conservation management plan. (f...

7 CFR 766.110 - Conservation Contract.

Code of Federal Regulations, 2011 CFR

2011-01-01

... floodplains; (iii) Areas of high water quality or scenic value; (iv) Historic or cultural properties listed in..., or 50 years. (e) Conservation management plan. The Agency, through the recommendations of the Conservation Contract review team, is responsible for approving the conservation management plan. (f...

A systematic conservation planning approach to fire risk management in Natura 2000 sites.

PubMed

Foresta, Massimiliano; Carranza, Maria Laura; Garfì, Vittorio; Di Febbraro, Mirko; Marchetti, Marco; Loy, Anna

2016-10-01

A primary challenge in conservation biology is to preserve the most representative biodiversity while simultaneously optimizing the efforts associated with conservation. In Europe, the implementation of the Natura 2000 network requires protocols to recognize and map threats to biodiversity and to identify specific mitigation actions. We propose a systematic conservation planning approach to optimize management actions against specific threats based on two fundamental parameters: biodiversity values and threat pressure. We used the conservation planning software Marxan to optimize a fire management plan in a Natura 2000 coastal network in southern Italy. We address three primary questions: i) Which areas are at high fire risk? ii) Which areas are the most valuable for threatened biodiversity? iii) Which areas should receive priority risk-mitigation actions for the optimal effect?, iv) which fire-prevention actions are feasible in the management areas?. The biodiversity values for the Natura 2000 spatial units were derived from the distribution maps of 18 habitats and 89 vertebrate species of concern in Europe (Habitat Directive 92/43/EEC). The threat pressure map, defined as fire probability, was obtained from digital layers of fire risk and of fire frequency. Marxan settings were defined as follows: a) planning units of 40 × 40 m, b) conservation features defined as all habitats and vertebrate species of European concern occurring in the study area, c) conservation targets defined according with fire sensitivity and extinction risk of conservation features, and d) costs determined as the complement of fire probabilities. We identified 23 management areas in which to concentrate efforts for the optimal reduction of fire-induced effects. Because traditional fire prevention is not feasible for most of policy habitats included in the management areas, alternative prevention practices were identified that allows the conservation of the vegetation structure. The

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

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

On the Role of Water Models in Quantifying the Binding Free Energy of Highly Conserved Water Molecules in Proteins: The Case of Concanavalin A.

PubMed

Fadda, Elisa; Woods, Robert J

2011-10-11

The ability of ligands to displace conserved water molecules in protein binding sites is of significant interest in drug design and is particularly pertinent in the case of glycomimetic drugs. This concept was explored in previous work [ Clarke et al. J. Am. Chem. Soc. 2001 , 123 , 12238 - 12247 and Kadirvelraj et al. J. Am. Chem. Soc. 2008 , 130 , 16933 - 16942 ] for a highly conserved water molecule located in the binding site of the prototypic carbohydrate-binding protein Concanavalin A (Con A). A synthetic ligand was designed with the aim of displacing such water. While the synthetic ligand bound to Con A in an analogous manner to that of the natural ligand, crystallographic analysis demonstrated that it did not displace the conserved water. In order to quantify the affinity of this particular water for the Con A surface, we report here the calculated standard binding free energy for this water in both ligand-bound and free Con A, employing three popular water models: TIP3P, TIP4P, and TIP5P. Although each model was developed to perform well in simulations of bulk-phase water, the computed binding energies for the isolated water molecule displayed a high sensitivity to the model. Both molecular dynamics simulation and free energy results indicate that the choice of water model may greatly influence the characterization of surface water molecules as conserved (TIP5P) or not (TIP3P) in protein binding sites, an observation of considerable significance to rational drug design. Structural and theoretical aspects at the basis of the different behaviors are identified and discussed.

Conserving rare species can have high opportunity costs for common species.

PubMed

Neeson, Thomas M; Doran, Patrick J; Ferris, Michael C; Fitzpatrick, Kimberly B; Herbert, Matthew; Khoury, Mary; Moody, Allison T; Ross, Jared; Yacobson, Eugene; McIntyre, Peter B

2018-04-13

Conservation practitioners face difficult choices in apportioning limited resources between rare species (to ensure their existence) and common species (to ensure their abundance and ecosystem contributions). We quantified the opportunity costs of conserving rare species of migratory fishes in the context of removing dams and retrofitting road culverts across 1,883 tributaries of the North American Great Lakes. Our optimization models show that maximizing total habitat gains across species can be very efficient in terms of benefits achieved per dollar spent, but disproportionately benefits common species. Conservation approaches that target rare species, or that ensure some benefits for every species (i.e., complementarity) enable strategic allocation of resources among species but reduce aggregate habitat gains. Thus, small habitat gains for the rarest species necessarily come at the expense of more than 20 times as much habitat for common ones. These opportunity costs are likely to occur in many ecosystems because range limits and conservation costs often vary widely among species. Given that common species worldwide are declining more rapidly than rare ones within major taxa, our findings provide incentive for triage among multiple worthy conservation targets. © 2018 John Wiley & Sons Ltd.

Identifying gaps in conservation networks: of indicators and uncertainty in geographic-based analyses

Treesearch

Curtis H. Flather; Kenneth R. Wilson; Denis J. Dean; William C. McComb

1997-01-01

Mapping of biodiversity elements to expose gaps in. conservation networks has become a common strategy in nature-reserve design. We review a set of critical assumptions and issues that influence the interpretation and implementation of gap analysis, including: (1) the assumption that a subset of taxa can be used to indicate overall diversity patterns, and (2) the...

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

ERIC Educational Resources Information Center

Massachusetts State Water Resources Authority, Boston.

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

Sequencing Conservation Actions Through Threat Assessments in the Southeastern United States

Treesearch

Robert D. Sutter; Christopher C. Szell

2006-01-01

The identification of conservation priorities is one of the leading issues in conservation biology. We present a project of The Nature Conservancy, called Sequencing Conservation Actions, which prioritizes conservation areas and identifies foci for crosscutting strategies at various geographic scales. We use the term “Sequencing” to mean an ordering of actions over...

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.

Significance of Perceived Social Expectation and Implications to Conservation Education: Turtle Conservation as a Case Study

NASA Astrophysics Data System (ADS)

Lo, Alex Y.; Chow, Alex T.; Cheung, Sze Man

2012-11-01

The likelihood of participating in wildlife conservation programs is dependent on social influences and circumstances. This view is validated by a case study of behavioral intention to support conservation of Asian turtles. A total of 776 college students in China completed a questionnaire survey designed to identify factors associated with their intention to support conservation. A regression model explained 48 % of variance in the level of intention. Perceived social expectation was the strongest predictor, followed by attitudes toward turtle protection and perceived behavioral control, altogether explaining 44 %. Strong ethics and socio-economic variables had some statistical significant impacts and accounted for 3 % of the variance. The effects of general environmental awareness, trust and responsibility ascription were modest. Knowledge about turtles was a weak predictor. We conclude that perceived social expectation is a limiting factor of conservation behavior. Sustained interest and commitment to conservation can be created by enhancing positive social influences. Conservation educators should explore the potential of professionally supported, group-based actions that can nurture a sense of collective achievement as part of an educational campaign.

Leadership: a new frontier in conservation science.

PubMed

Manolis, Jim C; Chan, Kai M; Finkelstein, Myra E; Stephens, Scott; Nelson, Cara R; Grant, Jacqualine B; Dombeck, Michael P

2009-08-01

Leadership is a critical tool for expanding the influence of conservation science, but recent advances in leadership concepts and practice remain underutilized by conservation scientists. Furthermore, an explicit conceptual foundation and definition of leadership in conservation science are not available in the literature. Here we drew on our diverse leadership experiences, our reading of leadership literature, and discussions with selected conservation science leaders to define conservation-science leadership, summarize an exploratory set of leadership principles that are applicable to conservation science, and recommend actions to expand leadership capacity among conservation scientists and practitioners. We define 2 types of conservation-science leadership: shaping conservation science through path-breaking research, and advancing the integration of conservation science into policy, management, and society at large. We focused on the second, integrative type of leadership because we believe it presents the greatest opportunity for improving conservation effectiveness. We identified 8 leadership principles derived mainly from the "adaptive leadership" literature: recognize the social dimension of the problem; cycle frequently through action and reflection; get and maintain attention; combine strengths of multiple leaders; extend your reach through networks of relationships; strategically time your effort; nurture productive conflict; and cultivate diversity. Conservation scientists and practitioners should strive to develop themselves as leaders, and the Society for Conservation Biology, conservation organizations, and academia should support this effort through professional development, mentoring, teaching, and research.

How research-prioritization exercises affect conservation policy.

PubMed

Rudd, Murray A

2011-10-01

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

Identifying priority areas for ecosystem service management in South African grasslands.

PubMed

Egoh, Benis N; Reyers, Belinda; Rouget, Mathieu; Richardson, David M

2011-06-01

Grasslands provide many ecosystem services required to support human well-being and are home to a diverse fauna and flora. Degradation of grasslands due to agriculture and other forms of land use threaten biodiversity and ecosystem services. Various efforts are underway around the world to stem these declines. The Grassland Programme in South Africa is one such initiative and is aimed at safeguarding both biodiversity and ecosystem services. As part of this developing programme, we identified spatial priority areas for ecosystem services, tested the effect of different target levels of ecosystem services used to identify priority areas, and evaluated whether biodiversity priority areas can be aligned with those for ecosystem services. We mapped five ecosystem services (below ground carbon storage, surface water supply, water flow regulation, soil accumulation and soil retention) and identified priority areas for individual ecosystem services and for all five services at the scale of quaternary catchments. Planning for individual ecosystem services showed that, depending on the ecosystem service of interest, between 4% and 13% of the grassland biome was required to conserve at least 40% of the soil and water services. Thirty-four percent of the biome was needed to conserve 40% of the carbon service in the grassland. Priority areas identified for five ecosystem services under three target levels (20%, 40%, 60% of the total amount) showed that between 17% and 56% of the grassland biome was needed to conserve these ecosystem services. There was moderate to high overlap between priority areas selected for ecosystem services and already-identified terrestrial and freshwater biodiversity priority areas. This level of overlap coupled with low irreplaceability values obtained when planning for individual ecosystem services makes it possible to combine biodiversity and ecosystem services in one plan using systematic conservation planning. Copyright © 2011 Elsevier Ltd. All

Mistaken identity: activating conservative political identities induces "conservative" financial decisions.

PubMed

Morris, Michael W; Carranza, Erica; Fox, Craig R

2008-11-01

Four studies investigated whether activating a social identity can lead group members to choose options that are labeled in words associated with that identity. When political identities were made salient, Republicans (but not Democrats) became more likely to choose the gamble or investment option labeled "conservative." This shift did not occur in a condition in which the same options were unlabeled. Thus, the mechanism underlying the effect appears to be not activated identity-related values prioritizing low risk, but rather activated identity-related language (the group label "conservative"). Indeed, when political identities were salient, Republicans favored options labeled "conservative" regardless of whether the options were low or high risk. Finally, requiring participants to explain the label "conservative" before making their choice did not diminish the effect, which suggests that it does not merely reflect inattention to content or construct accessibility. We discuss the implications of these results for the literatures on identity, priming, choice, politics, and marketing.

SELECTING INDICATORS OF BIODIVERSITY FOR CONSERVATION PLANNING: IDENTIFYING THE MECHANISMS BEHIND INDICATOR GROUP PERFORMANCE

EPA Science Inventory

Most conservation planning is constrained by time and funding. In particular, the selection of areas to protect biodiversity must often be completed with limited data on species distributions. Consequently, different groups of species have been proposed as indicators or surroga...

Conservation assessment for the Siskiyou Mountains salamander and Scott Bar salamander in northern California.

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

Vinikour, W. S.; LaGory, K. E.; Adduci, J. J.

2006-10-20

The purpose of this conservation assessment is to summarize existing knowledge regarding the biology and ecology of the Siskiyou Mountains salamander and Scott Bar salamander, identify threats to the two species, and identify conservation considerations to aid federal management for persistence of the species. The conservation assessment will serve as the basis for a conservation strategy for the species.

Screening of broad spectrum natural pesticides against conserved target arginine kinase in cotton pests by molecular modeling.

PubMed

Sakthivel, Seethalakshmi; Habeeb, S K M; Raman, Chandrasekar

2018-03-12

Cotton is an economically important crop and its production is challenged by the diversity of pests and related insecticide resistance. Identification of the conserved target across the cotton pest will help to design broad spectrum insecticide. In this study, we have identified conserved sequences by Expressed Sequence Tag profiling from three cotton pests namely Aphis gossypii, Helicoverpa armigera, and Spodoptera exigua. One target protein arginine kinase having a key role in insect physiology and energy metabolism was studied further using homology modeling, virtual screening, molecular docking, and molecular dynamics simulation to identify potential biopesticide compounds from the Zinc natural database. We have identified four compounds having excellent inhibitor potential against the identified broad spectrum target which are highly specific to invertebrates.

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

Of birds, carbon and water: integrating multiple ecosystem service impacts to identify locations for agricultural conservation practice adoption

EPA Science Inventory

Human use of the landscape for crop production can degrade ecosystem services. A number of agricultural conservation practices are touted as mitigating these impacts. Many of these practices are encouraged by incentive programs such as the Conservation Reserve Program administere...

Assessing Potential Conservation and Restoration Areas of Freshwater Fish Fauna in the Indian River Basins

NASA Astrophysics Data System (ADS)

Bhatt, Jay P.; Manish, Kumar; Mehta, Rajender; Pandit, Maharaj K.

2016-05-01

Conservation efforts globally are skewed toward terrestrial ecosystems. To date, conservation of aquatic ecosystems, in particular fish fauna, is largely neglected. We provide a country-wide assessment of Indian river ecosystems in order to identify and prioritize areas for protection and restoration of freshwater fish fauna. Using various biodiversity and anthropogenic attributes, coupled with tools of ecological modeling, we delineated areas for fish fauna conservation and restoration in the 20 major river basins of India. To do this, we used prioritization analyses and reserve selection algorithms to derive conservation value index (CVI) and vulnerability index (VI) of the river basins. CVI was estimated using endemicity, rarity, conservation value, and taxonomic singularity, while VI was estimated using a disturbance index derived from percent geographic area of the basin under human settlements, human population density, predominant land use, and total number of exotic fish species in each basin. The two indices, CVI and VI, were converted into geo-referenced maps, and each map was super-imposed onto species richness and forest cover maps, respectively. After superimposition, areas with high CVI and low VI shade intensities were delineated for conservation, while areas with high CVI and high VI shade intensities were demarcated for restoration. In view of the importance of freshwater fish for human livelihoods and consumption, and ecosystems of India's rivers, we call for urgent attention to the conservation of their fish fauna along with restoration of their degraded habitats.

Genomic analysis identified a potential novel molecular mechanism for high-altitude adaptation in sheep at the Himalayas.

PubMed

Gorkhali, Neena Amatya; Dong, Kunzhe; Yang, Min; Song, Shen; Kader, Adiljian; Shrestha, Bhola Shankar; He, Xiaohong; Zhao, Qianjun; Pu, Yabin; Li, Xiangchen; Kijas, James; Guan, Weijun; Han, Jianlin; Jiang, Lin; Ma, Yuehui

2016-07-22

Sheep has successfully adapted to the extreme high-altitude Himalayan region. To identify genes underlying such adaptation, we genotyped genome-wide single nucleotide polymorphisms (SNPs) of four major sheep breeds living at different altitudes in Nepal and downloaded SNP array data from additional Asian and Middle East breeds. Using a di value-based genomic comparison between four high-altitude and eight lowland Asian breeds, we discovered the most differentiated variants at the locus of FGF-7 (Keratinocyte growth factor-7), which was previously reported as a good protective candidate for pulmonary injuries. We further found a SNP upstream of FGF-7 that appears to contribute to the divergence signature. First, the SNP occurred at an extremely conserved site. Second, the SNP showed an increasing allele frequency with the elevated altitude in Nepalese sheep. Third, the electrophoretic mobility shift assays (EMSA) analysis using human lung cancer cells revealed the allele-specific DNA-protein interactions. We thus hypothesized that FGF-7 gene potentially enhances lung function by regulating its expression level in high-altitude sheep through altering its binding of specific transcription factors. Especially, FGF-7 gene was not implicated in previous studies of other high-altitude species, suggesting a potential novel adaptive mechanism to high altitude in sheep at the Himalayas.

Practical approaches for assessing local land use change and conservation priorities in the tropics

NASA Astrophysics Data System (ADS)

Rivas, Cassandra J.

Tropical areas typically support high biological diversity; however, many are experiencing rapid land-use change. The resulting loss, fragmentation, and degradation of habitats place biodiversity at risk. For these reasons, the tropics are frequently identified as global conservation hotspots. Safeguarding tropical biodiversity necessitates successful and efficient conservation planning and implementation at local scales, where land use decisions are made and enforced. Yet, despite considerable agreement on the need for improved practices, planning may be difficult due to limited resources, such as funding, data, and expertise, especially for small conservation organizations in tropical developing countries. My thesis aims to assist small, non-governmental organizations (NGOs), operating in tropical developing countries, in overcoming resource limitations by providing recommendations for improved conservation planning. Following a brief introduction in Chapter 1, I present a literature review of systematic conservation planning (SCP) projects in the developing tropics. Although SCP is considered an efficient, effective approach, it requires substantial data and expertise to conduct the analysis and may present challenges for implementation. I reviewed and synthesized the methods and results of 14 case studies to identify practical ways to implement and overcome limitations for employing SCP. I found that SCP studies in the peer-reviewed literature were primarily implemented by researchers in large organizations or institutions, as opposed to on-the-ground conservation planners. A variety of data types were used in the SCP analyses, many of which data are freely available. Few case studies involved stakeholders and intended to implement the assessment; instead, the case studies were carried out in the context of research and development, limiting local involvement and implementation. Nonetheless, the studies provided valuable strategies for employing each step of

Ten ways remote sensing can contribute to conservation

USGS Publications Warehouse

Rose, Robert A.; Byler, Dirck; Eastman, J. Ron; Fleishman, Erica; Geller, Gary; Goetz, Scott; Guild, Liane; Hamilton, Healy; Hansen, Matt; Headley, Rachel; Hewson, Jennifer; Horning, Ned; Kaplin, Beth A.; Laporte, Nadine; Leidner, Allison K.; Leimgruber, Peter; Morisette, Jeffrey T.; Musinsky, John; Pintea, Lilian; Prados, Ana; Radeloff, Volker C.; Rowen, Mary; Saatchi, Sassan; Schill, Steve; Tabor, Karyn; Turner, Woody; Vodacek, Anthony; Vogelmann, James; Wegmann, Martin; Wilkie, David; Wilson, Cara

2014-01-01

In an effort to increase conservation effectiveness through the use of Earth observation technologies, a group of remote sensing scientists affiliated with government and academic institutions and conservation organizations identified 10 questions in conservation for which the potential to be answered would be greatly increased by use of remotely sensed data and analyses of those data. Our goals were to increase conservation practitioners’ use of remote sensing to support their work, increase collaboration between the conservation science and remote sensing communities, identify and develop new and innovative uses of remote sensing for advancing conservation science, provide guidance to space agencies on how future satellite missions can support conservation science, and generate support from the public and private sector in the use of remote sensing data to address the 10 conservation questions. We identified a broad initial list of questions on the basis of an email chain-referral survey. We then used a workshop-based iterative and collaborative approach to whittle the list down to these final questions (which represent 10 major themes in conservation): How can global Earth observation data be used to model species distributions and abundances? How can remote sensing improve the understanding of animal movements? How can remotely sensed ecosystem variables be used to understand, monitor, and predict ecosystem response and resilience to multiple stressors? How can remote sensing be used to monitor the effects of climate on ecosystems? How can near real-time ecosystem monitoring catalyze threat reduction, governance and regulation compliance, and resource management decisions? How can remote sensing inform configuration of protected area networks at spatial extents relevant to populations of target species and ecosystem services? How can remote sensing-derived products be used to value and monitor changes in ecosystem services? How can remote sensing be used to

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.

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence.

PubMed

Meuleman, Wouter; Peric-Hupkes, Daan; Kind, Jop; Beaudry, Jean-Bernard; Pagie, Ludo; Kellis, Manolis; Reinders, Marcel; Wessels, Lodewyk; van Steensel, Bas

2013-02-01

In metazoans, the nuclear lamina is thought to play an important role in the spatial organization of interphase chromosomes, by providing anchoring sites for large genomic segments named lamina-associated domains (LADs). Some of these LADs are cell-type specific, while many others appear constitutively associated with the lamina. Constitutive LADs (cLADs) may contribute to a basal chromosome architecture. By comparison of mouse and human lamina interaction maps, we find that the sizes and genomic positions of cLADs are strongly conserved. Moreover, cLADs are depleted of synteny breakpoints, pointing to evolutionary selective pressure to keep cLADs intact. Paradoxically, the overall sequence conservation is low for cLADs. Instead, cLADs are universally characterized by long stretches of DNA of high A/T content. Cell-type specific LADs also tend to adhere to this "A/T rule" in embryonic stem cells, but not in differentiated cells. This suggests that the A/T rule represents a default positioning mechanism that is locally overruled during lineage commitment. Analysis of paralogs suggests that during evolution changes in A/T content have driven the relocation of genes to and from the nuclear lamina, in tight association with changes in expression level. Taken together, these results reveal that the spatial organization of mammalian genomes is highly conserved and tightly linked to local nucleotide composition.

Large-Scale Bioinformatics Analysis of Bacillus Genomes Uncovers Conserved Roles of Natural Products in Bacterial Physiology.

PubMed

Grubbs, Kirk J; Bleich, Rachel M; Santa Maria, Kevin C; Allen, Scott E; Farag, Sherif; Shank, Elizabeth A; Bowers, Albert A

2017-01-01

Bacteria possess an amazing capacity to synthesize a diverse range of structurally complex, bioactive natural products known as specialized (or secondary) metabolites. Many of these specialized metabolites are used as clinical therapeutics, while others have important ecological roles in microbial communities. The biosynthetic gene clusters (BGCs) that generate these metabolites can be identified in bacterial genome sequences using their highly conserved genetic features. We analyzed an unprecedented 1,566 bacterial genomes from Bacillus species and identified nearly 20,000 BGCs. By comparing these BGCs to one another as well as a curated set of known specialized metabolite BGCs, we discovered that the majority of Bacillus natural products are comprised of a small set of highly conserved, well-distributed, known natural product compounds. Most of these metabolites have important roles influencing the physiology and development of Bacillus species. We identified, in addition to these characterized compounds, many unique, weakly conserved BGCs scattered across the genus that are predicted to encode unknown natural products. Many of these "singleton" BGCs appear to have been acquired via horizontal gene transfer. Based on this large-scale characterization of metabolite production in the Bacilli , we go on to connect the alkylpyrones, natural products that are highly conserved but previously biologically uncharacterized, to a role in Bacillus physiology: inhibiting spore development. IMPORTANCE Bacilli are capable of producing a diverse array of specialized metabolites, many of which have gained attention for their roles as signals that affect bacterial physiology and development. Up to this point, however, the Bacillus genus's metabolic capacity has been underexplored. We undertook a deep genomic analysis of 1,566 Bacillus genomes to understand the full spectrum of metabolites that this bacterial group can make. We discovered that the majority of the specialized

[Identification of marine and coastal biodiversity conservation priorities in Costa Rica].

PubMed

Alvarado, Juan José; Herrera, Bernal; Corrales, Lenin; Asch, Jenny; Paaby, Pía

2011-06-01

Costa Rica is recognized as one of the most diverse countries in species and ecosystems, in their terrestrial realm as well as in the marine. Besides this relevance, the country presents a delay on conservation and management of marine and coastal biodiversity, with respect to terrestrial. For 2006, the marine protected surface was 5,208.8 km2, with 331.5 km of coastline, in 20 protected areas. The country has made progress on the conservation priority sites identification for terrestrial and freshwater biodiversity, with few efforts on marine planning. This research presents the analysis and results of the gap identification process, for marine and coastal biodiversity conservation in the protected areas system of Costa Rica. The analysis was built with the spatial information available on the presence and distribution of coastal and marine biodiversity, the establishment of the conservation goals and a threat analysis over the ecological integrity of this biodiversity. The selection of high-priority sites was carried out using spatial optimization techniques and the superposition over the current shape of marine protected areas, in order to identify representation gaps. A total of 19,076 km2 of conservation gaps were indentified, with 1,323 km2 in the Caribbean and 17,753 km2 in the Pacific. Recommendations are aimed at planning and strengthening the marine protected areas system, using the gaps identified as a framework. It is expected that the results of this study would be the scientific base needed for planning and sustainable use of marine biodiversity in the country.

7 CFR 1469.22 - Conservation practice operation and maintenance.

Code of Federal Regulations, 2011 CFR

2011-01-01

... life span of the conservation treatment, as identified in the contract or conservation stewardship plan... procedures as specified in § 1469.25. If an existing practice is part of a system that meets the quality...

7 CFR 1469.22 - Conservation practice operation and maintenance.

Code of Federal Regulations, 2010 CFR

2010-01-01

... life span of the conservation treatment, as identified in the contract or conservation stewardship plan... procedures as specified in § 1469.25. If an existing practice is part of a system that meets the quality...

High cumulants of conserved charges and their statistical uncertainties

NASA Astrophysics Data System (ADS)

Li-Zhu, Chen; Ye-Yin, Zhao; Xue, Pan; Zhi-Ming, Li; Yuan-Fang, Wu

2017-10-01

We study the influence of measured high cumulants of conserved charges on their associated statistical uncertainties in relativistic heavy-ion collisions. With a given number of events, the measured cumulants randomly fluctuate with an approximately normal distribution, while the estimated statistical uncertainties are found to be correlated with corresponding values of the obtained cumulants. Generally, with a given number of events, the larger the cumulants we measure, the larger the statistical uncertainties that are estimated. The error-weighted averaged cumulants are dependent on statistics. Despite this effect, however, it is found that the three sigma rule of thumb is still applicable when the statistics are above one million. Supported by NSFC (11405088, 11521064, 11647093), Major State Basic Research Development Program of China (2014CB845402) and Ministry of Science and Technology (MoST) (2016YFE0104800)

Disruption of long-distance highly conserved noncoding elements in neurocristopathies.

PubMed

Amiel, Jeanne; Benko, Sabina; Gordon, Christopher T; Lyonnet, Stanislas

2010-12-01

One of the key discoveries of vertebrate genome sequencing projects has been the identification of highly conserved noncoding elements (CNEs). Some characteristics of CNEs include their high frequency in mammalian genomes, their potential regulatory role in gene expression, and their enrichment in gene deserts nearby master developmental genes. The abnormal development of neural crest cells (NCCs) leads to a broad spectrum of congenital malformation(s), termed neurocristopathies, and/or tumor predisposition. Here we review recent findings that disruptions of CNEs, within or at long distance from the coding sequences of key genes involved in NCC development, result in neurocristopathies via the alteration of tissue- or stage-specific long-distance regulation of gene expression. While most studies on human genetic disorders have focused on protein-coding sequences, these examples suggest that investigation of genomic alterations of CNEs will provide a broader understanding of the molecular etiology of both rare and common human congenital malformations. © 2010 New York Academy of Sciences.

Conservation of high-flux backbone in alternate optimal and near-optimal flux distributions of metabolic networks.

PubMed

Samal, Areejit

2008-12-01

Constraint-based flux balance analysis (FBA) has proven successful in predicting the flux distribution of metabolic networks in diverse environmental conditions. FBA finds one of the alternate optimal solutions that maximizes the biomass production rate. Almaas et al. have shown that the flux distribution follows a power law, and it is possible to associate with most metabolites two reactions which maximally produce and consume a given metabolite, respectively. This observation led to the concept of high-flux backbone (HFB) in metabolic networks. In previous work, the HFB has been computed using a particular optima obtained using FBA. In this paper, we investigate the conservation of HFB of a particular solution for a given medium across different alternate optima and near-optima in metabolic networks of E. coli and S. cerevisiae. Using flux variability analysis (FVA), we propose a method to determine reactions that are guaranteed to be in HFB regardless of alternate solutions. We find that the HFB of a particular optima is largely conserved across alternate optima in E. coli, while it is only moderately conserved in S. cerevisiae. However, the HFB of a particular near-optima shows a large variation across alternate near-optima in both organisms. We show that the conserved set of reactions in HFB across alternate near-optima has a large overlap with essential reactions and reactions which are both uniquely consuming (UC) and uniquely producing (UP). Our findings suggest that the structure of the metabolic network admits a high degree of redundancy and plasticity in near-optimal flow patterns enhancing system robustness for a given environmental condition.

Conservation priorities for endangered Indian tigers through a genomic lens.

PubMed

Natesh, Meghana; Atla, Goutham; Nigam, Parag; Jhala, Yadvendradev V; Zachariah, Arun; Borthakur, Udayan; Ramakrishnan, Uma

2017-08-29

Tigers have lost 93% of their historical range worldwide. India plays a vital role in the conservation of tigers since nearly 60% of all wild tigers are currently found here. However, as protected areas are small (<300 km 2 on average), with only a few individuals in each, many of them may not be independently viable. It is thus important to identify and conserve genetically connected populations, as well as to maintain connectivity within them. We collected samples from wild tigers (Panthera tigris tigris) across India and used genome-wide SNPs to infer genetic connectivity. We genotyped 10,184 SNPs from 38 individuals across 17 protected areas and identified three genetically distinct clusters (corresponding to northwest, southern and central India). The northwest cluster was isolated with low variation and high relatedness. The geographically large central cluster included tigers from central, northeastern and northern India, and had the highest variation. Most genetic diversity (62%) was shared among clusters, while unique variation was highest in the central cluster (8.5%) and lowest in the northwestern one (2%). We did not detect signatures of differential selection or local adaptation. We highlight that the northwest population requires conservation attention to ensure persistence of these tigers.

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

PubMed Central

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

2014-01-01

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

Functionally conserved enhancers with divergent sequences in distant vertebrates

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

Yang, Song; Oksenberg, Nir; Takayama, Sachiko

To examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. In conclusion, our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species.

Functionally conserved enhancers with divergent sequences in distant vertebrates

DOE PAGES

Yang, Song; Oksenberg, Nir; Takayama, Sachiko; ...

2015-10-30

To examine the contributions of sequence and function conservation in the evolution of enhancers, we systematically identified enhancers whose sequences are not conserved among distant groups of vertebrate species, but have homologous function and are likely to be derived from a common ancestral sequence. In conclusion, our approach combined comparative genomics and epigenomics to identify potential enhancer sequences in the genomes of three groups of distantly related vertebrate species.

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

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

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.

Crowdfunding biodiversity conservation.

PubMed

Gallo-Cajiao, E; Archibald, C; Friedman, R; Steven, R; Fuller, R A; Game, E T; Morrison, T H; Ritchie, E G

2018-05-26

Raising funds is critical for conserving biodiversity and hence so too is scrutinizing emerging financial mechanisms that might help achieve this goal. In this context, anecdotal evidence indicates crowdfunding is being used to support a variety of activities needed for biodiversity conservation, yet its magnitude and allocation remain largely unknown. We conducted a global analysis to help address this knowledge gap, based on empirical data from conservation-focused projects extracted from crowdfunding platforms. For each project, we determined the funds raised, date, country of implementation, proponent characteristics, activity type, biodiversity realm, and target taxa. We identified 72 relevant platforms and 577 conservation-focused projects that have raised US$4 790 634 since 2009. Whilst proponents were based in 38 countries, projects were delivered across 80 countries, indicating a potential mechanism of resource mobilization. Proponents were from non-governmental organizations (35%), universities (30%), or were freelancers (26%). Most projects were for research (40%), persuasion (31%), and on-ground actions (21%). Projects have focused primarily on species (57.7%) and terrestrial ecosystems (20.3%), and less on marine (8.8%) and freshwater ecosystems (3.6%). Projects have focused on 208 species, including a disproportionate number of threatened bird and mammal species. Crowdfunding for biodiversity conservation has now become a global phenomenon and presents signals for potential expansion, despite possible pitfalls. Opportunities arise from its spatial amplifying effect, steady increase over time, inclusion of Cinderella species, adoption by multiple actors, and funding of a range of activities beyond research. Our study paves the way for further research on key questions, such as campaign success rates, effectiveness, and drivers of adoption. Even though the capital input of crowdfunding so far has been modest compared to other conservation finance

A comparative approach to assess drivers of success in mammalian conservation recovery programs.

PubMed

Crees, Jennifer J; Collins, Amy C; Stephenson, P J; Meredith, Helen M R; Young, Richard P; Howe, Caroline; Price, Mark R Stanley; Turvey, Samuel T

2016-08-01

The outcomes of species recovery programs have been mixed; high-profile population recoveries contrast with species-level extinctions. Each conservation intervention has its own challenges, but to inform more effective management it is imperative to assess whether correlates of wider recovery program success or failure can be identified. To contribute to evidence-based improvement of future conservation strategies, we conducted a global quantitative analysis of 48 mammalian recovery programs. We reviewed available scientific literature and conducted semistructured interviews with conservation professionals involved in different recovery programs to investigate ecological, management, and political factors associated with population recoveries or declines. Identifying and removing threats was significantly associated with increasing population trend and decreasing conservation dependence, emphasizing that populations are likely to continue to be compromised in the absence of effective threat mitigation and supporting the need for threat monitoring and adaptive management in response to new and potential threats. Lack of habitat and small population size were cited as limiting factors in 56% and 42% of recovery programs, respectively, and both were statistically associated with increased longer term dependence on conservation intervention, demonstrating the importance of increasing population numbers quickly and restoring and protecting habitat. Poor stakeholder coordination and management were also regularly cited by respondents as key weaknesses in recovery programs, indicating the importance of effective leadership and shared goals and management plans. Project outcomes were not influenced by biological or ecological variables such as body mass or habitat, which suggests that these insights into correlates of conservation success and failure are likely to be generalizable across mammals. © 2016 Society for Conservation Biology.

Descriptive study of important energy-conservation content for industrial arts in North Carolina and potential constraints to implementation of the content

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

Johnson, C.D.

The purpose of this study was to determine the important energy-conservation content for industrial arts in North Carolina. The continuing purpose was to identify constraints to implementation of the identified important content. Fifty-three energy-conservation-content items were identified from the literature. This content was rated on importance by seven industrial arts/energy-conservation specialists in North Carolina. An analysis of the specialists scores resulted in the identification of the 20 most important energy-conservation-content items for industrial arts in North Carolina. Identification of possible constraints to the implementation of the important content was accomplished by surveying the certified industrial arts teachers in North Carolina.more » On the survey, teachers rated each content item in relation to their instructional practices, knowledge level, and perception of content appropriateness. Almost 67% of the industrial arts teachers in North Carolina responded to the survey. The study revealed that overall, industrial arts teachers believed energy conservation was moderately to highly appropriate for industrial arts. Knowledge of energy conservation was at a comparatively lower level, and was considered a possible constraint to content implementation. Although energy-conservation instructional practices were at a low level, 88% of the teachers in the survey sample included at least one of the energy-conservation-content items in their curriculum.« less

Exceptional responders in conservation.

PubMed

Post, Gerald; Geldmann, Jonas

2017-08-30

Conservation operates within complex systems with incomplete knowledge of the system and the interventions utilized. This frequently results in the inability to find generally applicable methods to alleviate threats to Earth's vanishing wildlife. One approach used in medicine and the social sciences has been to develop a deeper understanding of positive outliers. Where such outliers share similar characteristics, they may be considered exceptional responders. We devised a 4-step framework for identifying exceptional responders in conservation: identification of the study system, identification of the response structure, identification of the threshold for exceptionalism, and identification of commonalities among outliers. Evaluation of exceptional responders provides additional information that is often ignored in randomized controlled trials and before-after control-intervention experiments. Interrogating the contextual factors that contribute to an exceptional outcome allow exceptional responders to become valuable pieces of information leading to unexpected discoveries and novel hypotheses. © 2017 Society for Conservation Biology.

Electric load management and energy conservation

NASA Technical Reports Server (NTRS)

Kheir, N. A.

1976-01-01

Electric load management and energy conservation relate heavily to the major problems facing power industry at present. The three basic modes of energy conservation are identified as demand reduction, increased efficiency and substitution for scarce fuels. Direct and indirect load management objectives are to reduce peak loads and have future growth in electricity requirements in such a manner to cause more of it to fall off the system's peak. In this paper, an overview of proposed and implemented load management options is presented. Research opportunities exist for the evaluation of socio-economic impacts of energy conservation and load management schemes specially on the electric power industry itself.

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.

On the relationship between residue structural environment and sequence conservation in proteins.

PubMed

Liu, Jen-Wei; Lin, Jau-Ji; Cheng, Chih-Wen; Lin, Yu-Feng; Hwang, Jenn-Kang; Huang, Tsun-Tsao

2017-09-01

Residues that are crucial to protein function or structure are usually evolutionarily conserved. To identify the important residues in protein, sequence conservation is estimated, and current methods rely upon the unbiased collection of homologous sequences. Surprisingly, our previous studies have shown that the sequence conservation is closely correlated with the weighted contact number (WCN), a measure of packing density for residue's structural environment, calculated only based on the C α positions of a protein structure. Moreover, studies have shown that sequence conservation is correlated with environment-related structural properties calculated based on different protein substructures, such as a protein's all atoms, backbone atoms, side-chain atoms, or side-chain centroid. To know whether the C α atomic positions are adequate to show the relationship between residue environment and sequence conservation or not, here we compared C α atoms with other substructures in their contributions to the sequence conservation. Our results show that C α positions are substantially equivalent to the other substructures in calculations of various measures of residue environment. As a result, the overlapping contributions between C α atoms and the other substructures are high, yielding similar structure-conservation relationship. Take the WCN as an example, the average overlapping contribution to sequence conservation is 87% between C α and all-atom substructures. These results indicate that only C α atoms of a protein structure could reflect sequence conservation at the residue level. © 2017 Wiley Periodicals, Inc.

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

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

PubMed

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

2014-04-01

Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in the tropics. We constructed a record of afro-alpine plants retrieved from DNA preserved in sediment cores from 2 volcanic crater sites in the Albertine Rift, eastern Africa. The record extended well beyond the onset of substantial anthropogenic effects on tropical mountains. To ensure high-quality taxonomic inference from the sedaDNA sequences, we built an extensive DNA reference library covering the majority of the afro-alpine flora, by sequencing DNA from taxonomically verified specimens. Comparisons with pollen records from the same sediment cores showed that plant diversity recovered with sedaDNA improved vegetation reconstructions based on pollen records by revealing both additional taxa and providing increased taxonomic resolution. Furthermore, combining the 2 measures assisted in distinguishing vegetation change at different geographic scales; sedaDNA almost exclusively reflects local vegetation, whereas pollen can potentially originate from a wide area that in highlands in particular can span several ecozones. Our results suggest that sedaDNA may provide information on restoration targets and the nature and magnitude of human-induced environmental changes, including in high conservation priority, biodiversity hotspots, where understanding of preanthropogenic impact (or reference) conditions is highly limited. © 2013 Society for Conservation Biology.

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

SPECIES RICHNESS AND BIODIVERSITY CONSERVATION PRIORITIES IN BRITISH COLUMBIA

EPA Science Inventory

Patterns in the geographic distribution of seven species groups were used to identify important areas for conservation in British Columbia, Canada. Potential priority sites for conservation were determined using an integer programming algorithm that maximized the number of speci...

Effect of local cultural context on the success of community-based conservation interventions.

PubMed

Waylen, Kerry A; Fischer, Anke; McGowan, Philip J K; Thirgood, Simon J; Milner-Gulland, E J

2010-08-01

Conservation interventions require evaluation to understand what factors predict success or failure. To date, there has been little systematic investigation of the effect of social and cultural context on conservation success, although a large body of literature argues it is important. We investigated whether local cultural context, particularly local institutions and the efforts of interventions to engage with this culture significantly influence conservation outcomes. We also tested the effects of community participation, conservation education, benefit provision, and market integration. We systematically reviewed the literature on community-based conservation and identified 68 interventions suitable for inclusion. We used a protocol to extract and code information and evaluated a range of measures of outcome success (attitudinal, behavioral, ecological, and economic). We also examined the association of each predictor with each outcome measure and the structure of predictor covariance. Local institutional context influenced intervention outcomes, and interventions that engaged with local institutions were more likely to succeed. Nevertheless, there was limited support for the role of community participation, conservation education, benefit provision, and market integration on intervention success. We recommend that conservation interventions seek to understand the societies they work with and tailor their activities accordingly. Systematic reviews are a valuable approach for assessing conservation evidence, although sensitive to the continuing lack of high-quality reporting on conservation interventions.

On biodiversity conservation and poverty traps.

PubMed

Barrett, Christopher B; Travis, Alexander J; Dasgupta, Partha

2011-08-23

This paper introduces a special feature on biodiversity conservation and poverty traps. We define and explain the core concepts and then identify four distinct classes of mechanisms that define important interlinkages between biodiversity and poverty. The multiplicity of candidate mechanisms underscores a major challenge in designing policy appropriate across settings. This framework is then used to introduce the ensuing set of papers, which empirically explore these various mechanisms linking poverty traps and biodiversity conservation.

Assessing Potential Conservation and Restoration Areas of Freshwater Fish Fauna in the Indian River Basins.

PubMed

Bhatt, Jay P; Manish, Kumar; Mehta, Rajender; Pandit, Maharaj K

2016-05-01

Conservation efforts globally are skewed toward terrestrial ecosystems. To date, conservation of aquatic ecosystems, in particular fish fauna, is largely neglected. We provide a country-wide assessment of Indian river ecosystems in order to identify and prioritize areas for protection and restoration of freshwater fish fauna. Using various biodiversity and anthropogenic attributes, coupled with tools of ecological modeling, we delineated areas for fish fauna conservation and restoration in the 20 major river basins of India. To do this, we used prioritization analyses and reserve selection algorithms to derive conservation value index (CVI) and vulnerability index (VI) of the river basins. CVI was estimated using endemicity, rarity, conservation value, and taxonomic singularity, while VI was estimated using a disturbance index derived from percent geographic area of the basin under human settlements, human population density, predominant land use, and total number of exotic fish species in each basin. The two indices, CVI and VI, were converted into geo-referenced maps, and each map was super-imposed onto species richness and forest cover maps, respectively. After superimposition, areas with high CVI and low VI shade intensities were delineated for conservation, while areas with high CVI and high VI shade intensities were demarcated for restoration. In view of the importance of freshwater fish for human livelihoods and consumption, and ecosystems of India's rivers, we call for urgent attention to the conservation of their fish fauna along with restoration of their degraded habitats.

Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)

PubMed Central

Yang, Yaodong; Mason, Annaliese S.; Lei, Xintao; Ma, Zilong

2013-01-01

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events. PMID:23951162

Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).

PubMed

Xiao, Yong; Xia, Wei; Yang, Yaodong; Mason, Annaliese S; Lei, Xintao; Ma, Zilong

2013-01-01

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.

Testing a two-scale focused conservation strategy for reducing phosphorus and sediment loads from agricultural watersheds

USGS Publications Warehouse

Carvin, Rebecca; Good, Laura W.; Fitzpatrick, Faith A.; Diehl, Curt; Songer, Katherine; Meyer, Kimberly J.; Panuska, John C.; Richter, Steve; Whalley, Kyle

2018-01-01

This study tested a focused strategy for reducing phosphorus (P) and sediment loads in agricultural streams. The strategy involved selecting small watersheds identified as likely to respond relatively quickly, and then focusing conservation practices on high-contributing fields within those watersheds. Two 5,000 ha (12,360 ac) watersheds in the Driftless Area of south central Wisconsin, previously ranked in the top 6% of similarly sized Wisconsin watersheds for expected responsiveness to conservation efforts to reduce high P and sediment loads, were chosen for the study. The stream outlets from both watersheds were monitored from October of 2006 through September of 2016 for streamflow and concentrations of sediment, total P, and, beginning in October of 2009, total dissolved P. Fields and pastures having the highest potential P delivery to the streams in each watershed were identified using the Wisconsin P Index (Good et al. 2012). After three years of baseline monitoring (2006 to 2009), farmers implemented both field- and farm-based conservation practices in one watershed (treatment) as a means to reduce sediment and P inputs to the stream from the highest contributing areas, whereas there were no out-of-the-ordinary conservation efforts in the second watershed (control). Implementation occurred primarily in 2011 and 2012. In the four years following implementation of conservation practices (2013 through 2016), there was a statistically significant reduction in storm-event suspended sediment loads in the treatment watershed compared to the control watershed when the ground was not frozen (p = 0.047). While there was an apparent reduction in year-round suspended sediment event loads, it was not statistically significant at the 95% confidence level (p = 0.15). Total P loads were significantly reduced for runoff events (p < 0.01) with a median reduction of 50%. Total P and total dissolved P concentrations for low-flow conditions were also significantly reduced (p

On nonepistemic values in conservation biology.

PubMed

Baumgaertner, Bert; Holthuijzen, Wieteke

2017-02-01

Conservation biology is a uniquely interdisciplinary science with strong roots in ecology, but it also embraces a value-laden and mission-oriented framework. This combination of science and values causes conservation biology to be at the center of critique regarding the discipline's scientific credibility-especially the division between the realms of theory and practice. We identify this dichotomy between seemingly objective (fact-based) and subjective (value-laden) practices as the measure-value dichotomy, whereby measure refers to methods and analyses used in conservation biology (i.e., measuring biodiversity) and value refers to nonepistemic values. We reviewed and evaluated several landmark articles central to the foundation of conservation biology and concepts of biodiversity with respect to their attempts to separate measures and values. We argue that the measure-value dichotomy is false and that conservation biology can make progress in ways unavailable to other disciplines because its practitioners are tasked with engaging in both the realm of theory and the realm of practice. The entanglement of measures and values is by no means a weakness of conservation biology. Because central concepts such as biodiversity contain both factual and evaluative aspects, conservation biologists can make theoretical progress by examining, reviewing, and forming the values that are an integral part of those concepts. We suggest that values should be included and analyzed with respect to the methods, results, and conclusions of scientific work in conservation biology. © 2016 Society for Conservation Biology.

A Conservation Plan for the Transylvania University Library.

ERIC Educational Resources Information Center

Bryson, Kathleen; Mayo, Lynn

This assessment of the conservation needs of the Frances Corrick Thomas Library begins with an examination of the architectural and environmental peculiarities of the existing building, which is seen as a major obstacle to achieving an effective conservation program. Needs are identified and recommendations for immediate and intermediate action,…

Fertility and obstetric outcome after conservative management of placenta accreta.

PubMed

Provansal, Magali; Courbiere, Blandine; Agostini, Aubert; D'Ercole, Claude; Boubli, Léon; Bretelle, Florence

2010-05-01

To determine the fertility and obstetric outcomes after conservative management of placenta accreta. A retrospective observational cohort study of all identified cases of placenta accreta from 1993 to 2007 in 2 tertiary university hospitals in France. For patients treated conservatively, maternal and fetal morbidity, reproductive function, fertility, and subsequent pregnancies were recorded. During the study period, 46 patients were treated by conservative management; 6 patients underwent a secondary hysterectomy. Of the remaining 40 patients, 35 were followed up for a median of 65 months (range 18-156 months). Patients resumed their menstrual cycles after a median of 130 days (range 48-176 days). Menses were irregular in 11 patients (31%), but none had amenorrhea. Twelve of the 14 patients desiring another pregnancy achieved a total of 15 pregnancies; 2 patients had recurrent placenta accreta. Five spontaneous abortions and 1 termination of pregnancy occurred during the first trimester. The median term at delivery was 37 weeks (range, 35-40 weeks). Four patients delivered prematurely. Conservative management of placenta accreta can preserve fertility, although the risk of recurrent placenta accreta appears to be high. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

Dissecting the Gene Network of Dietary Restriction to Identify Evolutionarily Conserved Pathways and New Functional Genes

PubMed Central

Wuttke, Daniel; Connor, Richard; Vora, Chintan; Craig, Thomas; Li, Yang; Wood, Shona; Vasieva, Olga; Shmookler Reis, Robert; Tang, Fusheng; de Magalhães, João Pedro

2012-01-01

Dietary restriction (DR), limiting nutrient intake from diet without causing malnutrition, delays the aging process and extends lifespan in multiple organisms. The conserved life-extending effect of DR suggests the involvement of fundamental mechanisms, although these remain a subject of debate. To help decipher the life-extending mechanisms of DR, we first compiled a list of genes that if genetically altered disrupt or prevent the life-extending effects of DR. We called these DR–essential genes and identified more than 100 in model organisms such as yeast, worms, flies, and mice. In order for other researchers to benefit from this first curated list of genes essential for DR, we established an online database called GenDR (http://genomics.senescence.info/diet/). To dissect the interactions of DR–essential genes and discover the underlying lifespan-extending mechanisms, we then used a variety of network and systems biology approaches to analyze the gene network of DR. We show that DR–essential genes are more conserved at the molecular level and have more molecular interactions than expected by chance. Furthermore, we employed a guilt-by-association method to predict novel DR–essential genes. In budding yeast, we predicted nine genes related to vacuolar functions; we show experimentally that mutations deleting eight of those genes prevent the life-extending effects of DR. Three of these mutants (OPT2, FRE6, and RCR2) had extended lifespan under ad libitum, indicating that the lack of further longevity under DR is not caused by a general compromise of fitness. These results demonstrate how network analyses of DR using GenDR can be used to make phenotypically relevant predictions. Moreover, gene-regulatory circuits reveal that the DR–induced transcriptional signature in yeast involves nutrient-sensing, stress responses and meiotic transcription factors. Finally, comparing the influence of gene expression changes during DR on the interactomes of multiple

Riverine threat indices to assess watershed condition and identify primary management capacity of agriculture natural resource management agencies.

PubMed

Fore, Jeffrey D; Sowa, Scott P; Galat, David L; Annis, Gust M; Diamond, David D; Rewa, Charles

2014-03-01

Managers can improve conservation of lotic systems over large geographies if they have tools to assess total watershed conditions for individual stream segments and can identify segments where conservation practices are most likely to be successful (i.e., primary management capacity). The goal of this research was to develop a suite of threat indices to help agriculture resource management agencies select and prioritize watersheds across Missouri River basin in which to implement agriculture conservation practices. We quantified watershed percentages or densities of 17 threat metrics that represent major sources of ecological stress to stream communities into five threat indices: agriculture, urban, point-source pollution, infrastructure, and all non-agriculture threats. We identified stream segments where agriculture management agencies had primary management capacity. Agriculture watershed condition differed by ecoregion and considerable local variation was observed among stream segments in ecoregions of high agriculture threats. Stream segments with high non-agriculture threats were most concentrated near urban areas, but showed high local variability. 60 % of stream segments in the basin were classified as under U.S. Department of Agriculture's Natural Resources Conservation Service (NRCS) primary management capacity and most segments were in regions of high agricultural threats. NRCS primary management capacity was locally variable which highlights the importance of assessing total watershed condition for multiple threats. Our threat indices can be used by agriculture resource management agencies to prioritize conservation actions and investments based on: (a) relative severity of all threats, (b) relative severity of agricultural threats, and (c) and degree of primary management capacity.

Conserving old-growth forest diversity in disturbance-prone landscapes.

PubMed

Spies, Thomas A; Hemstrom, Miles A; Youngblood, Andrew; Hummel, Susan

2006-04-01

A decade after its creation, the Northwest Forest Plan is contributing to the conservation of old-growth forests on federal land. However the success and outlook for the plan are questionable in the dry provinces, where losses of old growth to wildfire have been relatively high and risks of further loss remain. We summarize the state of knowledge of old-growth forests in the plan area, identify challenges to conserve them, and suggest some conservation approaches that might better meet the goals of the plan. Historically, old-growth forests in these provinces ranged from open, patchy stands, maintained by frequent low-severity fire, to a mosaic of dense and open stands maintained by mixed-severity fires. Old-growth structure and composition were spatially heterogeneous, varied strongly with topography and elevation, and were shaped by a complex disturbance regime of fire, insects, and disease. With fire suppression and cutting of large pines (Pinus spp.) and Douglas-firs (Pseudotsuga menziesii [Mirbel] Franco), old-growth diversity has declined and dense understories have developed across large areas. Challenges to conserving these forests include a lack of definitions needed for planning of fire-dependent old-growth stands and landscapes, and conflicts in conservation goals that can be resolved only at the landscape level. Fire suppression has increased the area of the dense, older forest favored by Northern Spotted Owls (Strix occidentalis caurina) but increased the probability of high-severity fire. The plan allows for fuel reduction in late-successional reserves; fuel treatments, however apparently have not happened at a high enough rate or been applied in a landscape-level approach. Landscape-level strategies are needed that prioritize fuel treatments by vegetation zones, develop shaded fuel breaks in strategic positions, and thin and apply prescribed fire to reduce ladder fuels around remaining old trees. Evaluations of the current and alternative strategies

An optimization-based approach for high-order accurate discretization of conservation laws with discontinuous solutions

NASA Astrophysics Data System (ADS)

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

2018-07-01

This work introduces a novel discontinuity-tracking framework for resolving discontinuous solutions of conservation laws with high-order numerical discretizations that support inter-element solution discontinuities, such as discontinuous Galerkin or finite volume methods. The proposed method aims to align inter-element boundaries with discontinuities in the solution by deforming the computational mesh. A discontinuity-aligned mesh ensures the discontinuity is represented through inter-element jumps while smooth basis functions interior to elements are only used to approximate smooth regions of the solution, thereby avoiding Gibbs' phenomena that create well-known stability issues. Therefore, very coarse high-order discretizations accurately resolve the piecewise smooth solution throughout the domain, provided the discontinuity is tracked. Central to the proposed discontinuity-tracking framework is a discrete PDE-constrained optimization formulation that simultaneously aligns the computational mesh with discontinuities in the solution and solves the discretized conservation law on this mesh. The optimization objective is taken as a combination of the deviation of the finite-dimensional solution from its element-wise average and a mesh distortion metric to simultaneously penalize Gibbs' phenomena and distorted meshes. It will be shown that our objective function satisfies two critical properties that are required for this discontinuity-tracking framework to be practical: (1) possesses a local minima at a discontinuity-aligned mesh and (2) decreases monotonically to this minimum in a neighborhood of radius approximately h / 2, whereas other popular discontinuity indicators fail to satisfy the latter. Another important contribution of this work is the observation that traditional reduced space PDE-constrained optimization solvers that repeatedly solve the conservation law at various mesh configurations are not viable in this context since severe overshoot and

The utility of transcriptomics in fish conservation.

PubMed

Connon, Richard E; Jeffries, Ken M; Komoroske, Lisa M; Todgham, Anne E; Fangue, Nann A

2018-01-29

There is growing recognition of the need to understand the mechanisms underlying organismal resilience (i.e. tolerance, acclimatization) to environmental change to support the conservation management of sensitive and economically important species. Here, we discuss how functional genomics can be used in conservation biology to provide a cellular-level understanding of organismal responses to environmental conditions. In particular, the integration of transcriptomics with physiological and ecological research is increasingly playing an important role in identifying functional physiological thresholds predictive of compensatory responses and detrimental outcomes, transforming the way we can study issues in conservation biology. Notably, with technological advances in RNA sequencing, transcriptome-wide approaches can now be applied to species where no prior genomic sequence information is available to develop species-specific tools and investigate sublethal impacts that can contribute to population declines over generations and undermine prospects for long-term conservation success. Here, we examine the use of transcriptomics as a means of determining organismal responses to environmental stressors and use key study examples of conservation concern in fishes to highlight the added value of transcriptome-wide data to the identification of functional response pathways. Finally, we discuss the gaps between the core science and policy frameworks and how thresholds identified through transcriptomic evaluations provide evidence that can be more readily used by resource managers. © 2018. Published by The Company of Biologists Ltd.

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.

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

Biodiversity conservation in a changing climate: a review of threats and implications for conservation planning in Myanmar.

PubMed

Rao, Madhu; Saw Htun; Platt, Steven G; Tizard, Robert; Poole, Colin; Than Myint; Watson, James E M

2013-11-01

High levels of species richness and endemism make Myanmar a regional priority for conservation. However, decades of economic and political sanctions have resulted in low conservation investment to effectively tackle threats to biodiversity. Recent sweeping political reforms have placed Myanmar on the fast track to economic development-the expectation is increased economic investments focused on the exploitation of the country's rich, and relatively intact, natural resources. Within a context of weak regulatory capacity and inadequate environmental safeguards, rapid economic development is likely to have far-reaching negative implications for already threatened biodiversity and natural-resource-dependent human communities. Climate change will further exacerbate prevailing threats given Myanmar's high exposure and vulnerability. The aim of this review is to examine the implications of increased economic growth and a changing climate within the larger context of biodiversity conservation in Myanmar. We summarize conservation challenges, assess direct climatological impacts on biodiversity and conclude with recommendations for long-term adaptation approaches for biodiversity conservation.

High overlap between traditional ecological knowledge and forest conservation found in the Bolivian Amazon.

PubMed

Paneque-Gálvez, Jaime; Pérez-Llorente, Irene; Luz, Ana Catarina; Guèze, Maximilien; Mas, Jean-François; Macía, Manuel J; Orta-Martínez, Martí; Reyes-García, Victoria

2018-03-12

It has been suggested that traditional ecological knowledge (TEK) may play a key role in forest conservation. However, empirical studies assessing to what extent TEK is associated with forest conservation compared with other variables are rare. Furthermore, to our knowledge, the spatial overlap of TEK and forest conservation has not been evaluated at fine scales. In this paper, we address both issues through a case study with Tsimane' Amerindians in the Bolivian Amazon. We sampled 624 households across 59 villages to estimate TEK and used remote sensing data to assess forest conservation. We ran statistical and spatial analyses to evaluate whether TEK was associated and spatially overlapped with forest conservation at the village level. We find that Tsimane' TEK is significantly and positively associated with forest conservation although acculturation variables bear stronger and negative associations with forest conservation. We also find a very significant spatial overlap between levels of Tsimane' TEK and forest conservation. We discuss the potential reasons underpinning our results, which provide insights that may be useful for informing policies in the realms of development, conservation, and climate. We posit that the protection of indigenous cultural systems is vital and urgent to create more effective policies in such realms.

Social-psychological principles of community-based conservation and conservancy motivation: attaining goals within an autonomy-supportive environment.

PubMed

Decaro, Daniel; Stokes, Michael

2008-12-01

Community-based natural resource conservation programs in developing nations face many implementation challenges underpinned by social-psychological mechanisms. One challenge is garnering local support in an economically and socially sustainable fashion despite economic hardship and historical alienation from local resources. Unfortunately, conservationists' limited understanding of the social-psychological mechanisms underlying participatory conservation impedes the search for appropriate solutions. We address this issue by revealing key underlying social-psychological mechanisms of participatory conservation. Different administrative designs create social atmospheres that differentially affect endorsement of conservation goals. Certain forms of endorsement may be less effective motivators and less economically and socially sustainable than others. From a literature review we found that conservation initiatives endorsed primarily for nonautonomous instrumental reasons, such as to avoid economic fines or to secure economic rewards, are less motivating than those endorsed for autonomous reasons, such as for the opportunity for personal expression and growth. We suggest that successful participatory programs promote autonomous endorsement of conservation through an administrative framework of autonomy support-free and open democratic participation in management, substantive recognition and inclusion of local stakeholder identity, and respectful, noncoercive social interaction. This framework of the autonomy-supportive environment (self-determination theory) has important implications for future research into program design and incentive-based conservation and identifies a testable social-psychological theory of conservancy motivation.

Graduate student's guide to necessary skills for nonacademic conservation careers.

PubMed

Blickley, Jessica L; Deiner, Kristy; Garbach, Kelly; Lacher, Iara; Meek, Mariah H; Porensky, Lauren M; Wilkerson, Marit L; Winford, Eric M; Schwartz, Mark W

2013-02-01

Graduate education programs in conservation science generally focus on disciplinary training and discipline-specific research skills. However, nonacademic conservation professionals often require an additional suite of skills. This discrepancy between academic training and professional needs can make it difficult for graduate students to identify the skills and experiences that will best prepare them for the conservation job market. We analyzed job advertisements for conservation-science positions and interviewed conservation professionals with experience hiring early-career conservation scientists to determine what skills employers of conservation professionals seek; whether the relative importance of skills varies by job sector (government, nonprofit, and private); and how graduate students interested in careers in conservation science might signal competency in key skills to potential employers. In job advertisements, disciplinary, interpersonal, and project-management skills were in the top 5 skills mentioned across all job sectors. Employers' needs for additional skills, like program leadership, conflict resolution and negotiation, and technical and information technology skills, varied across sectors. Our interview results demonstrated that some skills are best signaled to employers via experiences obtained outside thesis or dissertation work. Our findings suggest that graduate students who wish to be competitive in the conservation job market can benefit by gaining skills identified as important to the job sector in which they hope to work and should not necessarily expect to be competent in these skills simply by completing their chosen degree path. © 2012 Society for Conservation Biology.

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

PubMed

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

2002-02-01

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

Transportation Energy Conservation Policy: Implications for Social Science Research.

ERIC Educational Resources Information Center

Zerega, Anne Marie

1981-01-01

Examines the role social science plays in federal transportation energy conservation policy; assesses the current forms and degree of consideration of social issues in transportation energy policy; and identifies contributions that the social sciences could make in achieving energy conservation goals. (Author/MK)

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...

On biodiversity conservation and poverty traps

PubMed Central

Barrett, Christopher B.; Travis, Alexander J.; Dasgupta, Partha

2011-01-01

This paper introduces a special feature on biodiversity conservation and poverty traps. We define and explain the core concepts and then identify four distinct classes of mechanisms that define important interlinkages between biodiversity and poverty. The multiplicity of candidate mechanisms underscores a major challenge in designing policy appropriate across settings. This framework is then used to introduce the ensuing set of papers, which empirically explore these various mechanisms linking poverty traps and biodiversity conservation. PMID:21873176

Identification of priority conservation areas and potential corridors for jaguars in the Caatinga biome, Brazil.

PubMed

Morato, Ronaldo Gonçalves; Ferraz, Katia Maria Paschoaletto Micchi de Barros; de Paula, Rogério Cunha; de Campos, Cláudia Bueno

2014-01-01

The jaguar, Panthera onca, is a top predator with the extant population found within the Brazilian Caatinga biome now known to be on the brink of extinction. Designing new conservation units and potential corridors are therefore crucial for the long-term survival of the species within the Caatinga biome. Thus, our aims were: 1) to recognize suitable areas for jaguar occurrence, 2) to delineate areas for jaguar conservation (PJCUs), 3) to design corridors among priority areas, and 4) to prioritize PJCUs. A total of 62 points records of jaguar occurrence and 10 potential predictors were analyzed in a GIS environment. A predictive distributional map was obtained using Species Distribution Modeling (SDM) as performed by the Maximum Entropy (Maxent) algorithm. Areas equal to or higher than the median suitability value of 0.595 were selected as of high suitability for jaguar occurrence and named as Priority Jaguar Conservation Units (PJCU). Ten PJCUs with sizes varying from 23.6 km2 to 4,311.0 km2 were identified. Afterwards, we combined the response curve, as generated by SDM, and expert opinions to create a permeability matrix and to identify least cost corridors and buffer zones between each PJCU pair. Connectivity corridors and buffer zone for jaguar movement included an area of 8.884,26 km2 and the total corridor length is about 160.94 km. Prioritizing criteria indicated the PJCU representing c.a. 68.61% of the total PJCU area (PJCU # 1) as of high priority for conservation and connectivity with others PJCUs (PJCUs # 4, 5 and 7) desirable for the long term survival of the species. In conclusion, by using the jaguar as a focal species and combining SDM and expert opinion we were able to create a valid framework for practical conservation actions at the Caatinga biome. The same approach could be used for the conservation of other carnivores.

Weighting issues in recreation research and in identifying support for resource conservation management alternatives

Treesearch

Amy L. Sheaffer; Jay Beaman; Joseph T. O' Leary; Rebecca L. Williams; Doran M. Mason

2001-01-01

Sampling for research in recreation settings in an ongoing challenge. Often certain groups of users are more likely to be sampled. It is important in measuring public support for resource conservation and in understanding use of natural resources for recreation to evaluate issues of bias in survey methodologies. Important methodological issues emerged from a statewide...

Bicycle transportation for energy conservation

DOT National Transportation Integrated Search

1980-05-01

The study was mandated by Section 682 of the National Energy Conservation Policy Act of 1978. The study's objectives were to: (1) identify the obstacles to increased bicycle use; (2) develop a Comprehensive Bicycle Transportation Program (CBTP) to ov...

Distinct activation phenotype of a highly conserved novel HLA-B57-restricted epitope during dengue virus infection

PubMed Central

Townsley, Elizabeth; Woda, Marcia; Thomas, Stephen J; Kalayanarooj, Siripen; Gibbons, Robert V; Nisalak, Ananda; Srikiatkhachorn, Anon; Green, Sharone; Stephens, Henry AF; Rothman, Alan L; Mathew, Anuja

2014-01-01

Variation in the sequence of T-cell epitopes between dengue virus (DENV) serotypes is believed to alter memory T-cell responses during second heterologous infections. We identified a highly conserved, novel, HLA-B57-restricted epitope on the DENV NS1 protein. We predicted higher frequencies of B57-NS126–34-specific CD8+ T cells in peripheral blood mononuclear cells from individuals undergoing secondary rather than primary DENV infection. However, high tetramer-positive T-cell frequencies during acute infection were seen in only one of nine subjects with secondary infection. B57-NS126–34-specific and other DENV epitope-specific CD8+ T cells, as well as total CD8+ T cells, expressed an activated phenotype (CD69+ and/or CD38+) during acute infection. In contrast, expression of CD71 was largely limited to DENV epitope-specific CD8+ T cells. In vitro stimulation of cell lines indicated that CD71 expression was differentially sensitive to stimulation by homologous and heterologous variant peptides. CD71 may represent a useful marker of antigen-specific T-cell activation. PMID:23941420

Distinct activation phenotype of a highly conserved novel HLA-B57-restricted epitope during dengue virus infection.

PubMed

Townsley, Elizabeth; Woda, Marcia; Thomas, Stephen J; Kalayanarooj, Siripen; Gibbons, Robert V; Nisalak, Ananda; Srikiatkhachorn, Anon; Green, Sharone; Stephens, Henry A F; Rothman, Alan L; Mathew, Anuja

2014-01-01

Variation in the sequence of T-cell epitopes between dengue virus (DENV) serotypes is believed to alter memory T-cell responses during second heterologous infections. We identified a highly conserved, novel, HLA-B57-restricted epitope on the DENV NS1 protein. We predicted higher frequencies of B57-NS1(26-34) -specific CD8(+) T cells in peripheral blood mononuclear cells from individuals undergoing secondary rather than primary DENV infection. However, high tetramer-positive T-cell frequencies during acute infection were seen in only one of nine subjects with secondary infection. B57-NS1(26-34) -specific and other DENV epitope-specific CD8(+) T cells, as well as total CD8(+) T cells, expressed an activated phenotype (CD69(+) and/or CD38(+)) during acute infection. In contrast, expression of CD71 was largely limited to DENV epitope-specific CD8(+) T cells. In vitro stimulation of cell lines indicated that CD71 expression was differentially sensitive to stimulation by homologous and heterologous variant peptides. CD71 may represent a useful marker of antigen-specific T-cell activation. © 2013 John Wiley & Sons Ltd.

Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure

PubMed Central

Cooper, Vaughn S.; Hatcher, Philip J.; Verheyde, Bart; Carlier, Aurélien; Vandamme, Peter

2017-01-01

The natural environment serves as a reservoir of opportunistic pathogens. A well-established method for studying the epidemiology of such opportunists is multilocus sequence typing, which in many cases has defined strains predisposed to causing infection. Burkholderia multivorans is an important pathogen in people with cystic fibrosis (CF) and its epidemiology suggests that strains are acquired from non-human sources such as the natural environment. This raises the central question of whether the isolation source (CF or environment) or the multilocus sequence type (ST) of B. multivorans better predicts their genomic content and functionality. We identified four pairs of B. multivorans isolates, representing distinct STs and consisting of one CF and one environmental isolate each. All genomes were sequenced using the PacBio SMRT sequencing technology, which resulted in eight high-quality B. multivorans genome assemblies. The present study demonstrated that the genomic structure of the examined B. multivorans STs is highly conserved and that the B. multivorans genomic lineages are defined by their ST. Orthologous protein families were not uniformly distributed among chromosomes, with core orthologs being enriched on the primary chromosome and ST-specific orthologs being enriched on the second and third chromosome. The ST-specific orthologs were enriched in genes involved in defense mechanisms and secondary metabolism, corroborating the strain-specificity of these virulence characteristics. Finally, the same B. multivorans genomic lineages occur in both CF and environmental samples and on different continents, demonstrating their ubiquity and evolutionary persistence. PMID:28430818

State of the interface between conservation and physiology: a bibliometric analysis

PubMed Central

Lennox, Robert; Cooke, Steven J.

2014-01-01

Contemporary conservation science benefits from the perspectives of a variety of different disciplines, including a recent synergy with physiology, an interface known as ‘conservation physiology’. To evaluate the degree of interaction between conservation and animal/plant physiology, we conducted three bibliometric analyses. We first pursued the use of the term ‘conservation physiology’ since its first definition in 2006 to determine how frequently it has been used and in which publications. Secondly, we evaluated the occurrence of conservation terms in animal and plant physiology journals, physiological terms in conservation journals, and a combination of terms in ecology journals. Thirdly, we explored trends in a subset of conservation physiology articles published between 2006 and 2012. We identified a surge in the use of the term ‘conservation physiology’ in 2012, after only a slow increase in usage between 2006 and 2011. Conservation journals tend to have been significantly more active in publishing conservation physiology than animal physiology, plant physiology or ecology journals. However, we found evidence that ecology and animal physiology journals began to incorporate more conservation physiology after 2006, while conservation- and plant physiology-themed journals did not. Among 299 conservation physiology articles that we identified, vertebrate taxa have been over-represented in conservation physiology compared with their relative taxonomic abundance, invertebrate taxa have been under-represented, and plants have been represented in proportion to their relative taxonomic abundance; however, those findings are reasonably consistent with publication trends in conservation biology. Diffuse distribution of conservation physiology papers throughout the literature may have been a barrier to the growth of the subdiscipline when the interface was emerging. The introduction of the focused journal Conservation Physiology in 2013 may address that

State of the interface between conservation and physiology: a bibliometric analysis.

PubMed

Lennox, Robert; Cooke, Steven J

2014-01-01

Contemporary conservation science benefits from the perspectives of a variety of different disciplines, including a recent synergy with physiology, an interface known as 'conservation physiology'. To evaluate the degree of interaction between conservation and animal/plant physiology, we conducted three bibliometric analyses. We first pursued the use of the term 'conservation physiology' since its first definition in 2006 to determine how frequently it has been used and in which publications. Secondly, we evaluated the occurrence of conservation terms in animal and plant physiology journals, physiological terms in conservation journals, and a combination of terms in ecology journals. Thirdly, we explored trends in a subset of conservation physiology articles published between 2006 and 2012. We identified a surge in the use of the term 'conservation physiology' in 2012, after only a slow increase in usage between 2006 and 2011. Conservation journals tend to have been significantly more active in publishing conservation physiology than animal physiology, plant physiology or ecology journals. However, we found evidence that ecology and animal physiology journals began to incorporate more conservation physiology after 2006, while conservation- and plant physiology-themed journals did not. Among 299 conservation physiology articles that we identified, vertebrate taxa have been over-represented in conservation physiology compared with their relative taxonomic abundance, invertebrate taxa have been under-represented, and plants have been represented in proportion to their relative taxonomic abundance; however, those findings are reasonably consistent with publication trends in conservation biology. Diffuse distribution of conservation physiology papers throughout the literature may have been a barrier to the growth of the subdiscipline when the interface was emerging. The introduction of the focused journal Conservation Physiology in 2013 may address that deficiency

Conserved and variable domains of RNase MRP RNA.

PubMed

Dávila López, Marcela; Rosenblad, Magnus Alm; Samuelsson, Tore

2009-01-01

Ribonuclease MRP is a eukaryotic ribonucleoprotein complex consisting of one RNA molecule and 7-10 protein subunits. One important function of MRP is to catalyze an endonucleolytic cleavage during processing of rRNA precursors. RNase MRP is evolutionary related to RNase P which is critical for tRNA processing. A large number of MRP RNA sequences that now are available have been used to identify conserved primary and secondary structure features of the molecule. MRP RNA has structural features in common with P RNA such as a conserved catalytic core, but it also has unique features and is characterized by a domain highly variable between species. Information regarding primary and secondary structure features is of interest not only in basic studies of the function of MRP RNA, but also because mutations in the RNA give rise to human genetic diseases such as cartilage-hair hypoplasia.

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

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.

Efficacy of the core DNA barcodes in identifying processed and poorly conserved plant materials commonly used in South African traditional medicine

PubMed Central

Mankga, Ledile T.; Yessoufou, Kowiyou; Moteetee, Annah M.; Daru, Barnabas H.; van der Bank, Michelle

2013-01-01

Abstract Medicinal plants cover a broad range of taxa, which may be phylogenetically less related but morphologically very similar. Such morphological similarity between species may lead to misidentification and inappropriate use. Also the substitution of a medicinal plant by a cheaper alternative (e.g. other non-medicinal plant species), either due to misidentification, or deliberately to cheat consumers, is an issue of growing concern. In this study, we used DNA barcoding to identify commonly used medicinal plants in South Africa. Using the core plant barcodes, matK and rbcLa, obtained from processed and poorly conserved materials sold at the muthi traditional medicine market, we tested efficacy of the barcodes in species discrimination. Based on genetic divergence, PCR amplification efficiency and BLAST algorithm, we revealed varied discriminatory potentials for the DNA barcodes. In general, the barcodes exhibited high discriminatory power, indicating their effectiveness in verifying the identity of the most common plant species traded in South African medicinal markets. BLAST algorithm successfully matched 61% of the queries against a reference database, suggesting that most of the information supplied by sellers at traditional medicinal markets in South Africa is correct. Our findings reinforce the utility of DNA barcoding technique in limiting false identification that can harm public health. PMID:24453559

Conservation and variability of West Nile virus proteins.

PubMed

Koo, Qi Ying; Khan, Asif M; Jung, Keun-Ok; Ramdas, Shweta; Miotto, Olivo; Tan, Tin Wee; Brusic, Vladimir; Salmon, Jerome; August, J Thomas

2009-01-01

West Nile virus (WNV) has emerged globally as an increasingly important pathogen for humans and domestic animals. Studies of the evolutionary diversity of the virus over its known history will help to elucidate conserved sites, and characterize their correspondence to other pathogens and their relevance to the immune system. We describe a large-scale analysis of the entire WNV proteome, aimed at identifying and characterizing evolutionarily conserved amino acid sequences. This study, which used 2,746 WNV protein sequences collected from the NCBI GenPept database, focused on analysis of peptides of length 9 amino acids or more, which are immunologically relevant as potential T-cell epitopes. Entropy-based analysis of the diversity of WNV sequences, revealed the presence of numerous evolutionarily stable nonamer positions across the proteome (entropy value of < or = 1). The representation (frequency) of nonamers variant to the predominant peptide at these stable positions was, generally, low (< or = 10% of the WNV sequences analyzed). Eighty-eight fragments of length 9-29 amino acids, representing approximately 34% of the WNV polyprotein length, were identified to be identical and evolutionarily stable in all analyzed WNV sequences. Of the 88 completely conserved sequences, 67 are also present in other flaviviruses, and several have been associated with the functional and structural properties of viral proteins. Immunoinformatic analysis revealed that the majority (78/88) of conserved sequences are potentially immunogenic, while 44 contained experimentally confirmed human T-cell epitopes. This study identified a comprehensive catalogue of completely conserved WNV sequences, many of which are shared by other flaviviruses, and majority are potential epitopes. The complete conservation of these immunologically relevant sequences through the entire recorded WNV history suggests they will be valuable as components of peptide-specific vaccines or other therapeutic

24 CFR 968.115 - Modernization and energy conservation standards.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 24 Housing and Urban Development 4 2013-04-01 2013-04-01 false Modernization and energy... energy conservation standards. All improvements funded under this part shall: (a) Meet the modernization standards as prescribed by HUD; (b) Incorporate cost-effective energy conservation measures, identified in...

24 CFR 968.115 - Modernization and energy conservation standards.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 24 Housing and Urban Development 4 2011-04-01 2011-04-01 false Modernization and energy... energy conservation standards. All improvements funded under this part shall: (a) Meet the modernization standards as prescribed by HUD; (b) Incorporate cost-effective energy conservation measures, identified in...

24 CFR 968.115 - Modernization and energy conservation standards.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 24 Housing and Urban Development 4 2012-04-01 2012-04-01 false Modernization and energy... energy conservation standards. All improvements funded under this part shall: (a) Meet the modernization standards as prescribed by HUD; (b) Incorporate cost-effective energy conservation measures, identified in...

24 CFR 968.115 - Modernization and energy conservation standards.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 24 Housing and Urban Development 4 2010-04-01 2010-04-01 false Modernization and energy... energy conservation standards. All improvements funded under this part shall: (a) Meet the modernization standards as prescribed by HUD; (b) Incorporate cost-effective energy conservation measures, identified in...

Alkylation sensitivity screens reveal a conserved cross-species functionome

PubMed Central

Svilar, David; Dyavaiah, Madhu; Brown, Ashley R.; Tang, Jiang-bo; Li, Jianfeng; McDonald, Peter R.; Shun, Tong Ying; Braganza, Andrea; Wang, Xiao-hong; Maniar, Salony; St Croix, Claudette M.; Lazo, John S.; Pollack, Ian F.; Begley, Thomas J.; Sobol, Robert W.

2013-01-01

To identify genes that contribute to chemotherapy resistance in glioblastoma, we conducted a synthetic lethal screen in a chemotherapy-resistant glioblastoma derived cell line with the clinical alkylator temozolomide (TMZ) and an siRNA library tailored towards “druggable” targets. Select DNA repair genes in the screen were validated independently, confirming the DNA glycosylases UNG and MYH as well as MPG to be involved in the response to high dose TMZ. The involvement of UNG and MYH is likely the result of a TMZ-induced burst of reactive oxygen species. We then compared the human TMZ sensitizing genes identified in our screen with those previously identified from alkylator screens conducted in E. coli and S. cerevisiae. The conserved biological processes across all three species composes an Alkylation Functionome that includes many novel proteins not previously thought to impact alkylator resistance. This high-throughput screen, validation and cross-species analysis was then followed by a mechanistic analysis of two essential nodes: base excision repair (BER) DNA glycosylases (UNG, human and mag1, S. cerevisiae) and protein modification systems, including UBE3B and ICMT in human cells or pby1, lip22, stp22 and aim22 in S. cerevisiae. The conserved processes of BER and protein modification were dual targeted and yielded additive sensitization to alkylators in S. cerevisiae. In contrast, dual targeting of BER and protein modification genes in human cells did not increase sensitivity, suggesting an epistatic relationship. Importantly, these studies provide potential new targets to overcome alkylating agent resistance. PMID:23038810

Conservation biogeography of red oaks (Quercus, section Lobatae) in Mexico and Central America.

PubMed

Torres-Miranda, Andrés; Luna-Vega, Isolda; Oyama, Ken

2011-02-01

Oaks are dominant trees and key species in many temperate and subtropical forests in the world. In this study, we analyzed patterns of distribution of red oaks (Quercus, section Lobatae) occurring in Mexico and Central America to determine areas of species richness and endemism to propose areas of conservation. Patterns of richness and endemism of 75 red oak species were analyzed using three different units. Two complementarity algorithms based on species richness and three algorithms based on species rarity were used to identify important areas for conservation. A simulated annealing analysis was performed to evaluate and formulate effective new reserves for red oaks that are useful for conserving the ecosystems associated with them after the systematic conservation planning approach. Two main centers of species richness were detected. The northern Sierra Madre Oriental and Serranías Meridionales of Jalisco had the highest values of endemism. Fourteen areas were considered as priorities for conservation of red oak species based on the 26 priority political entities, 11 floristic units and the priority grid-cells obtained in the complementarity analysis. In the present network of Natural Protected Areas in Mexico and Central America, only 41.3% (31 species) of the red oak species are protected. The simulated annealing analysis indicated that to protect all 75 species of red oaks, 12 current natural protected areas need to be expanded by 120000 ha of additional land, and 26 new natural protected areas with 512500 ha need to be created. Red oaks are a useful model to identify areas for conservation based on species richness and endemism as a result of their wide geographic distribution and a high number of species. We evaluated and reformulated new reserves for red oaks that are also useful for the conservation of ecosystems associated with them.

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

PubMed Central

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

2013-01-01

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

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.

Differences in evolutionary pressure acting within highly conserved ortholog groups.

PubMed

Przytycka, Teresa M; Jothi, Raja; Aravind, L; Lipman, David J

2008-07-17

In highly conserved widely distributed ortholog groups, the main evolutionary force is assumed to be purifying selection that enforces sequence conservation, with most divergence occurring by accumulation of neutral substitutions. Using a set of ortholog groups from prokaryotes, with a single representative in each studied organism, we asked the question if this evolutionary pressure is acting similarly on different subgroups of orthologs defined as major lineages (e.g. Proteobacteria or Firmicutes). Using correlations in entropy measures as a proxy for evolutionary pressure, we observed two distinct behaviors within our ortholog collection. The first subset of ortholog groups, called here informational, consisted mostly of proteins associated with information processing (i.e. translation, transcription, DNA replication) and the second, the non-informational ortholog groups, mostly comprised of proteins involved in metabolic pathways. The evolutionary pressure acting on non-informational proteins is more uniform relative to their informational counterparts. The non-informational proteins show higher level of correlation between entropy profiles and more uniformity across subgroups. The low correlation of entropy profiles in the informational ortholog groups suggest that the evolutionary pressure acting on the informational ortholog groups is not uniform across different clades considered this study. This might suggest "fine-tuning" of informational proteins in each lineage leading to lineage-specific differences in selection. This, in turn, could make these proteins less exchangeable between lineages. In contrast, the uniformity of the selective pressure acting on the non-informational groups might allow the exchange of the genetic material via lateral gene transfer.

Harmonizing recreational fisheries and conservation objectives for aquatic biodiversity in inland waters.

PubMed

Cowx, I G; Arlinghaus, R; Cooke, S J

2010-06-01

The importance of recreational fisheries to local and national economies, and as a generator of immense social welfare throughout the developed world, is well established. Development in the sector and its interaction with non-fishery-related nature conservation objectives for aquatic biodiversity, however, have the potential to generate conflict. This article reviews the intersection between recreational fisheries and nature conservation goals for aquatic biodiversity with specific reference to inland waters in industrialized countries, and the principal management activities and constraints that can lead to conflicts. A SWOT (strengths, weaknesses, opportunities and threats) analysis was used to review the issues facing sectoral development and identify options for future advancement of recreational fisheries to ameliorate potential conflicts with nature conservation goals. It is concluded that reconciliation of recreational fisheries and modern conservation perspectives is both possible and desirable, because many conservation problems also benefit fisheries quality. Angler buy-in to conservation is probable if (1) management scales are small, (2) threats to conservation originate from outside the fisheries sectors and (3) ecological awareness for the conservation problem is high. If these aspects are not present, reconciliation of recreational fisheries and nature conservation goals is less likely, risking both the aquatic biodiversity and the future of angling. To address these issues, enforcement of legislation and continued communication with angler communities is necessary, as well as development of integrated management policies that build on the instrumental values of aquatic biodiversity for recreational fisheries, while curtailing the more insidious threats to such biodiversity that originate directly from the recreational fisheries sector.

Identifying Centres of Plant Biodiversity in South Australia

PubMed Central

Guerin, Greg R.; Biffin, Ed; Baruch, Zdravko; Lowe, Andrew J.

2016-01-01

We aimed to identify regional centres of plant biodiversity in South Australia, a sub-continental land area of 983,482 km2, by mapping a suite of metrics. Broad-brush conservation issues associated with the centres were mapped, specifically climate sensitivity, exposure to habitat fragmentation, introduced species and altered fire regimes. We compiled 727,417 plant species records from plot-based field surveys and herbarium records and mapped the following: species richness (all species; South Australian endemics; conservation-dependent species; introduced species); georeferenced weighted endemism, phylogenetic diversity, georeferenced phylogenetic endemism; and measures of beta diversity at local and state-wide scales. Associated conservation issues mapped were: climate sensitivity measured via ordination and non-linear modelling; habitat fragmentation represented by the proportion of remnant vegetation within a moving window; fire prone landscapes assessed using fire history records; invasive species assessed through diversity metrics, species distribution and literature. Compared to plots, herbarium data had higher spatial and taxonomic coverage but records were more biased towards major transport corridors. Beta diversity was influenced by sampling intensity and scale of comparison. We identified six centres of high plant biodiversity for South Australia: Western Kangaroo Island; Southern Mount Lofty Ranges; Anangu Pitjantjatjara Yankunytjatjara lands; Southern Flinders Ranges; Southern Eyre Peninsula; Lower South East. Species composition in the arid-mediterranean ecotone was the most climate sensitive. Fragmentation mapping highlighted the dichotomy between extensive land-use and high remnancy in the north and intensive land-use and low remnancy in the south. Invasive species were most species rich in agricultural areas close to population centres. Fire mapping revealed large variation in frequency across the state. Biodiversity scores were not always

Hydration in drug design. 3. Conserved water molecules at the ligand-binding sites of homologous proteins

NASA Astrophysics Data System (ADS)

Poornima, C. S.; Dean, P. M.

1995-12-01

Water molecules are known to play an important rôle in mediating protein-ligand interactions. If water molecules are conserved at the ligand-binding sites of homologous proteins, such a finding may suggest the structural importance of water molecules in ligand binding. Structurally conserved water molecules change the conventional definition of `binding sites' by changing the shape and complementarity of these sites. Such conserved water molecules can be important for site-directed ligand/drug design. Therefore, five different sets of homologous protein/protein-ligand complexes have been examined to identify the conserved water molecules at the ligand-binding sites. Our analysis reveals that there are as many as 16 conserved water molecules at the FAD binding site of glutathione reductase between the crystal structures obtained from human and E. coli. In the remaining four sets of high-resolution crystal structures, 2-4 water molecules have been found to be conserved at the ligand-binding sites. The majority of these conserved water molecules are either bound in deep grooves at the protein-ligand interface or completely buried in cavities between the protein and the ligand. All these water molecules, conserved between the protein/protein-ligand complexes from different species, have identical or similar apolar and polar interactions in a given set. The site residues interacting with the conserved water molecules at the ligand-binding sites have been found to be highly conserved among proteins from different species; they are more conserved compared to the other site residues interacting with the ligand. These water molecules, in general, make multiple polar contacts with protein-site residues.

Identifying impediments to long-distance mammal migrations.

PubMed

Seidler, Renee G; Long, Ryan A; Berger, Joel; Bergen, Scott; Beckmann, Jon P

2015-02-01

In much of the world, the persistence of long-distance migrations by mammals is threatened by development. Even where human population density is relatively low, there are roads, fencing, and energy development that present barriers to animal movement. If we are to conserve species that rely on long-distance migration, then it is critical that we identify existing migration impediments. To delineate stopover sites associated with anthropogenic development, we applied Brownian bridge movement models to high-frequency locations of pronghorn (Antilocapra americana) in the Greater Yellowstone Ecosystem. We then used resource utilization functions to assess the threats to long-distance migration of pronghorn that were due to fences and highways. Migrating pronghorn avoided dense developments of natural gas fields. Highways with relatively high volumes of traffic and woven-wire sheep fence acted as complete barriers. At crossings with known migration bottlenecks, use of high-quality forage and shrub habitat by pronghorn as they approached the highway was lower than expected based on availability of those resources. In contrast, pronghorn consistently utilized high-quality forage close to the highway at crossings with no known migration bottlenecks. Our findings demonstrate the importance of minimizing development in migration corridors in the future and of mitigating existing pressure on migratory animals by removing barriers, reducing the development footprint, or installing crossing structures. © 2014 Society for Conservation Biology.