Comparative Genomics of the Listeria monocytogenes ST204 Subgroup.

PubMed

Fox, Edward M; Allnutt, Theodore; Bradbury, Mark I; Fanning, Séamus; Chandry, P Scott

2016-01-01

The ST204 subgroup of Listeria monocytogenes is among the most frequently isolated in Australia from a range of environmental niches. In this study we provide a comparative genomics analysis of food and food environment isolates from geographically diverse sources. Analysis of the ST204 genomes showed a highly conserved core genome with the majority of variation seen in mobile genetic elements such as plasmids, transposons and phage insertions. Most strains (13/15) harbored plasmids, which although varying in size contained highly conserved sequences. Interestingly 4 isolates contained a conserved plasmid of 91,396 bp. The strains examined were isolated over a period of 12 years and from different geographic locations suggesting plasmids are an important component of the genetic repertoire of this subgroup and may provide a range of stress tolerance mechanisms. In addition to this 4 phage insertion sites and 2 transposons were identified among isolates, including a novel transposon. These genetic elements were highly conserved across isolates that harbored them, and also contained a range of genetic markers linked to stress tolerance and virulence. The maintenance of conserved mobile genetic elements in the ST204 population suggests these elements may contribute to the diverse range of niches colonized by ST204 isolates. Environmental stress selection may contribute to maintaining these genetic features, which in turn may be co-selecting for virulence markers relevant to clinical infection with ST204 isolates.

Phylogenetic analysis of conservation priorities for aquatic mammals and their terrestrial relatives, with a comparison of methods.

PubMed

May-Collado, Laura J; Agnarsson, Ingi

2011-01-01

Habitat loss and overexploitation are among the primary factors threatening populations of many mammal species. Recently, aquatic mammals have been highlighted as particularly vulnerable. Here we test (1) if aquatic mammals emerge as more phylogenetically urgent conservation priorities than their terrestrial relatives, and (2) if high priority species are receiving sufficient conservation effort. We also compare results among some phylogenetic conservation methods. A phylogenetic analysis of conservation priorities for all 620 species of Cetartiodactyla and Carnivora, including most aquatic mammals. Conservation priority ranking of aquatic versus terrestrial species is approximately proportional to their diversity. However, nearly all obligated freshwater cetartiodactylans are among the top conservation priority species. Further, ∼74% and 40% of fully aquatic cetartiodactylans and carnivores, respectively, are either threatened or data deficient, more so than their terrestrial relatives. Strikingly, only 3% of all 'high priority' species are thought to be stable. An overwhelming 97% of these species thus either show decreasing population trends (87%) or are insufficiently known (10%). Furthermore, a disproportional number of highly evolutionarily distinct species are experiencing population decline, thus, such species should be closely monitored even if not currently threatened. Comparison among methods reveals that exact species ranking differs considerably among methods, nevertheless, most top priority species consistently rank high under any method. While we here favor one approach, we also suggest that a consensus approach may be useful when methods disagree. These results reinforce prior findings, suggesting there is an urgent need to gather basic conservation data for aquatic mammals, and special conservation focus is needed on those confined to freshwater. That evolutionarily distinct--and thus 'biodiverse'--species are faring relatively poorly is alarming and requires further study. Our results offer a detailed guide to phylogeny-based conservation prioritization for these two orders.

Soil particulate organic matter dynamics after conservation reserve program land is converted to cropland

USDA-ARS?s Scientific Manuscript database

The objective of this project is to compare the soil C quality in Conservation Reserve Program (CRP) vs. land under Sorghum cropping or rangeland in the Southern High Plains. Whole soils as well as light fraction particulate organic matter (lfPOM) was assessed using diffuse reflectance Fourier trans...

Wildlife Abundance and Diversity as Indicators of Tourism Potential in Northern Botswana.

PubMed

Winterbach, Christiaan W; Whitesell, Carolyn; Somers, Michael J

2015-01-01

Wildlife tourism can provide economic incentives for conservation. Due to the abundance of wildlife and the presence of charismatic species some areas are better suited to wildlife tourism. Our first objective was to develop criteria based on wildlife abundance and diversity to evaluate tourism potential in the Northern Conservation Zone of Botswana. Secondly we wanted to quantify and compare tourism experiences in areas with high and low tourism potential. We used aerial survey data to estimate wildlife biomass and diversity to determine tourism potential, while data from ground surveys quantified the tourist experience. Areas used for High Paying Low Volume tourism had significantly higher mean wildlife biomass and wildlife diversity than the areas avoided for this type of tourism. Only 22% of the Northern Conservation Zone has intermediate to high tourism potential. The areas with high tourism potential, as determined from the aerial survey data, provided tourists with significantly better wildlife sightings (ground surveys) than the low tourism potential areas. Even Low Paying tourism may not be economically viable in concessions that lack areas with intermediate to high tourism potential. The largest part of the Northern Conservation Zone has low tourism potential, but low tourism potential is not equal to low conservation value. Alternative conservation strategies should be developed to complement the economic incentive provided by wildlife-based tourism in Botswana.

Wildlife Abundance and Diversity as Indicators of Tourism Potential in Northern Botswana

PubMed Central

Winterbach, Christiaan W.; Whitesell, Carolyn; Somers, Michael J.

2015-01-01

Wildlife tourism can provide economic incentives for conservation. Due to the abundance of wildlife and the presence of charismatic species some areas are better suited to wildlife tourism. Our first objective was to develop criteria based on wildlife abundance and diversity to evaluate tourism potential in the Northern Conservation Zone of Botswana. Secondly we wanted to quantify and compare tourism experiences in areas with high and low tourism potential. We used aerial survey data to estimate wildlife biomass and diversity to determine tourism potential, while data from ground surveys quantified the tourist experience. Areas used for High Paying Low Volume tourism had significantly higher mean wildlife biomass and wildlife diversity than the areas avoided for this type of tourism. Only 22% of the Northern Conservation Zone has intermediate to high tourism potential. The areas with high tourism potential, as determined from the aerial survey data, provided tourists with significantly better wildlife sightings (ground surveys) than the low tourism potential areas. Even Low Paying tourism may not be economically viable in concessions that lack areas with intermediate to high tourism potential. The largest part of the Northern Conservation Zone has low tourism potential, but low tourism potential is not equal to low conservation value. Alternative conservation strategies should be developed to complement the economic incentive provided by wildlife-based tourism in Botswana. PMID:26308859

Relevance of genetics for conservation policies: the case of Minorcan cork oaks

PubMed Central

Lorenzo, Zaida; Burgarella, Concetta; de Heredia, Unai López; Lumaret, Roselyne; Petit, Rémy J.; Soto, Álvaro; Gil, Luis

2009-01-01

Background and Aims Marginal populations of widely distributed species can be of high conservation interest when they hold a significant or unique portion of the genetic diversity of the species. However, such genetic information is frequently lacking. Here the relevance of genetic surveys to develop efficient conservation strategies for such populations is illustrated using cork oak (Quercus suber) from Minorca (Balearic Islands, Spain) as a case study. Cork oak is highly endangered on the island, where no more than 67 individuals live in small, isolated stands in siliceous sites. As a consequence, it was recently granted protected status. Methods Two Bayesian clustering approaches were used to analyse the genetic structure of the Minorcan population, on the basis of nuclear microsatellite data. The different groups within the island were also compared with additional island and continental populations surrounding Minorca. Key Results Very high genetic diversity was found, with values comparable with those observed in continental parts of the species' range. Furthermore, the Minorcan oak stands were highly differentiated from one another and were genetically related to different continental populations of France and Spain. Conclusions The high levels of genetic diversity and inter-stands differentiation make Minorcan cork oak eligible for specific conservation efforts. The relationship of Minorcan stands to different continental populations in France and Spain probably reflects multiple colonization events. However, discrepancy between chloroplast DNA- and nuclear DNA-based groups does not support a simple scenario of recent introduction. Gene exchanges between neighbouring cork oak stands and with holm oak have created specific and exceptional genetic combinations. They also constitute a wide range of potential genetic resources for research on adaptation to new environmental conditions. Conservation guidelines that take into account these findings are provided. PMID:19671575

Phase I: energy conservation potential of Portland Cement particle size distribution control. Progress report, November 1978-January 1979

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

Helmuth, R.A.

1979-03-01

Progress is reported on the energy conservation potential of Portland cement particle size distribution control. Results of preliminary concrete tests, Series IIIa and Series IIIb, effects of particle size ranges on strength and drying shrinkage, are presented. Series IV, effects of mixing and curing temperature, tests compare the properties of several good particle size controlled cements with normally ground cements at low and high temperatures. The work on the effects of high alkali and high sulfate clinker cements (Series V) has begun.

Assessing the shelf life of cost-efficient conservation plans for species at risk across gradients of agricultural land use.

PubMed

Robillard, Cassandra M; Kerr, Jeremy T

2017-08-01

High costs of land in agricultural regions warrant spatial prioritization approaches to conservation that explicitly consider land prices to produce protected-area networks that accomplish targets efficiently. However, land-use changes in such regions and delays between plan design and implementation may render optimized plans obsolete before implementation occurs. To measure the shelf life of cost-efficient conservation plans, we simulated a land-acquisition and restoration initiative aimed at conserving species at risk in Canada's farmlands. We accounted for observed changes in land-acquisition costs and in agricultural intensity based on censuses of agriculture taken from 1986 to 2011. For each year of data, we mapped costs and areas of conservation priority designated using Marxan. We compared plans to test for changes through time in the arrangement of high-priority sites and in the total cost of each plan. For acquisition costs, we measured the savings from accounting for prices during site selection. Land-acquisition costs and land-use intensity generally rose over time independent of inflation (24-78%), although rates of change were heterogeneous through space and decreased in some areas. Accounting for spatial variation in land price lowered the cost of conservation plans by 1.73-13.9%, decreased the range of costs by 19-82%, and created unique solutions from which to choose. Despite the rise in plan costs over time, the high conservation priority of particular areas remained consistent. Delaying conservation in these critical areas may compromise what optimized conservation plans can achieve. In the case of Canadian farmland, rapid conservation action is cost-effective, even with moderate levels of uncertainty in how to implement restoration goals. © 2016 Society for Conservation Biology.

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

PubMed

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

2011-02-01

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

Efficacy of Gastrografin® Compared with Standard Conservative Treatment in Management of Adhesive Small Bowel Obstruction at Mulago National Referral Hospital

PubMed Central

Haule, Caspar; Ongom, Peter A; Kimuli, Timothy

2013-01-01

Introduction The treatment of adhesive small bowel obstruction is controversial, with both operative and non-operative management practiced in different centers worldwide. Non-operative management is increasingly getting popular, though operative rates still remain high. A study to compare the efficacy of an oral water-soluble medium (Gastrografin®) with standard conservative management, both non-operative methods, in the management of this condition was conducted in a tertiary Sub Saharan hospital. Methods An open randomised controlled clinical trial was conducted between September 2012 and March 2013 at Mulago National Referral and Teaching Hospital, Uganda. Fifty patients of both genders, with adhesive small bowel obstruction, in the hospital’s emergency and general surgical wards were included. Randomisation was to Gastrografin® and standard conservative treatment groups. The primary outcomes were: the time interval between admission and relief of obstruction, the length of hospital stay, and the rates of operative surgery. Results All 50 recruited patients were followed up and analysed; 25 for each group. In the Gastrografin® group, 22 (88%) patients had relief of obstruction following the intervention, with 3 (12%) requiring surgery. The conservative treatment group had 16 (64%) patients relieved of obstruction conservatively, and 9 (36%) required surgery. The difference in operative rates between the two groups was not statistically significance (P = 0.67). Average time to relief of obstruction was shorter in the Gastrografin® group (72.52 hrs) compared to the conservative treatment group (117.75 hrs), a significant difference (P = 0.023). The average length of hospital stay was shorter in the Gastrografin® group (5.62 days) compared to the conservative treatment group (10.88 days), a significant difference (P = 0.04). Conclusion The use of Gastrografin® in patients with adhesive small bowel obstruction helps in earlier resolution of obstruction and reduces the length of hospital stay compared with standard conservative management. Its role in reducing the rate of laparotomies remains inconclusive. PMID:24729947

Efficacy of Gastrografin® Compared with Standard Conservative Treatment in Management of Adhesive Small Bowel Obstruction at Mulago National Referral Hospital.

PubMed

Haule, Caspar; Ongom, Peter A; Kimuli, Timothy

2013-12-01

The treatment of adhesive small bowel obstruction is controversial, with both operative and non-operative management practiced in different centers worldwide. Non-operative management is increasingly getting popular, though operative rates still remain high. A study to compare the efficacy of an oral water-soluble medium (Gastrografin ® ) with standard conservative management, both non-operative methods, in the management of this condition was conducted in a tertiary Sub Saharan hospital. An open randomised controlled clinical trial was conducted between September 2012 and March 2013 at Mulago National Referral and Teaching Hospital, Uganda. Fifty patients of both genders, with adhesive small bowel obstruction, in the hospital's emergency and general surgical wards were included. Randomisation was to Gastrografin ® and standard conservative treatment groups. The primary outcomes were: the time interval between admission and relief of obstruction, the length of hospital stay, and the rates of operative surgery. All 50 recruited patients were followed up and analysed; 25 for each group. In the Gastrografin ® group, 22 (88%) patients had relief of obstruction following the intervention, with 3 (12%) requiring surgery. The conservative treatment group had 16 (64%) patients relieved of obstruction conservatively, and 9 (36%) required surgery. The difference in operative rates between the two groups was not statistically significance ( P = 0.67 ). Average time to relief of obstruction was shorter in the Gastrografin ® group (72.52 hrs) compared to the conservative treatment group (117.75 hrs), a significant difference ( P = 0.023 ). The average length of hospital stay was shorter in the Gastrografin ® group (5.62 days) compared to the conservative treatment group (10.88 days), a significant difference ( P = 0.04 ). The use of Gastrografin ® in patients with adhesive small bowel obstruction helps in earlier resolution of obstruction and reduces the length of hospital stay compared with standard conservative management. Its role in reducing the rate of laparotomies remains inconclusive.

Analysis of hepatitis B virus preS1 variability and prevalence of the rs2296651 polymorphism in a Spanish population

PubMed Central

Casillas, Rosario; Tabernero, David; Gregori, Josep; Belmonte, Irene; Cortese, Maria Francesca; González, Carolina; Riveiro-Barciela, Mar; López, Rosa Maria; Quer, Josep; Esteban, Rafael; Buti, Maria; Rodríguez-Frías, Francisco

2018-01-01

AIM To determine the variability/conservation of the domain of hepatitis B virus (HBV) preS1 region that interacts with sodium-taurocholate cotransporting polypeptide (hereafter, NTCP-interacting domain) and the prevalence of the rs2296651 polymorphism (S267F, NTCP variant) in a Spanish population. METHODS Serum samples from 246 individuals were included and divided into 3 groups: patients with chronic HBV infection (CHB) (n = 41, 73% Caucasians), patients with resolved HBV infection (n = 100, 100% Caucasians) and an HBV-uninfected control group (n = 105, 100% Caucasians). Variability/conservation of the amino acid (aa) sequences of the NTCP-interacting domain, (aa 2-48 in viral genotype D) and a highly conserved preS1 domain associated with virion morphogenesis (aa 92-103 in viral genotype D) were analyzed by next-generation sequencing and compared in 18 CHB patients with viremia > 4 log IU/mL. The rs2296651 polymorphism was determined in all individuals in all 3 groups using an in-house real-time PCR melting curve analysis. RESULTS The HBV preS1 NTCP-interacting domain showed a high degree of conservation among the examined viral genomes especially between aa 9 and 21 (in the genotype D consensus sequence). As compared with the virion morphogenesis domain, the NTCP-interacting domain had a smaller proportion of HBV genotype-unrelated changes comprising > 1% of the quasispecies (25.5% vs 31.8%), but a larger proportion of genotype-associated viral polymorphisms (34% vs 27.3%), according to consensus sequences from GenBank patterns of HBV genotypes A to H. Variation/conservation in both domains depended on viral genotype, with genotype C being the most highly conserved and genotype E the most variable (limited finding, only 2 genotype E included). Of note, proline residues were highly conserved in both domains, and serine residues showed changes only to threonine or tyrosine in the virion morphogenesis domain. The rs2296651 polymorphism was not detected in any participant. CONCLUSION In our CHB population, the NTCP-interacting domain was highly conserved, particularly the proline residues and essential amino acids related with the NTCP interaction, and the prevalence of rs2296651 was low/null. PMID:29456407

The Most Deeply Conserved Noncoding Sequences in Plants Serve Similar Functions to Those in Vertebrates Despite Large Differences in Evolutionary Rates[W

PubMed Central

Burgess, Diane; Freeling, Michael

2014-01-01

In vertebrates, conserved noncoding elements (CNEs) are functionally constrained sequences that can show striking conservation over >400 million years of evolutionary distance and frequently are located megabases away from target developmental genes. Conserved noncoding sequences (CNSs) in plants are much shorter, and it has been difficult to detect conservation among distantly related genomes. In this article, we show not only that CNS sequences can be detected throughout the eudicot clade of flowering plants, but also that a subset of 37 CNSs can be found in all flowering plants (diverging ∼170 million years ago). These CNSs are functionally similar to vertebrate CNEs, being highly associated with transcription factor and development genes and enriched in transcription factor binding sites. Some of the most highly conserved sequences occur in genes encoding RNA binding proteins, particularly the RNA splicing–associated SR genes. Differences in sequence conservation between plants and animals are likely to reflect differences in the biology of the organisms, with plants being much more able to tolerate genomic deletions and whole-genome duplication events due, in part, to their far greater fecundity compared with vertebrates. PMID:24681619

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 and Role of Electrostatics in Thymidylate Synthase.

PubMed

Garg, Divita; Skouloubris, Stephane; Briffotaux, Julien; Myllykallio, Hannu; Wade, Rebecca C

2015-11-27

Conservation of function across families of orthologous enzymes is generally accompanied by conservation of their active site electrostatic potentials. To study the electrostatic conservation in the highly conserved essential enzyme, thymidylate synthase (TS), we conducted a systematic species-based comparison of the electrostatic potential in the vicinity of its active site. Whereas the electrostatics of the active site of TS are generally well conserved, the TSs from minimal organisms do not conform to the overall trend. Since the genomes of minimal organisms have a high thymidine content compared to other organisms, the observation of non-conserved electrostatics was surprising. Analysis of the symbiotic relationship between minimal organisms and their hosts, and the genetic completeness of the thymidine synthesis pathway suggested that TS from the minimal organism Wigglesworthia glossinidia (W.g.b.) must be active. Four residues in the vicinity of the active site of Escherichia coli TS were mutated individually and simultaneously to mimic the electrostatics of W.g.b TS. The measured activities of the E. coli TS mutants imply that conservation of electrostatics in the region of the active site is important for the activity of TS, and suggest that the W.g.b. TS has the minimal activity necessary to support replication of its reduced genome.

What Data to Use for Forest Conservation Planning? A Comparison of Coarse Open and Detailed Proprietary Forest Inventory Data in Finland

PubMed Central

Lehtomäki, Joona; Tuominen, Sakari; Toivonen, Tuuli; Leinonen, Antti

2015-01-01

The boreal region is facing intensifying resource extraction pressure, but the lack of comprehensive biodiversity data makes operative forest conservation planning difficult. Many countries have implemented forest inventory schemes and are making extensive and up-to-date forest databases increasingly available. Some of the more detailed inventory databases, however, remain proprietary and unavailable for conservation planning. Here, we investigate how well different open and proprietary forest inventory data sets suit the purpose of conservation prioritization in Finland. We also explore how much priorities are affected by using the less accurate but open data. First, we construct a set of indices for forest conservation value based on quantitative information commonly found in forest inventories. These include the maturity of the trees, tree species composition, and site fertility. Secondly, using these data and accounting for connectivity between forest types, we investigate the patterns in conservation priority. For prioritization, we use Zonation, a method and software for spatial conservation prioritization. We then validate the prioritizations by comparing them to known areas of high conservation value. We show that the overall priority patterns are relatively consistent across different data sources and analysis options. However, the coarse data cannot be used to accurately identify the high-priority areas as it misses much of the fine-scale variation in forest structures. We conclude that, while inventory data collected for forestry purposes may be useful for forest conservation purposes, it needs to be detailed enough to be able to account for more fine-scaled features of high conservation value. These results underline the importance of making detailed inventory data publicly available. Finally, we discuss how the prioritization methodology we used could be integrated into operative forest management, especially in countries in the boreal zone. PMID:26317227

What Data to Use for Forest Conservation Planning? A Comparison of Coarse Open and Detailed Proprietary Forest Inventory Data in Finland.

PubMed

Lehtomäki, Joona; Tuominen, Sakari; Toivonen, Tuuli; Leinonen, Antti

2015-01-01

The boreal region is facing intensifying resource extraction pressure, but the lack of comprehensive biodiversity data makes operative forest conservation planning difficult. Many countries have implemented forest inventory schemes and are making extensive and up-to-date forest databases increasingly available. Some of the more detailed inventory databases, however, remain proprietary and unavailable for conservation planning. Here, we investigate how well different open and proprietary forest inventory data sets suit the purpose of conservation prioritization in Finland. We also explore how much priorities are affected by using the less accurate but open data. First, we construct a set of indices for forest conservation value based on quantitative information commonly found in forest inventories. These include the maturity of the trees, tree species composition, and site fertility. Secondly, using these data and accounting for connectivity between forest types, we investigate the patterns in conservation priority. For prioritization, we use Zonation, a method and software for spatial conservation prioritization. We then validate the prioritizations by comparing them to known areas of high conservation value. We show that the overall priority patterns are relatively consistent across different data sources and analysis options. However, the coarse data cannot be used to accurately identify the high-priority areas as it misses much of the fine-scale variation in forest structures. We conclude that, while inventory data collected for forestry purposes may be useful for forest conservation purposes, it needs to be detailed enough to be able to account for more fine-scaled features of high conservation value. These results underline the importance of making detailed inventory data publicly available. Finally, we discuss how the prioritization methodology we used could be integrated into operative forest management, especially in countries in the boreal zone.

Reducing Energy Consumption and Creating a Conservation Culture in Organizations: A Case Study of One Public School District

ERIC Educational Resources Information Center

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

2011-01-01

How can existing schools significantly reduce their energy use? With energy costs rising and school budgets shrinking, energy use is a substantial cost that can be reduced through conservation efforts. Using a case study methodology, the authors compare two public high schools from the same school district, one that has achieved moderate energy…

Conservation value of low-productivity forests measured as the amount and diversity of dead wood and saproxylic beetles.

PubMed

Hämäläinen, Aino; Strengbom, Joachim; Ranius, Thomas

2018-06-01

In many managed landscapes, low-productivity land comprises most of the remaining relatively untouched areas, and is often over-represented within protected areas. The relationship between the productivity and conservational value of a site is poorly known; however, it has been hypothesized that biodiversity increases with productivity due to higher resource abundance or heterogeneity, and that the species communities of low-productivity land are a nested subset of communities from more productive land. We tested these hypotheses for dead-wood-dependent beetles by comparing their species richness and composition, as well as the amount and diversity of dead wood, between low-productivity (potential forest growth <1 m 3 ·ha -1 ·yr -1 ) and high-productivity Scots pine-dominated stands in Sweden. We included four stand types: stands situated on (1) thin soils and (2) mires (both low-productivity), (3) managed stands, and (4) unmanaged stands set aside for conservation purposes (both high-productivity). Beetle species richness and number of red-listed species were highest in the high-productivity set-asides. Species richness was positively correlated with the volume and diversity of dead wood, but volume appeared to be a better predictor than diversity for the higher species richness in set-asides. Beetle species composition was similar among stand types, and the assemblages in low-productivity stands were largely subsets of those in high-productivity set-asides. However, 11% of all species and 40% of red-listed species only occurred in high-productivity stands, while no species were unique to low-productivity stands. We conclude that low-productivity forests are less valuable for conservation than high-productivity forest land. Given the generally similar species composition among stand types, a comparable conservational effect could be obtained by setting aside a larger area of low-productivity forest in comparison to the high-productivity. In terms of dead wood volumes, 1.8-3.6 ha of low-productivity forest has the same value as 1 ha of unmanaged high-productivity forest. This figure can be used to estimate the conservation value of low-productivity forests; however, as high-productivity forests harbored some unique species, they are not completely exchangeable. © 2018 The Authors. Ecological Applications published by Wiley Periodicals, Inc. on behalf of Ecological Society of America.

Can private land conservation reduce wildfire risk to homes? A case study in San Diego County, California, USA

USGS Publications Warehouse

Butsic, Van; Syphard, Alexandra D.; Keeley, Jon E.; Bar-Massada, Avi

2017-01-01

The purchase of private land for conservation purposes is a common way to prevent the exploitation of sensitive ecological areas. However, private land conservation can also provide other benefits, one of these being natural hazard reduction. Here, we investigated the impacts of private land conservation on fire risk to homes in San Diego County, California. We coupled an econometric land use change model with a model that estimates the probability of house loss due to fire in order to compare fire risk at the county and municipality scale under alternative private land purchasing schemes and over a 20 year time horizon. We found that conservation purchases could reduce fire risk on this landscape, and the amount of risk reduction was related to the targeting approach used to choose which parcels were conserved. Conservation land purchases that targeted parcels designated as high fire hazard resulted in lower fire risk to homes than purchases that targeted low costs or high likelihood to subdivide. This result was driven by (1) preventing home placement in fire prone areas and (2) taking land off the market, and hence increasing development densities in other areas. These results raise the possibility that resource conservation and fire hazard reduction may benefit from combining efforts. With adequate planning, future conservation purchases could have synergistic effects beyond just protecting ecologically sensitive areas.

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.

Phylogenetic Analysis of Conservation Priorities for Aquatic Mammals and Their Terrestrial Relatives, with a Comparison of Methods

PubMed Central

May-Collado, Laura J.; Agnarsson, Ingi

2011-01-01

Background Habitat loss and overexploitation are among the primary factors threatening populations of many mammal species. Recently, aquatic mammals have been highlighted as particularly vulnerable. Here we test (1) if aquatic mammals emerge as more phylogenetically urgent conservation priorities than their terrestrial relatives, and (2) if high priority species are receiving sufficient conservation effort. We also compare results among some phylogenetic conservation methods. Methodology/Principal Findings A phylogenetic analysis of conservation priorities for all 620 species of Cetartiodactyla and Carnivora, including most aquatic mammals. Conservation priority ranking of aquatic versus terrestrial species is approximately proportional to their diversity. However, nearly all obligated freshwater cetartiodactylans are among the top conservation priority species. Further, ∼74% and 40% of fully aquatic cetartiodactylans and carnivores, respectively, are either threatened or data deficient, more so than their terrestrial relatives. Strikingly, only 3% of all ‘high priority’ species are thought to be stable. An overwhelming 97% of these species thus either show decreasing population trends (87%) or are insufficiently known (10%). Furthermore, a disproportional number of highly evolutionarily distinct species are experiencing population decline, thus, such species should be closely monitored even if not currently threatened. Comparison among methods reveals that exact species ranking differs considerably among methods, nevertheless, most top priority species consistently rank high under any method. While we here favor one approach, we also suggest that a consensus approach may be useful when methods disagree. Conclusions/Significance These results reinforce prior findings, suggesting there is an urgent need to gather basic conservation data for aquatic mammals, and special conservation focus is needed on those confined to freshwater. That evolutionarily distinct—and thus ‘biodiverse’—species are faring relatively poorly is alarming and requires further study. Our results offer a detailed guide to phylogeny-based conservation prioritization for these two orders. PMID:21799899

Targeting climate diversity in conservation planning to build resilience to climate change

USGS Publications Warehouse

Heller, Nicole E.; Kreitler, Jason R.; Ackerly, David; Weiss, Stuart; Recinos, Amanda; Branciforte, Ryan; Flint, Lorraine E.; Flint, Alan L.; Micheli, Elisabeth

2015-01-01

Climate change is raising challenging concerns for systematic conservation planning. Are methods based on the current spatial patterns of biodiversity effective given long-term climate change? Some conservation scientists argue that planning should focus on protecting the abiotic diversity in the landscape, which drives patterns of biological diversity, rather than focusing on the distribution of focal species, which shift in response to climate change. Climate is one important abiotic driver of biodiversity patterns, as different climates host different biological communities and genetic pools. We propose conservation networks that capture the full range of climatic diversity in a region will improve the resilience of biotic communities to climate change compared to networks that do not. In this study we used historical and future hydro-climate projections from the high resolution Basin Characterization Model to explore the utility of directly targeting climatic diversity in planning. Using the spatial planning tool, Marxan, we designed conservation networks to capture the diversity of climate types, at the regional and sub-regional scale, and compared them to networks we designed to capture the diversity of vegetation types. By focusing on the Conservation Lands Network (CLN) of the San Francisco Bay Area as a real-world case study, we compared the potential resilience of networks by examining two factors: the range of climate space captured, and climatic stability to 18 future climates, reflecting different emission scenarios and global climate models. We found that the climate-based network planned at the sub-regional scale captured a greater range of climate space and showed higher climatic stability than the vegetation and regional based-networks. At the same time, differences among network scenarios are small relative to the variance in climate stability across global climate models. Across different projected futures, topographically heterogeneous areas consistently show greater climate stability than homogenous areas. The analysis suggests that utilizing high-resolution climate and hydrological data in conservation planning improves the likely resilience of biodiversity to climate change. We used these analyses to suggest new conservation priorities for the San Francisco Bay Area.

Ultrasonic Spray Drying vs High Vacuum and Microwaves Technology for Blueberries

NASA Astrophysics Data System (ADS)

Candia-Muñoz, N.; Ramirez-Bunster, M.; Vargas-Hernández, Y.; Gaete-Garretón, L.

Interest in high quality foods: good taste and a high content of nutrients with healthy beneficial effects are increasing. Fruits have good properties but, they are lost because the oxidation process, additionally, for different reasons a 40% of harvested fruit are lost. To conserve the fruit properties an ultrasonic assisted spray dryer was developed and tested, comparing its results with microwave-vacuum drying technology. Results did shown taste, color, smell, particle shape and size distribution better than the conventional one. The antioxidants conservation were quite good except in the anthocyanins, in which the microwave and vacuum technology shown best results.

Territorial user rights for fisheries as ancillary instruments for marine coastal conservation in Chile.

PubMed

Gelcich, Stefan; Fernández, Miriam; Godoy, Natalio; Canepa, Antonio; Prado, Luis; Castilla, Juan Carlos

2012-12-01

Territorial user rights for fisheries have been advocated as a way to achieve sustainable resource management. However, few researchers have empirically assessed their potential as ancillary marine conservation instruments by comparing them to no-take marine protected areas. In kelp (Lessonia trabeculata) forests of central Chile, we compared species richness, density, and biomass of macroinvertebrates and reef fishes among territorial-user-right areas with low-level and high-level enforcement, no-take marine protected areas, and open-access areas in 42 100-m subtidal transects. We also assessed structural complexity of the kelp forest and substratum composition. Multivariate randomized permutation tests indicated macroinvertebrate and reef fish communities associated with the different access regimes differed significantly. Substratum composition and structural complexity of kelp forest did not differ among access regimes. Univariate analyses showed species richness, biomass, and density of macroinvertebrates and reef fishes were greater in highly enforced territorial-user-right areas and no-take marine protected areas than in open-access areas. Densities of macroinvertebrates and reef fishes of economic importance were not significantly different between highly enforced territorial-user-right and no-take marine protected areas. Densities of economically important macroinvertebrates in areas with low-level enforcement were significantly lower than those in areas with high-level enforcement and no-take marine protected areas but were significantly higher than in areas with open access. Territorial-user-right areas could be important ancillary conservation instruments if they are well enforced. ©2012 Society for Conservation Biology.

A simple mass-conserved level set method for simulation of multiphase flows

NASA Astrophysics Data System (ADS)

Yuan, H.-Z.; Shu, C.; Wang, Y.; Shu, S.

2018-04-01

In this paper, a modified level set method is proposed for simulation of multiphase flows with large density ratio and high Reynolds number. The present method simply introduces a source or sink term into the level set equation to compensate the mass loss or offset the mass increase. The source or sink term is derived analytically by applying the mass conservation principle with the level set equation and the continuity equation of flow field. Since only a source term is introduced, the application of the present method is as simple as the original level set method, but it can guarantee the overall mass conservation. To validate the present method, the vortex flow problem is first considered. The simulation results are compared with those from the original level set method, which demonstrates that the modified level set method has the capability of accurately capturing the interface and keeping the mass conservation. Then, the proposed method is further validated by simulating the Laplace law, the merging of two bubbles, a bubble rising with high density ratio, and Rayleigh-Taylor instability with high Reynolds number. Numerical results show that the mass is a well-conserved by the present method.

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.

Sustainability of three modified soil conservation methods in agriculture area

NASA Astrophysics Data System (ADS)

Setiawan, M. A.; Sara, F. H.; Christanto, N.; Sartohadi, J.; Samodra, G.; Widicahyono, A.; Ardiana, N.; Widiyati, C. N.; Astuti, E. M.; Martha, G. K.; Malik, R. F.; Sambodo, A. P.; Rokhmaningtyas, R. P.; Swastanto, G. A.; Gomez, C.

2018-04-01

Recent innovations in soil conservation methods do not present any breakthrough. Providing more attractive soil conservation methods from the farmer’s perspective is however still of critical importance. Contributing to this soil research gap we attempt to evaluate the sustainable use of three modified conservation methods, namely JALAPA (Jala Sabut Kelapa - geotextile made of coconut fibres), wood sediment trap, and polybag system compared to traditional tillage without conservation method. This research provides both qualitative and quantitative analysis on the performance of each conservation measures. Therefore, in addition to the total sediment yield value and investment cost – as quantitative analysis, we also evaluate qualitatively the indicator of soil loss, installation, maintenance, and the durability of conservation medium. Those criteria define the sustainability use of each conservation method. The results show that JALAPA is the most effective method for controlling soil loss, but it also requires the most expensive cost for installation. However, our finding confirms that geotextile is sensitive to sun heating by which the coconut fibre can become dry and shrink. Wood sediment trap is the cheapest and easiest to install; however it is easily damaged by termite. Polybag method results in the highest productivity, but requires more time during the first installation. In terms of the farmer’s perspective, soil conservation using polybag system was the most accepted technique due to its high benefits; even if it is less effective at reducing soil loss compared to JALAPA.

Supporting local diversity of habitats and species on farmland: a comparison of three wildlife-friendly schemes.

PubMed

Hardman, Chloe J; Harrison, Dominic P G; Shaw, Pete J; Nevard, Tim D; Hughes, Brin; Potts, Simon G; Norris, Ken

2016-02-01

Restoration and maintenance of habitat diversity have been suggested as conservation priorities in farmed landscapes, but how this should be achieved and at what scale are unclear. This study makes a novel comparison of the effectiveness of three wildlife-friendly farming schemes for supporting local habitat diversity and species richness on 12 farms in England.The schemes were: (i) Conservation Grade (Conservation Grade: a prescriptive, non-organic, biodiversity-focused scheme), (ii) organic agriculture and (iii) a baseline of Entry Level Stewardship (Entry Level Stewardship: a flexible widespread government scheme). Conservation Grade farms supported a quarter higher habitat diversity at the 100-m radius scale compared to Entry Level Stewardship farms. Conservation Grade and organic farms both supported a fifth higher habitat diversity at the 250-m radius scale compared to Entry Level Stewardship farms. Habitat diversity at the 100-m and 250-m scales significantly predicted species richness of butterflies and plants. Habitat diversity at the 100-m scale also significantly predicted species richness of birds in winter and solitary bees. There were no significant relationships between habitat diversity and species richness for bumblebees or birds in summer.Butterfly species richness was significantly higher on organic farms (50% higher) and marginally higher on Conservation Grade farms (20% higher), compared with farms in Entry Level Stewardship. Organic farms supported significantly more plant species than Entry Level Stewardship farms (70% higher) but Conservation Grade farms did not (10% higher). There were no significant differences between the three schemes for species richness of bumblebees, solitary bees or birds. Policy implications . The wildlife-friendly farming schemes which included compulsory changes in management, Conservation Grade and organic, were more effective at increasing local habitat diversity and species richness compared with the less prescriptive Entry Level Stewardship scheme. We recommend that wildlife-friendly farming schemes should aim to enhance and maintain high local habitat diversity, through mechanisms such as option packages, where farmers are required to deliver a combination of several habitats.

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 for NADDA, ADDA, and MKDOM2, respectively, for a data set comprised of approximately 2500 sequences. PMID:27552220

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.

Recreational Use of the Countryside: No Evidence that High Nature Value Enhances a Key Ecosystem Service

PubMed Central

Hornigold, Karen; Lake, Iain; Dolman, Paul

2016-01-01

In Western Europe, recreational amenity is presented as an important cultural ecosystem service that, along with other values, helps justify policies to conserve biodiversity. However, whether recreational use by the public is enhanced at protected areas designated for nature conservation is unknown. This is the first study to model outdoor recreation at a national scale, examining habitat preferences with statutory designation (Site of Special Scientific Interest) as an indicator of nature conservation importance. Models were based on a massive, three year national household survey providing spatially-referenced recreational visits to the natural environment. Site characteristics including land cover were compared between these observed visit sites (n = 31,502) and randomly chosen control sites (n = 63,000). Recreationists preferred areas of coast, freshwater, broadleaved woodland and higher densities of footpaths and avoided arable, coniferous woodland and lowland heath. Although conservation designation offers similar or greater public access than undesignated areas of the same habitat, statutory designation decreased the probability of visitation to coastal and freshwater sites and gave no effect for broadleaved woodland. Thus general recreational use by the public did not represent an important ecosystem service of protected high-nature-value areas, so that intrinsic and existence values remain as the primary justifications for conservation of high nature value areas. Management of ‘green infrastructure’ sites of lower conservation value that offer desirable habitats and enhanced provision of footpaths, could mitigate recreational impacts on nearby valuable conservation areas. PMID:27828990

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

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.

Conserved and divergent functions of Pax6 underlie species-specific neurogenic patterns in the developing amniote brain.

PubMed

Yamashita, Wataru; Takahashi, Masanori; Kikkawa, Takako; Gotoh, Hitoshi; Osumi, Noriko; Ono, Katsuhiko; Nomura, Tadashi

2018-04-16

The evolution of unique organ structures is associated with changes in conserved developmental programs. However, characterizing the functional conservation and variation of homologous transcription factors (TFs) that dictate species-specific cellular dynamics has remained elusive. Here, we dissect shared and divergent functions of Pax6 during amniote brain development. Comparative functional analyses revealed that the neurogenic function of Pax6 is highly conserved in the developing mouse and chick pallium, whereas stage-specific binary functions of Pax6 in neurogenesis are unique to mouse neuronal progenitors, consistent with Pax6-dependent temporal regulation of Notch signaling. Furthermore, we identified that Pax6-dependent enhancer activity of Dbx1 is extensively conserved between mammals and chick, although Dbx1 expression in the developing pallium is highly divergent in these species. Our results suggest that spatiotemporal changes in Pax6-dependent regulatory programs contributed to species-specific neurogenic patterns in mammalian and avian lineages, which underlie the morphological divergence of the amniote pallial architectures. © 2018. Published by The Company of Biologists Ltd.

Cross-species Extrapolation of EDC Toxicity: Consequences for Screening Programs

EPA Science Inventory

Many structural and functional aspects of the vertebrate hypothalamic-pituitary-gonadal (HPG) axis are known to be highly conserved, but the full significance of this from a toxicological perspective has received comparatively little attention. High-quality data generated through...

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.

Ain't no mountain high enough: plant invasions reaching new elevations

Treesearch

An& iacute Pauchard; bal; Christoph Kueffer; Hansj& ouml Dietz; rg; Curtis C. Daehler; Jake Alexander; Peter J. Edwards; Ar& eacute; Jos& eacute valo; Ram& oacute; n; Lohengrin A. Cavieres; Antoine Guisan; Sylvia Haider; Gabi Jakobs; Keith McDougall; Constance I. Millar; Bridgett J. Naylor; Catherine G. Parks; Lisa J. Rew; Tim Seipel

2009-01-01

Most studies of invasive species have been in highly modified, lowland environments, with comparatively little attention directed to less disturbed, high-elevation environments. However, increasing evidence indicates that plant invasions do occur in these environments, which often have high conservation value and provide important ecosystem services. Over a thousand...

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

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.

Comparative Sequence and X-Inactivation Analyses of a Domain of Escape in Human Xp11.2 and the Conserved Segment in Mouse

PubMed Central

Tsuchiya, Karen D.; Greally, John M.; Yi, Yajun; Noel, Kevin P.; Truong, Jean-Pierre; Disteche, Christine M.

2004-01-01

We have performed X-inactivation and sequence analyses on 350 kb of sequence from human Xp11.2, a region shown previously to contain a cluster of genes that escape X inactivation, and we compared this region with the region of conserved synteny in mouse. We identified several new transcripts from this region in human and in mouse, which defined the full extent of the domain escaping X inactivation in both species. In human, escape from X inactivation involves an uninterrupted 235-kb domain of multiple genes. Despite highly conserved gene content and order between the two species, Smcx is the only mouse gene from the conserved segment that escapes inactivation. As repetitive sequences are believed to facilitate spreading of X inactivation along the chromosome, we compared the repetitive sequence composition of this region between the two species. We found that long terminal repeats (LTRs) were decreased in the human domain of escape, but not in the majority of the conserved mouse region adjacent to Smcx in which genes were subject to X inactivation, suggesting that these repeats might be excluded from escape domains to prevent spreading of silencing. Our findings indicate that genomic context, as well as gene-specific regulatory elements, interact to determine expression of a gene from the inactive X-chromosome. PMID:15197169

Surgical Versus Conservative Intervention for Acute Achilles Tendon Rupture: A PRISMA-Compliant Systematic Review of Overlapping Meta-Analyses.

PubMed

Zhang, Hao; Tang, Hao; He, Qianyun; Wei, Qiang; Tong, Dake; Wang, Chuangfeng; Wu, Dajiang; Wang, Guangchao; Zhang, Xin; Ding, Wenbin; Li, Di; Ding, Chen; Liu, Kang; Ji, Fang

2015-11-01

Although many meta-analyses comparing surgical intervention with conservative treatment have been conducted for acute Achilles tendon rupture, discordant conclusions are shown. This study systematically reviewed the overlapping meta-analyses relating to surgical versus conservative intervention of acute Achilles tendon rupture to assist decision makers select among conflicting meta-analyses, and to offer intervention recommendations based on the currently best evidence.Multiple databases were comprehensively searched for meta-analyses comparing surgical with conservative treatment of acute Achilles tendon rupture. Meta-analyses only comprising randomized controlled trials (RCTs) were included. Two authors independently evaluated the meta-analysis quality and extracted data. The Jadad decision algorithm was applied to ascertain which meta-analysis offered the best evidence.A total of 9 meta-analyses were included. Only RCTs were determined as Level-II evidence. The scores of Assessment of Multiple Systematic Reviews (AMSTAR) ranged from 5 to 10 (median 7). A high-quality meta-analysis with more RCTs was selected according to the Jadad decision algorithm. This study found that when functional rehabilitation was used, conservative intervention was equal to surgical treatment regarding the incidence of rerupture, range of motion, calf circumference, and functional outcomes, while reducing the incidence of other complications. Where functional rehabilitation was not performed, conservative intervention could significantly increase rerupture rate.Conservative intervention may be preferred for acute Achilles tendon rupture at centers offering functional rehabilitation, because it shows a similar rerupture rate with a lower risk of other complications when compared with surgical treatment. However, surgical treatment should be considered at centers without functional rehabilitation as this can reduce the incidence of rerupture.

Comparative Study of Regulatory Circuits in Two Sea Urchin Species Reveals Tight Control of Timing and High Conservation of Expression Dynamics

PubMed Central

Gildor, Tsvia; Ben-Tabou de-Leon, Smadar

2015-01-01

Accurate temporal control of gene expression is essential for normal development and must be robust to natural genetic and environmental variation. Studying gene expression variation within and between related species can delineate the level of expression variability that development can tolerate. Here we exploit the comprehensive model of sea urchin gene regulatory networks and generate high-density expression profiles of key regulatory genes of the Mediterranean sea urchin, Paracentrotus lividus (Pl). The high resolution of our studies reveals highly reproducible gene initiation times that have lower variation than those of maximal mRNA levels between different individuals of the same species. This observation supports a threshold behavior of gene activation that is less sensitive to input concentrations. We then compare Mediterranean sea urchin gene expression profiles to those of its Pacific Ocean relative, Strongylocentrotus purpuratus (Sp). These species shared a common ancestor about 40 million years ago and show highly similar embryonic morphologies. Our comparative analyses of five regulatory circuits operating in different embryonic territories reveal a high conservation of the temporal order of gene activation but also some cases of divergence. A linear ratio of 1.3-fold between gene initiation times in Pl and Sp is partially explained by scaling of the developmental rates with temperature. Scaling the developmental rates according to the estimated Sp-Pl ratio and normalizing the expression levels reveals a striking conservation of relative dynamics of gene expression between the species. Overall, our findings demonstrate the ability of biological developmental systems to tightly control the timing of gene activation and relative dynamics and overcome expression noise induced by genetic variation and growth conditions. PMID:26230518

Exclusion of agricultural lands in spatial conservation prioritization strategies: consequences for biodiversity and ecosystem service representation

PubMed Central

Durán, América P.; Duffy, James P.; Gaston, Kevin J.

2014-01-01

Agroecosystems have traditionally been considered incompatible with biological conservation goals, and often been excluded from spatial conservation prioritization strategies. The consequences for the representativeness of identified priority areas have been little explored. Here, we evaluate these for biodiversity and carbon storage representation when agricultural land areas are excluded from a spatial prioritization strategy for South America. Comparing different prioritization approaches, we also assess how the spatial overlap of priority areas changes. The exclusion of agricultural lands was detrimental to biodiversity representation, indicating that priority areas for agricultural production overlap with areas of relatively high occurrence of species. By contrast, exclusion of agricultural lands benefits representation of carbon storage within priority areas, as lands of high value for agriculture and carbon storage overlap little. When agricultural lands were included and equally weighted with biodiversity and carbon storage, a balanced representation resulted. Our findings suggest that with appropriate management, South American agroecosystems can significantly contribute to biodiversity conservation. PMID:25143040

Evaluation of patients with hepatic portal venous gas who can be treated with conservative therapy.

PubMed

Higashi, Takaaki; Hayashi, Hiromitsu; Takeyama, Hideaki; Arima, Kota; Taki, Katsunobu; Takamori, Hiroshi; Baba, Hideo

2016-01-01

Hepatic portal venous gas is an indication for emergency surgery and reportedly has a high mortality rate. However, these days, cases of hepatic portal venous gas associated with milder disease are increasing. In this report, we compared two groups to investigate whether there were any objective indicators for selecting conservative therapy. From July 2007 to August 2011, 19 patients with hepatic portal venous gas were evaluated at our hospital. The condition was diagnosed by computed tomography imaging. Vital signs, laboratory test results, and physical examination findings were compared. The A group included 12 patients who could be treated with conservative therapy. The B group included 7 patients who could not be treated with conservative therapy. The combined mortality rate was 31.5% (6/19 patients). There was a significant difference in the pulse rate and shock index. In the A group, none of the patients had signs of peritoneal irritation. However, in the B group, physical examination revealed signs of peritoneal irritation in all patients. Conservative therapy may be possible in patients with hepatic portal venous gas, depending on the cause. Evaluation of vital signs and serial changes on physical examination are important.

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 < 0.01) compared to the control watershed. This study demonstrated that a strategy that first identifies watersheds likely to respond to conservation efforts and then focuses implementation on relatively high-contributing fields within those watersheds can be successful in reducing stream P concentrations and loads.

Invasive mammal eradication on islands results in substantial conservation gains

PubMed Central

Jones, Holly P.; Holmes, Nick D.; Butchart, Stuart H. M.; Tershy, Bernie R.; Kappes, Peter J.; Corkery, Ilse; Aguirre-Muñoz, Alfonso; Armstrong, Doug P.; Bonnaud, Elsa; Burbidge, Andrew A.; Campbell, Karl; Courchamp, Franck; Cowan, Philip E.; Cuthbert, Richard J.; Ebbert, Steve; Genovesi, Piero; Howald, Gregg R.; Keitt, Bradford S.; Kress, Stephen W.; Miskelly, Colin M.; Oppel, Steffen; Poncet, Sally; Rauzon, Mark J.; Rocamora, Gérard; Russell, James C.; Samaniego-Herrera, Araceli; Seddon, Philip J.; Spatz, Dena R.; Towns, David R.; Croll, Donald A.

2016-01-01

More than US$21 billion is spent annually on biodiversity conservation. Despite their importance for preventing or slowing extinctions and preserving biodiversity, conservation interventions are rarely assessed systematically for their global impact. Islands house a disproportionately higher amount of biodiversity compared with mainlands, much of which is highly threatened with extinction. Indeed, island species make up nearly two-thirds of recent extinctions. Islands therefore are critical targets of conservation. We used an extensive literature and database review paired with expert interviews to estimate the global benefits of an increasingly used conservation action to stem biodiversity loss: eradication of invasive mammals on islands. We found 236 native terrestrial insular faunal species (596 populations) that benefitted through positive demographic and/or distributional responses from 251 eradications of invasive mammals on 181 islands. Seven native species (eight populations) were negatively impacted by invasive mammal eradication. Four threatened species had their International Union for the Conservation of Nature (IUCN) Red List extinction-risk categories reduced as a direct result of invasive mammal eradication, and no species moved to a higher extinction-risk category. We predict that 107 highly threatened birds, mammals, and reptiles on the IUCN Red List—6% of all these highly threatened species—likely have benefitted from invasive mammal eradications on islands. Because monitoring of eradication outcomes is sporadic and limited, the impacts of global eradications are likely greater than we report here. Our results highlight the importance of invasive mammal eradication on islands for protecting the world's most imperiled fauna. PMID:27001852

Invasive mammal eradication on islands results in substantial conservation gains.

PubMed

Jones, Holly P; Holmes, Nick D; Butchart, Stuart H M; Tershy, Bernie R; Kappes, Peter J; Corkery, Ilse; Aguirre-Muñoz, Alfonso; Armstrong, Doug P; Bonnaud, Elsa; Burbidge, Andrew A; Campbell, Karl; Courchamp, Franck; Cowan, Philip E; Cuthbert, Richard J; Ebbert, Steve; Genovesi, Piero; Howald, Gregg R; Keitt, Bradford S; Kress, Stephen W; Miskelly, Colin M; Oppel, Steffen; Poncet, Sally; Rauzon, Mark J; Rocamora, Gérard; Russell, James C; Samaniego-Herrera, Araceli; Seddon, Philip J; Spatz, Dena R; Towns, David R; Croll, Donald A

2016-04-12

More than US$21 billion is spent annually on biodiversity conservation. Despite their importance for preventing or slowing extinctions and preserving biodiversity, conservation interventions are rarely assessed systematically for their global impact. Islands house a disproportionately higher amount of biodiversity compared with mainlands, much of which is highly threatened with extinction. Indeed, island species make up nearly two-thirds of recent extinctions. Islands therefore are critical targets of conservation. We used an extensive literature and database review paired with expert interviews to estimate the global benefits of an increasingly used conservation action to stem biodiversity loss: eradication of invasive mammals on islands. We found 236 native terrestrial insular faunal species (596 populations) that benefitted through positive demographic and/or distributional responses from 251 eradications of invasive mammals on 181 islands. Seven native species (eight populations) were negatively impacted by invasive mammal eradication. Four threatened species had their International Union for the Conservation of Nature (IUCN) Red List extinction-risk categories reduced as a direct result of invasive mammal eradication, and no species moved to a higher extinction-risk category. We predict that 107 highly threatened birds, mammals, and reptiles on the IUCN Red List-6% of all these highly threatened species-likely have benefitted from invasive mammal eradications on islands. Because monitoring of eradication outcomes is sporadic and limited, the impacts of global eradications are likely greater than we report here. Our results highlight the importance of invasive mammal eradication on islands for protecting the world's most imperiled fauna.

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.

Linking Livelihoods and Conservation: An Examination of Local Residents' Perceived Linkages Between Conservation and Livelihood Benefits Around Nepal's Chitwan National Park

NASA Astrophysics Data System (ADS)

Nepal, Sanjay; Spiteri, Arian

2011-05-01

This paper investigates local recognition of the link between incentive-based program (IBP) benefits and conservation, and how perceptions of benefits and linkage influence attitudes in communities surrounding Chitwan National Park, Nepal. A survey of 189 households conducted between October and December 2004 examined local residents' perceived benefits, their attitudes toward park management, and perception of linkages between conservation and livelihoods. Linkage perceptions were measured by a scale compared with a respondent's recognition of benefits to determine whether IBPs establish a connection between benefits and livelihoods. An attitude scale was also created to compare attitudes toward park management with perceptions of benefits and linkage to determine if IBPs led to positive attitudes, and if the recognition of a direct tie between livelihoods and natural resources made attitudes more favorable. Research results indicate that as acknowledgement of benefit increases, so does the perception of linkage between the resource and livelihoods. Similarly, when perceived benefit increases, so too does attitude towards management. Positive attitude towards park management is influenced more by perception of livelihood dependence on resources than on benefits received from the park. However, overwhelming positive support voiced for conservation did not coincide with conduct. In spite of the positive attitudes and high perception of linkage, people did not necessarily behave in a way compatible with conservation. This suggests that while benefits alone can lead to positive attitudes, without clear linkages to conservation, the IBP may lose persuasion when alternative options—conflicting with conservation objectives—arise promising to provide greater economic benefit.

In-silico and in-vivo analyses of EST databases unveil conserved miRNAs from Carthamus tinctorius and Cynara cardunculus

PubMed Central

2012-01-01

Background MicroRNAs (miRNAs) are small RNAs (21-24 bp) providing an RNA-based system of gene regulation highly conserved in plants and animals. In plants, miRNAs control mRNA degradation or restrain translation, affecting development and responses to stresses. Plant miRNAs show imperfect but extensive complementarity to mRNA targets, making their computational prediction possible, useful when data mining is applied on different species. In this study we used a comparative approach to identify both miRNAs and their targets, in artichoke and safflower. Results Two complete expressed sequence tags (ESTs) datasets from artichoke (3.6·104 entries) and safflower (4.2·104), were analysed with a bioinformatic pipeline and in vitro experiments, identifying 17 potential miRNAs. For each EST, using RNAhybrid program and 953 non redundant miRNA mature sequences, available in mirBase as reference, we searched matching putative targets. 8730 out of 42011 ESTs from safflower and 7145 of 36323 ESTs from artichoke showed at least one predicted miRNA target. BLAST analysis showed that 75% of all ESTs shared at least a common homologous region (E-value < 10-4) and about 50% of these displayed 400 bp or longer aligned sequences as conserved homologous/orthologous (COS) regions. 960 and 890 ESTs of safflower and artichoke organized in COS shared 79 different miRNA targets, considered functionally conserved, and statistically significant when compared with random sequences (signal to noise ratio > 2 and specificity ≥ 0.85). Four highly significant miRNAs selected from in silico data were experimentally validated in globe artichoke leaves. Conclusions Mature miRNAs and targets were predicted within EST sequences of safflower and artichoke. Most of the miRNA targets appeared highly/moderately conserved, highlighting an important and conserved function. In this study we introduce a stringent parameter for the comparative sequence analysis, represented by the identification of the same target in the COS region. After statistical analysis 79 targets, found on the COS regions and belonging to 60 miRNA families, have a signal to noise ratio > 2, with ≥ 0.85 specificity. The putative miRNAs identified belong to 55 dicotyledon plants and to 24 families only in monocotyledon. PMID:22536958

CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison

PubMed Central

Castrignanò, Tiziana; Canali, Alessandro; Grillo, Giorgio; Liuni, Sabino; Mignone, Flavio; Pesole, Graziano

2004-01-01

The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences. Indeed, such sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome sequences, is able to identify statistically significant conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features. PMID:15215464

Comparative interrogation of the developing xylem transcriptomes of two wood-forming species: Populus trichocarpa and Eucalyptus grandis.

PubMed

Hefer, Charles A; Mizrachi, Eshchar; Myburg, Alexander A; Douglas, Carl J; Mansfield, Shawn D

2015-06-01

Wood formation is a complex developmental process governed by genetic and environmental stimuli. Populus and Eucalyptus are fast-growing, high-yielding tree genera that represent ecologically and economically important species suitable for generating significant lignocellulosic biomass. Comparative analysis of the developing xylem and leaf transcriptomes of Populus trichocarpa and Eucalyptus grandis together with phylogenetic analyses identified clusters of homologous genes preferentially expressed during xylem formation in both species. A conserved set of 336 single gene pairs showed highly similar xylem preferential expression patterns, as well as evidence of high functional constraint. Individual members of multi-gene orthologous clusters known to be involved in secondary cell wall biosynthesis also showed conserved xylem expression profiles. However, species-specific expression as well as opposite (xylem versus leaf) expression patterns observed for a subset of genes suggest subtle differences in the transcriptional regulation important for xylem development in each species. Using sequence similarity and gene expression status, we identified functional homologs likely to be involved in xylem developmental and biosynthetic processes in Populus and Eucalyptus. Our study suggests that, while genes involved in secondary cell wall biosynthesis show high levels of gene expression conservation, differential regulation of some xylem development genes may give rise to unique xylem properties. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

A Portable Dynamic Laser Speckle System for Sensing Long-Term Changes Caused by Treatments in Painting Conservation.

PubMed

Pérez, Alberto J; González-Peña, Rolando J; Braga, Roberto; Perles, Ángel; Pérez-Marín, Eva; García-Diego, Fernando J

2018-01-11

Dynamic laser speckle (DLS) is used as a reliable sensor of activity for all types of materials. Traditional applications are based on high-rate captures (usually greater than 10 frames-per-second, fps). Even for drying processes in conservation treatments, where there is a high level of activity in the first moments after the application and slower activity after some minutes or hours, the process is based on the acquisition of images at a time rate that is the same in moments of high and low activity. In this work, we present an alternative approach to track the drying process of protective layers and other painting conservation processes that take a long time to reduce their levels of activity. We illuminate, using three different wavelength lasers, a temporary protector (cyclododecane) and a varnish, and monitor them using a low fps rate during long-term drying. The results are compared to the traditional method. This work also presents a monitoring method that uses portable equipment. The results present the feasibility of using the portable device and show the improved sensitivity of the dynamic laser speckle when sensing the long-term process for drying cyclododecane and varnish in conservation.

G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences.

PubMed

Lenis, Vasileios Panagiotis E; Swain, Martin; Larkin, Denis M

2018-05-01

Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses, ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high-performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available from multiple projects, there is an increasing demand for genome comparative analyses. Here, we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species' reference genome. G-Anchor makes novel use of a databank of highly conserved DNA sequence elements. We demonstrate how these elements may be aligned to a pair of genomes, creating anchors. These anchors enable the rapid mapping of scaffolds from a de novo assembled genome to chromosome assemblies of a reference species. Our results demonstrate that G-Anchor can successfully anchor a vertebrate genome onto a phylogenetically related reference species genome using a desktop or laptop computer within a few hours and with comparable accuracy to that achieved by a highly accurate whole-genome alignment tool such as LASTZ. G-Anchor thus makes whole-genome comparisons accessible to researchers with limited computational resources. G-Anchor is a ready-to-use tool for anchoring a pair of vertebrate genomes. It may be used with large genomes that contain a significant fraction of evolutionally conserved DNA sequences and that are not highly repetitive, polypoid, or excessively fragmented. G-Anchor is not a substitute for whole-genome aligning software but can be used for fast and accurate initial genome comparisons. G-Anchor is freely available and a ready-to-use tool for the pairwise comparison of two genomes.

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.

Comparative Microbial Modules Resource: Generation and Visualization of Multi-species Biclusters

PubMed Central

Bate, Ashley; Eichenberger, Patrick; Bonneau, Richard

2011-01-01

The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures – results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation. PMID:22144874

Comparative microbial modules resource: generation and visualization of multi-species biclusters.

PubMed

Kacmarczyk, Thadeous; Waltman, Peter; Bate, Ashley; Eichenberger, Patrick; Bonneau, Richard

2011-12-01

The increasing abundance of large-scale, high-throughput datasets for many closely related organisms provides opportunities for comparative analysis via the simultaneous biclustering of datasets from multiple species. These analyses require a reformulation of how to organize multi-species datasets and visualize comparative genomics data analyses results. Recently, we developed a method, multi-species cMonkey, which integrates heterogeneous high-throughput datatypes from multiple species to identify conserved regulatory modules. Here we present an integrated data visualization system, built upon the Gaggle, enabling exploration of our method's results (available at http://meatwad.bio.nyu.edu/cmmr.html). The system can also be used to explore other comparative genomics datasets and outputs from other data analysis procedures - results from other multiple-species clustering programs or from independent clustering of different single-species datasets. We provide an example use of our system for two bacteria, Escherichia coli and Salmonella Typhimurium. We illustrate the use of our system by exploring conserved biclusters involved in nitrogen metabolism, uncovering a putative function for yjjI, a currently uncharacterized gene that we predict to be involved in nitrogen assimilation. © 2011 Kacmarczyk et al.

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.

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 related projects. PMID:26815653

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.

Examining current or future trade-offs for biodiversity conservation in north-eastern Australia.

PubMed

Reside, April E; VanDerWal, Jeremy; Moilanen, Atte; Graham, Erin M

2017-01-01

With the high rate of ecosystem change already occurring and predicted to occur in the coming decades, long-term conservation has to account not only for current biodiversity but also for the biodiversity patterns anticipated for the future. The trade-offs between prioritising future biodiversity at the expense of current priorities must be understood to guide current conservation planning, but have been largely unexplored. To fill this gap, we compared the performance of four conservation planning solutions involving 662 vertebrate species in the Wet Tropics Natural Resource Management Cluster Region in north-eastern Australia. Input species data for the four planning solutions were: 1) current distributions; 2) projected distributions for 2055; 3) projected distributions for 2085; and 4) current, 2055 and 2085 projected distributions, and the connectivity between each of the three time periods for each species. The four planning solutions were remarkably similar (up to 85% overlap), suggesting that modelling for either current or future scenarios is sufficient for conversation planning for this region, with little obvious trade-off. Our analyses also revealed that overall, species with small ranges occurring across steep elevation gradients and at higher elevations were more likely to be better represented in all solutions. Given that species with these characteristics are of high conservation significance, our results provide confidence that conservation planning focused on either current, near- or distant-future biodiversity will account for these species.

Examining current or future trade-offs for biodiversity conservation in north-eastern Australia

PubMed Central

VanDerWal, Jeremy; Moilanen, Atte; Graham, Erin M.

2017-01-01

With the high rate of ecosystem change already occurring and predicted to occur in the coming decades, long-term conservation has to account not only for current biodiversity but also for the biodiversity patterns anticipated for the future. The trade-offs between prioritising future biodiversity at the expense of current priorities must be understood to guide current conservation planning, but have been largely unexplored. To fill this gap, we compared the performance of four conservation planning solutions involving 662 vertebrate species in the Wet Tropics Natural Resource Management Cluster Region in north-eastern Australia. Input species data for the four planning solutions were: 1) current distributions; 2) projected distributions for 2055; 3) projected distributions for 2085; and 4) current, 2055 and 2085 projected distributions, and the connectivity between each of the three time periods for each species. The four planning solutions were remarkably similar (up to 85% overlap), suggesting that modelling for either current or future scenarios is sufficient for conversation planning for this region, with little obvious trade-off. Our analyses also revealed that overall, species with small ranges occurring across steep elevation gradients and at higher elevations were more likely to be better represented in all solutions. Given that species with these characteristics are of high conservation significance, our results provide confidence that conservation planning focused on either current, near- or distant-future biodiversity will account for these species. PMID:28222199

Clinical outcome in acute small bowel obstruction after surgical or conservative management.

PubMed

Meier, Raphael P H; de Saussure, Wassila Oulhaci; Orci, Lorenzo A; Gutzwiller, Eveline M; Morel, Philippe; Ris, Frédéric; Schwenter, Frank

2014-12-01

Small bowel obstruction (SBO) is characterized by a high rate of recurrence. In the present study, we aimed to compare the outcomes of patients managed either by conservative treatment or surgical operation for an episode of SBO. The outcomes of all patients hospitalized at a single center for acute SBO between 2004 and 2007 were assessed. The occurrence of recurrent hospitalization, surgery, SBO symptoms at home, and mortality was determined. Among 221 patients admitted with SBO, 136 underwent a surgical procedure (surgical group) and 85 were managed conservatively (conservative group). Baseline characteristics were similar between treatment groups. The median follow-up time (interquartile range) was 4.7 (3.7-5.8) years. Nineteen patients (14.0 %) of the surgical group were hospitalized for recurrent SBO versus 25 (29.4 %) of the conservative group [hazard ratio (HR), 0.5; 95 % CI, 0.3-0.9]. The need for a surgical management of a new SBO episode was similar between the two groups, ten patients (7.4 %) in the surgical group and six patients (7.1 %) in the conservative group (HR, 1.1; 95 % CI, 0.4-3.1). Five-year mortality from the date of hospital discharge was not significantly different between the two groups (age- and sex-adjusted HR, 1.1; 95 % CI, 0.6-2.1). A follow-up evaluation was obtained for 130 patients. Among them, 24 patients (34.8 %) of the surgical group and 35 patients (57.4 %) of the conservative group had recurrent SBO symptoms (odds ratio, 0.4; 95 % CI, 0.2-0.8). The recurrence of SBO symptoms and new hospitalizations were significantly lower after surgical management of SBO compared with conservative treatment.

Exclusion of agricultural lands in spatial conservation prioritization strategies: consequences for biodiversity and ecosystem service representation.

PubMed

Durán, América P; Duffy, James P; Gaston, Kevin J

2014-10-07

Agroecosystems have traditionally been considered incompatible with biological conservation goals, and often been excluded from spatial conservation prioritization strategies. The consequences for the representativeness of identified priority areas have been little explored. Here, we evaluate these for biodiversity and carbon storage representation when agricultural land areas are excluded from a spatial prioritization strategy for South America. Comparing different prioritization approaches, we also assess how the spatial overlap of priority areas changes. The exclusion of agricultural lands was detrimental to biodiversity representation, indicating that priority areas for agricultural production overlap with areas of relatively high occurrence of species. By contrast, exclusion of agricultural lands benefits representation of carbon storage within priority areas, as lands of high value for agriculture and carbon storage overlap little. When agricultural lands were included and equally weighted with biodiversity and carbon storage, a balanced representation resulted. Our findings suggest that with appropriate management, South American agroecosystems can significantly contribute to biodiversity conservation. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.

PubMed

Eastman, Alexander W; Heinrichs, David E; Yuan, Ze-Chun

2014-10-03

Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported. Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp. Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine. Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.

On the Evolution of the Cardiac Pacemaker

PubMed Central

Burkhard, Silja; van Eif, Vincent; Garric, Laurence; Christoffels, Vincent M.; Bakkers, Jeroen

2017-01-01

The rhythmic contraction of the heart is initiated and controlled by an intrinsic pacemaker system. Cardiac contractions commence at very early embryonic stages and coordination remains crucial for survival. The underlying molecular mechanisms of pacemaker cell development and function are still not fully understood. Heart form and function show high evolutionary conservation. Even in simple contractile cardiac tubes in primitive invertebrates, cardiac function is controlled by intrinsic, autonomous pacemaker cells. Understanding the evolutionary origin and development of cardiac pacemaker cells will help us outline the important pathways and factors involved. Key patterning factors, such as the homeodomain transcription factors Nkx2.5 and Shox2, and the LIM-homeodomain transcription factor Islet-1, components of the T-box (Tbx), and bone morphogenic protein (Bmp) families are well conserved. Here we compare the dominant pacemaking systems in various organisms with respect to the underlying molecular regulation. Comparative analysis of the pathways involved in patterning the pacemaker domain in an evolutionary context might help us outline a common fundamental pacemaker cell gene programme. Special focus is given to pacemaker development in zebrafish, an extensively used model for vertebrate development. Finally, we conclude with a summary of highly conserved key factors in pacemaker cell development and function. PMID:29367536

Ferritin gene organization: differences between plants and animals suggest possible kingdom-specific selective constraints.

PubMed

Proudhon, D; Wei, J; Briat, J; Theil, E C

1996-03-01

Ferritin, a protein widespread in nature, concentrates iron approximately 10(11)-10(12)-fold above the solubility within a spherical shell of 24 subunits; it derives in plants and animals from a common ancestor (based on sequence) but displays a cytoplasmic location in animals compared to the plastid in contemporary plants. Ferritin gene regulation in plants and animals is altered by development, hormones, and excess iron; iron signals target DNA in plants but mRNA in animals. Evolution has thus conserved the two end points of ferritin gene expression, the physiological signals and the protein structure, while allowing some divergence of the genetic mechanisms. Comparison of ferritin gene organization in plants and animals, made possible by the cloning of a dicot (soybean) ferritin gene presented here and the recent cloning of two monocot (maize) ferritin genes, shows evolutionary divergence in ferritin gene organization between plants and animals but conservation among plants or among animals; divergence in the genetic mechanism for iron regulation is reflected by the absence in all three plant genes of the IRE, a highly conserved, noncoding sequence in vertebrate animal ferritin mRNA. In plant ferritin genes, the number of introns (n = 7) is higher than in animals (n = 3). Second, no intron positions are conserved when ferritin genes of plants and animals are compared, although all ferritin gene introns are in the coding region; within kingdoms, the intron positions in ferritin genes are conserved. Finally, secondary protein structure has no apparent relationship to intron/exon boundaries in plant ferritin genes, whereas in animal ferritin genes the correspondence is high. The structural differences in introns/exons among phylogenetically related ferritin coding sequences and the high conservation of the gene structure within plant or animal kingdoms of the gene structure within plant or animal kingdoms suggest that kingdom-specific functional constraints may exist to maintain a particular intron/exon pattern within ferritin genes. In the case of plants, where ferritin gene intron placement is unrelated to triplet codons or protein structure, and where ferritin is targeted to the plastid, the selection pressure on gene organization may relate to RNA function and plastid/nuclear signaling.

Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication*

PubMed Central

Kito, Keiji; Ito, Haruka; Nohara, Takehiro; Ohnishi, Mihoko; Ishibashi, Yuko; Takeda, Daisuke

2016-01-01

Omics analysis is a versatile approach for understanding the conservation and diversity of molecular systems across multiple taxa. In this study, we compared the proteome expression profiles of four yeast species (Saccharomyces cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) grown on glucose- or glycerol-containing media. Conserved expression changes across all species were observed only for a small proportion of all proteins differentially expressed between the two growth conditions. Two Kluyveromyces species, both of which exhibited a high growth rate on glycerol, a nonfermentative carbon source, showed distinct species-specific expression profiles. In K. waltii grown on glycerol, proteins involved in the glyoxylate cycle and gluconeogenesis were expressed in high abundance. In K. lactis grown on glycerol, the expression of glycolytic and ethanol metabolic enzymes was unexpectedly low, whereas proteins involved in cytoplasmic translation, including ribosomal proteins and elongation factors, were highly expressed. These marked differences in the types of predominantly expressed proteins suggest that K. lactis optimizes the balance of proteome resource allocation between metabolism and protein synthesis giving priority to cellular growth. In S. cerevisiae, about 450 duplicate gene pairs were retained after whole-genome duplication. Intriguingly, we found that in the case of duplicates with conserved sequences, the total abundance of proteins encoded by a duplicate pair in S. cerevisiae was similar to that of protein encoded by nonduplicated ortholog in Kluyveromyces yeast. Given the frequency of haploinsufficiency, this observation suggests that conserved duplicate genes, even though minor cases of retained duplicates, do not exhibit a dosage effect in yeast, except for ribosomal proteins. Thus, comparative proteomic analyses across multiple species may reveal not only species-specific characteristics of metabolic processes under nonoptimal culture conditions but also provide valuable insights into intriguing biological principles, including the balance of proteome resource allocation and the role of gene duplication in evolutionary history. PMID:26560065

Yeast Interspecies Comparative Proteomics Reveals Divergence in Expression Profiles and Provides Insights into Proteome Resource Allocation and Evolutionary Roles of Gene Duplication.

PubMed

Kito, Keiji; Ito, Haruka; Nohara, Takehiro; Ohnishi, Mihoko; Ishibashi, Yuko; Takeda, Daisuke

2016-01-01

Omics analysis is a versatile approach for understanding the conservation and diversity of molecular systems across multiple taxa. In this study, we compared the proteome expression profiles of four yeast species (Saccharomyces cerevisiae, Saccharomyces mikatae, Kluyveromyces waltii, and Kluyveromyces lactis) grown on glucose- or glycerol-containing media. Conserved expression changes across all species were observed only for a small proportion of all proteins differentially expressed between the two growth conditions. Two Kluyveromyces species, both of which exhibited a high growth rate on glycerol, a nonfermentative carbon source, showed distinct species-specific expression profiles. In K. waltii grown on glycerol, proteins involved in the glyoxylate cycle and gluconeogenesis were expressed in high abundance. In K. lactis grown on glycerol, the expression of glycolytic and ethanol metabolic enzymes was unexpectedly low, whereas proteins involved in cytoplasmic translation, including ribosomal proteins and elongation factors, were highly expressed. These marked differences in the types of predominantly expressed proteins suggest that K. lactis optimizes the balance of proteome resource allocation between metabolism and protein synthesis giving priority to cellular growth. In S. cerevisiae, about 450 duplicate gene pairs were retained after whole-genome duplication. Intriguingly, we found that in the case of duplicates with conserved sequences, the total abundance of proteins encoded by a duplicate pair in S. cerevisiae was similar to that of protein encoded by nonduplicated ortholog in Kluyveromyces yeast. Given the frequency of haploinsufficiency, this observation suggests that conserved duplicate genes, even though minor cases of retained duplicates, do not exhibit a dosage effect in yeast, except for ribosomal proteins. Thus, comparative proteomic analyses across multiple species may reveal not only species-specific characteristics of metabolic processes under nonoptimal culture conditions but also provide valuable insights into intriguing biological principles, including the balance of proteome resource allocation and the role of gene duplication in evolutionary history. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Soil, water and nutrient conservation in mountain farming systems: case-study from the Sikkim Himalaya.

PubMed

Sharma, E; Rai, S C; Sharma, R

2001-02-01

The Khanikhola watershed in Sikkim is agrarian with about 50% area under rain-fed agriculture representing the conditions of the middle mountains all over the Himalaya. The study was conducted to assess overland flow, soil loss and subsequent nutrient losses from different land uses in the watershed, and identify biotechnological inputs for management of mountain farming systems. Overland flow, soil and nutrient losses were very high from open agricultural (cropped) fields compared to other land uses, and more than 72% of nutrient losses were attributable to agriculture land use. Forests and large cardamom agroforestry conserved more soil compared to other land uses. Interventions, like cultivation of broom grass upon terrace risers, N2-fixing Albizia trees for maintenance of soil fertility and plantation of horticulture trees, have reduced the soil loss (by 22%). Soil and water conservation values (> 80%) of both large cardamom and broom grass were higher compared to other crops. Use of N2-fixing Albizia tree in large cardamom agroforestry and croplands contributed to soil fertility, and increased productivity and yield. Bio-composting of farm resources ensured increase in nutrient availability specially phosphorus in cropped areas. Agricultural practices in mountain areas should be strengthened with more agroforestry components, and cash crops like large cardamom and broom grass in agroforestry provide high economic return and are hydroecologically sustainable.

Cost-effectiveness of duloxetine: the Stress Urinary Incontinence Treatment (SUIT) study.

PubMed

Mihaylova, Borislava; Pitman, Richard; Tincello, Douglas; van der Vaart, Huub; Tunn, Ralf; Timlin, Louise; Quail, Deborah; Johns, Adam; Sculpher, Mark

2010-08-01

To assess the cost-effectiveness of duloxetine compared with conservative therapy in women with stress urinary incontinence (SUI). Cost and outcome data were taken from the Stress Urinary Incontinence Treatment (SUIT) study, a 12-month, prospective, observational, naturalistic, multicenter, multicountry study. Costs were assessed in UK pound and outcomes in quality adjusted life years using responses to the EuroQol (EQ-5D); numbers of urine leaks were also estimated. Potential selection bias was countered using multivariate regression and propensity score analysis. Duloxetine alone, duloxetine in combination with conservative treatment, and conservative treatment alone were associated with roughly two fewer leaks per week compared with no treatment. Duloxetine alone and with conservative treatment for SUI were associated with incremental quality-adjusted life-years (QALYs) of about 0.03 over a year compared with no treatment or with conservative treatment alone. Conservative treatment alone did not show an effect on QALYs. None of the interventions appeared to have marked impacts on costs over a year. Depending on the form of matching, duloxetine either dominated or had an incremental cost-effectiveness ratio (ICER) below pound900 per QALY gained compared with no treatment and with conservative treatment alone. Duloxetine plus conservative therapy had an ICER below pound5500 compared with no treatment or conservative treatment alone. Duloxetine compared with duloxetine plus conservative therapy showed similar outcomes but an additional cost for the combined intervention. Although the limitations of the use of SUIT's observational data for this purpose need to be acknowledged, the study suggests that initiating duloxetine therapy in SUI is a cost-effective treatment alternative.

[Case control study of fractures-dislocations of ankle joint with conservative and operative treatment].

PubMed

Zhang, Song-Tu; Lin, Yi-Rong; Chen, Lian-Yuan

2010-10-01

To compare the clinical efficacy of grade III, IV supination-eversion fractures-dislocations of ankle joint between manipulative treatment and operative treatment. From September 2007 to December 2008, the clinical data of 60 patients with grade III, IV supination-eversion fractures-dislocations of ankle joint were retrospectively analyzed. There were 32 males and 28 females, ranging in age from 18 to 70 years with an average age of 38.17 years. All patients were respectively treated with manipulative treatment (conservative group, 30 cases) and operative treatment (operative group, 30 cases). The joint function was compared with Mazur standard; the reduction and shifting of fractures were observed with X-ray; the hospitalization day and the therapeutic cost were compared between two groups. All patients were followed up with an average of 15.27 months (ranged, 6 to 25 months). In conservative group, 16 cases got excellent result in joint function, 10 good, 3 fair, 1 poor; in operative group, 20 cases got excellent result, 8 good, 2 fair, 0 poor. In conservative group in the X-ray showed 25 cases obtained excellent and good reduction, 4 fair, 1 poor; and in operative group in the X-ray showed 28 cases obtained excellent and good reduction, 2 fair, 0 poor. There was no significant difference at the joint function and X-ray film after treatment between two groups (P > 0.05). The hospital day was respectively (7.87 +/- 3.34), (17.37 +/- 4.64) d in conservative group and operative group; and the therapeutic cost was respectively (2 506.67 +/- 649.10), (11 473.33 +/- 1 564.90) yuan. There was significant difference at hospital day and therapeutic cost between two groups (P < 0.05). Conservative treatment and operative treatment can both reach a very good result in treating grade III, IV supination-eversion fractures and dislocations of ankle joint. However, conservative treatment has advantage of high safety factor, low therapeutic cost, can reduce medical costs for patients.

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.

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 model, we are able to identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA. PMID:24564200

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 identify conserved regions fast or even interactively using a standard PC. Our method has many potential applications such as finding characteristic signature sequences for families of organisms and studying conserved and variable regions in, for example, 16S rRNA.

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.

Ecosystem Services and Opportunity Costs Shift Spatial Priorities for Conserving Forest Biodiversity

PubMed Central

Schröter, Matthias; Rusch, Graciela M.; Barton, David N.; Blumentrath, Stefan; Nordén, Björn

2014-01-01

Inclusion of spatially explicit information on ecosystem services in conservation planning is a fairly new practice. This study analyses how the incorporation of ecosystem services as conservation features can affect conservation of forest biodiversity and how different opportunity cost constraints can change spatial priorities for conservation. We created spatially explicit cost-effective conservation scenarios for 59 forest biodiversity features and five ecosystem services in the county of Telemark (Norway) with the help of the heuristic optimisation planning software, Marxan with Zones. We combined a mix of conservation instruments where forestry is either completely (non-use zone) or partially restricted (partial use zone). Opportunity costs were measured in terms of foregone timber harvest, an important provisioning service in Telemark. Including a number of ecosystem services shifted priority conservation sites compared to a case where only biodiversity was considered, and increased the area of both the partial (+36.2%) and the non-use zone (+3.2%). Furthermore, opportunity costs increased (+6.6%), which suggests that ecosystem services may not be a side-benefit of biodiversity conservation in this area. Opportunity cost levels were systematically changed to analyse their effect on spatial conservation priorities. Conservation of biodiversity and ecosystem services trades off against timber harvest. Currently designated nature reserves and landscape protection areas achieve a very low proportion (9.1%) of the conservation targets we set in our scenario, which illustrates the high importance given to timber production at present. A trade-off curve indicated that large marginal increases in conservation target achievement are possible when the budget for conservation is increased. Forty percent of the maximum hypothetical opportunity costs would yield an average conservation target achievement of 79%. PMID:25393951

Ecosystem services and opportunity costs shift spatial priorities for conserving forest biodiversity.

PubMed

Schröter, Matthias; Rusch, Graciela M; Barton, David N; Blumentrath, Stefan; Nordén, Björn

2014-01-01

Inclusion of spatially explicit information on ecosystem services in conservation planning is a fairly new practice. This study analyses how the incorporation of ecosystem services as conservation features can affect conservation of forest biodiversity and how different opportunity cost constraints can change spatial priorities for conservation. We created spatially explicit cost-effective conservation scenarios for 59 forest biodiversity features and five ecosystem services in the county of Telemark (Norway) with the help of the heuristic optimisation planning software, Marxan with Zones. We combined a mix of conservation instruments where forestry is either completely (non-use zone) or partially restricted (partial use zone). Opportunity costs were measured in terms of foregone timber harvest, an important provisioning service in Telemark. Including a number of ecosystem services shifted priority conservation sites compared to a case where only biodiversity was considered, and increased the area of both the partial (+36.2%) and the non-use zone (+3.2%). Furthermore, opportunity costs increased (+6.6%), which suggests that ecosystem services may not be a side-benefit of biodiversity conservation in this area. Opportunity cost levels were systematically changed to analyse their effect on spatial conservation priorities. Conservation of biodiversity and ecosystem services trades off against timber harvest. Currently designated nature reserves and landscape protection areas achieve a very low proportion (9.1%) of the conservation targets we set in our scenario, which illustrates the high importance given to timber production at present. A trade-off curve indicated that large marginal increases in conservation target achievement are possible when the budget for conservation is increased. Forty percent of the maximum hypothetical opportunity costs would yield an average conservation target achievement of 79%.

ε-Aminocaproic acid and clinical value in cardiac anesthesia.

PubMed

Raghunathan, Karthik; Connelly, Neil Roy; Kanter, Gary J

2011-02-01

The primary aim was to compare the "clinical value" of tranexamic acid (TXA) with ε-aminocaproic acid (EACA) when used for blood conservation during high-risk cardiac surgery. Data previously reported by the Blood Conservation Using Antifibrinolytics in a Randomized Trial (BART) study investigators were reanalyzed independently after appropriate statistical adjustment. The authors compared TXA with EACA for important primary and secondary outcomes and applied the "clinical value" equation to this comparison. BART, the largest blinded multicenter study on this topic to date, compared all 3 commonly used antifibrinolytics head-to-head in a randomized dose-equivalent fashion during high-risk cardiac surgery. Comparisons of TXA with EACA with application of the clinical value equation was not performed specifically by the BART investigators. One thousand five hundred fifty patients enrolled in 2 of the 3 arms of the BART study were included in the analysis (TXA, n= 770 and EACA, n = 780, with data reported by the investigators in the New England Journal of Medicine). The major finding was that there were no significant differences in overall safety and clinically important efficacy between TXA and EACA. Considering the substantial difference in costs and with the increasing volume of high-risk cardiac surgery, EACA has increased "clinical value" when compared with TXA. EACA should be the antifibrinolytic medication of choice for high-risk cardiac surgery. Copyright © 2011 Elsevier Inc. All rights reserved.

Assessing shortfalls and complementary conservation areas for national plant biodiversity in South Korea.

PubMed

Choe, Hyeyeong; Thorne, James H; Huber, Patrick R; Lee, Dongkun; Quinn, James F

2018-01-01

Protected areas (PAs) are often considered the most important biodiversity conservation areas in national plans, but PAs often do not represent national-scale biodiversity. We evaluate the current conservation status of plant biodiversity within current existing PAs, and identify potential additional PAs for South Korea. We modeled species ranges for 2,297 plant species using Multivariate Adaptive Regression Splines and compared the level of mean range representation in South Korea's existing PAs, which comprise 5.7% of the country's mainland area, with an equal-area alternative PA strategy selected with the reserve algorithm Marxan. We also used Marxan to model two additional conservation scenarios that add lands to approach the Aichi Biodiversity Target objectives (17% of the country). Existing PAs in South Korea contain an average of 6.3% of each plant species' range, compared to 5.9% in the modeled equal-area alternative. However, existing PAs primarily represent a high percentage of the ranges for high-elevation and small range size species. The additional PAs scenario that adds lands to the existing PAs covers 14,587.55 km2, and would improve overall plant range representation to a mean of 16.8% of every species' range. The other additional PAs scenario, which selects new PAs from all lands and covers 13,197.35 km2, would improve overall plant range representation to a mean of 13.5%. Even though the additional PAs that includes existing PAs represents higher percentages of species' ranges, it is missing many biodiversity hotspots in non-mountainous areas and the additional PAs without locking in the existing PAs represent almost all species' ranges evenly, including low-elevation ones with larger ranges. Some priority conservation areas we identified are expansions of, or near, existing PAs, especially in northeastern and southern South Korea. However, lowland coastal areas and areas surrounding the capital city, Seoul, are also critical for biodiversity conservation in South Korea.

Assessing shortfalls and complementary conservation areas for national plant biodiversity in South Korea

PubMed Central

Thorne, James H.; Huber, Patrick R.; Lee, Dongkun; Quinn, James F.

2018-01-01

Protected areas (PAs) are often considered the most important biodiversity conservation areas in national plans, but PAs often do not represent national-scale biodiversity. We evaluate the current conservation status of plant biodiversity within current existing PAs, and identify potential additional PAs for South Korea. We modeled species ranges for 2,297 plant species using Multivariate Adaptive Regression Splines and compared the level of mean range representation in South Korea’s existing PAs, which comprise 5.7% of the country’s mainland area, with an equal-area alternative PA strategy selected with the reserve algorithm Marxan. We also used Marxan to model two additional conservation scenarios that add lands to approach the Aichi Biodiversity Target objectives (17% of the country). Existing PAs in South Korea contain an average of 6.3% of each plant species’ range, compared to 5.9% in the modeled equal-area alternative. However, existing PAs primarily represent a high percentage of the ranges for high-elevation and small range size species. The additional PAs scenario that adds lands to the existing PAs covers 14,587.55 km2, and would improve overall plant range representation to a mean of 16.8% of every species’ range. The other additional PAs scenario, which selects new PAs from all lands and covers 13,197.35 km2, would improve overall plant range representation to a mean of 13.5%. Even though the additional PAs that includes existing PAs represents higher percentages of species’ ranges, it is missing many biodiversity hotspots in non-mountainous areas and the additional PAs without locking in the existing PAs represent almost all species’ ranges evenly, including low-elevation ones with larger ranges. Some priority conservation areas we identified are expansions of, or near, existing PAs, especially in northeastern and southern South Korea. However, lowland coastal areas and areas surrounding the capital city, Seoul, are also critical for biodiversity conservation in South Korea. PMID:29474355

A Portable Dynamic Laser Speckle System for Sensing Long-Term Changes Caused by Treatments in Painting Conservation

PubMed Central

Pérez, Alberto J.; Braga, Roberto; Perles, Ángel; Pérez–Marín, Eva; García-Diego, Fernando J.

2018-01-01

Dynamic laser speckle (DLS) is used as a reliable sensor of activity for all types of materials. Traditional applications are based on high-rate captures (usually greater than 10 frames-per-second, fps). Even for drying processes in conservation treatments, where there is a high level of activity in the first moments after the application and slower activity after some minutes or hours, the process is based on the acquisition of images at a time rate that is the same in moments of high and low activity. In this work, we present an alternative approach to track the drying process of protective layers and other painting conservation processes that take a long time to reduce their levels of activity. We illuminate, using three different wavelength lasers, a temporary protector (cyclododecane) and a varnish, and monitor them using a low fps rate during long-term drying. The results are compared to the traditional method. This work also presents a monitoring method that uses portable equipment. The results present the feasibility of using the portable device and show the improved sensitivity of the dynamic laser speckle when sensing the long-term process for drying cyclododecane and varnish in conservation. PMID:29324692

Cost-effectiveness of alternative conservation strategies with application to the Pacific leatherback turtle.

PubMed

Gjertsen, Heidi; Squires, Dale; Dutton, Peter H; Eguchi, Tomoharu

2014-02-01

Although holistic conservation addressing all sources of mortality for endangered species or stocks is the preferred conservation strategy, limited budgets require a criterion to prioritize conservation investments. We compared the cost-effectiveness of nesting site and at-sea conservation strategies for Pacific leatherback turtles (Dermochelys coriacea). We sought to determine which conservation strategy or mix of strategies would produce the largest increase in population growth rate per dollar. Alternative strategies included protection of nesters and their eggs at nesting beaches in Indonesia, gear changes, effort restrictions, and caps on turtle takes in the Hawaiian (U.S.A.) longline swordfish fishery, and temporal and area closures in the California (U.S.A.) drift gill net fishery. We used a population model with a biological metric to measure the effects of conservation alternatives. We normalized all effects by cost to prioritize those strategies with the greatest biological effect relative to its economic cost. We used Monte Carlo simulation to address uncertainty in the main variables and to calculate probability distributions for cost-effectiveness measures. Nesting beach protection was the most cost-effective means of achieving increases in leatherback populations. This result creates the possibility of noncompensatory bycatch mitigation, where high-bycatch fisheries invest in protecting nesting beaches. An example of this practice is U.S. processors of longline tuna and California drift gill net fishers that tax themselves to finance low-cost nesting site protection. Under certain conditions, fisheries interventions, such as technologies that reduce leatherback bycatch without substantially decreasing target species catch, can be cost-effective. Reducing bycatch in coastal areas where bycatch is high, particularly adjacent to nesting beaches, may be cost-effective, particularly, if fisheries in the area are small and of little commercial value. © 2014 Society for Conservation Biology.

An Evolutionary Landscape of A-to-I RNA Editome across Metazoan Species

PubMed Central

Hung, Li-Yuan; Chen, Yen-Ju; Mai, Te-Lun; Chen, Chia-Ying; Yang, Min-Yu; Chiang, Tai-Wei; Wang, Yi-Da

2018-01-01

Abstract Adenosine-to-inosine (A-to-I) editing is widespread across the kingdom Metazoa. However, for the lack of comprehensive analysis in nonmodel animals, the evolutionary history of A-to-I editing remains largely unexplored. Here, we detect high-confidence editing sites using clustering and conservation strategies based on RNA sequencing data alone, without using single-nucleotide polymorphism information or genome sequencing data from the same sample. We thereby unveil the first evolutionary landscape of A-to-I editing maps across 20 metazoan species (from worm to human), providing unprecedented evidence on how the editing mechanism gradually expands its territory and increases its influence along the history of evolution. Our result revealed that highly clustered and conserved editing sites tended to have a higher editing level and a higher magnitude of the ADAR motif. The ratio of the frequencies of nonsynonymous editing to that of synonymous editing remarkably increased with increasing the conservation level of A-to-I editing. These results thus suggest potentially functional benefit of highly clustered and conserved editing sites. In addition, spatiotemporal dynamics analyses reveal a conserved enrichment of editing and ADAR expression in the central nervous system throughout more than 300 Myr of divergent evolution in complex animals and the comparability of editing patterns between invertebrates and between vertebrates during development. This study provides evolutionary and dynamic aspects of A-to-I editome across metazoan species, expanding this important but understudied class of nongenomically encoded events for comprehensive characterization. PMID:29294013

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-wide analysis to improved alignment quality, suggesting that enhanced genomic alignments may reveal many more conserved intronic sequences.

Comparative analysis on the structural features of the 5' flanking region of κ-casein genes from six different species

PubMed Central

Gerencsér, Ákos; Barta, Endre; Boa, Simon; Kastanis, Petros; Bösze, Zsuzsanna; Whitelaw, C Bruce A

2002-01-01

κ-casein plays an essential role in the formation, stabilisation and aggregation of milk micelles. Control of κ-casein expression reflects this essential role, although an understanding of the mechanisms involved lags behind that of the other milk protein genes. We determined the 5'-flanking sequences for the murine, rabbit and human κ-casein genes and compared them to the published ruminant sequences. The most conserved region was not the proximal promoter region but an approximately 400 bp long region centred 800 bp upstream of the TATA box. This region contained two highly conserved MGF/STAT5 sites with common spacing relative to each other. In this region, six conserved short stretches of similarity were also found which did not correspond to known transcription factor consensus sites. On the contrary to ruminant and human 5' regulatory sequences, the rabbit and murine 5'-flanking regions did not harbour any kind of repetitive elements. We generated a phylogenetic tree of the six species based on multiple alignment of the κ-casein sequences. This study identified conserved candidate transcriptional regulatory elements within the κ-casein gene promoter. PMID:11929628

Evolution of coding and non-coding genes in HOX clusters of a marsupial.

PubMed

Yu, Hongshi; Lindsay, James; Feng, Zhi-Ping; Frankenberg, Stephen; Hu, Yanqiu; Carone, Dawn; Shaw, Geoff; Pask, Andrew J; O'Neill, Rachel; Papenfuss, Anthony T; Renfree, Marilyn B

2012-06-18

The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial.

Evolution of coding and non-coding genes in HOX clusters of a marsupial

PubMed Central

2012-01-01

Background The HOX gene clusters are thought to be highly conserved amongst mammals and other vertebrates, but the long non-coding RNAs have only been studied in detail in human and mouse. The sequencing of the kangaroo genome provides an opportunity to use comparative analyses to compare the HOX clusters of a mammal with a distinct body plan to those of other mammals. Results Here we report a comparative analysis of HOX gene clusters between an Australian marsupial of the kangaroo family and the eutherians. There was a strikingly high level of conservation of HOX gene sequence and structure and non-protein coding genes including the microRNAs miR-196a, miR-196b, miR-10a and miR-10b and the long non-coding RNAs HOTAIR, HOTAIRM1 and HOXA11AS that play critical roles in regulating gene expression and controlling development. By microRNA deep sequencing and comparative genomic analyses, two conserved microRNAs (miR-10a and miR-10b) were identified and one new candidate microRNA with typical hairpin precursor structure that is expressed in both fibroblasts and testes was found. The prediction of microRNA target analysis showed that several known microRNA targets, such as miR-10, miR-414 and miR-464, were found in the tammar HOX clusters. In addition, several novel and putative miRNAs were identified that originated from elsewhere in the tammar genome and that target the tammar HOXB and HOXD clusters. Conclusions This study confirms that the emergence of known long non-coding RNAs in the HOX clusters clearly predate the marsupial-eutherian divergence 160 Ma ago. It also identified a new potentially functional microRNA as well as conserved miRNAs. These non-coding RNAs may participate in the regulation of HOX genes to influence the body plan of this marsupial. PMID:22708672

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...

Greater sage-grouse as an umbrella species for sagebrush-associated vertebrates

USGS Publications Warehouse

Rowland, M.M.; Wisdom, M.J.; Suring, L.H.; Meinke, C.W.

2006-01-01

Widespread degradation of the sagebrush ecosystem in the western United States, including the invasion of cheatgrass, has prompted resource managers to consider a variety of approaches to restore and conserve habitats for sagebrush-associated species. One such approach involves the use of greater sage-grouse, a species of prominent conservation interest, as an umbrella species. This shortcut approach assumes that managing habitats to conserve sage-grouse will simultaneously benefit other species of conservation concern. The efficacy of using sage-grouse as an umbrella species for conservation management, however, has not been fully evaluated. We tested that concept by comparing: (1) commonality in land-cover associations, and (2) spatial overlap in habitats between sage-grouse and 39 other sagebrush-associated vertebrate species of conservation concern in the Great Basin ecoregion. Overlap in species' land-cover associations with those of sage-grouse, based on the ?? (phi) correlation coefficient, was substantially greater for sagebrush obligates (x??=0.40) than non-obligates (x??=0.21). Spatial overlap between habitats of target species and those associated with sage-grouse was low (mean ?? = 0.23), but somewhat greater for habitats at high risk of displacement by cheatgrass (mean ?? = 0.33). Based on our criteria, management of sage-grouse habitats likely would offer relatively high conservation coverage for sagebrush obligates such as pygmy rabbit (mean ?? = 0.84), but far less for other species we addressed, such as lark sparrow (mean ?? = 0.09), largely due to lack of commonality in land-cover affinity and geographic ranges of these species and sage-grouse.

Aerobic stability of maize silage stored under plastic films with different oxygen permeability.

PubMed

Borreani, Giorgio; Piano, Serenella; Tabacco, Ernesto

2014-10-01

The most important factor that can influence silage quality is the degree of anaerobiosis maintained during conservation. The quality of the plastic film is a key factor, since the permeability of polyethylene to oxygen is too high for silage conservation. The aim of this work was to assess the effects of the interaction between three plastic films with different degrees of oxygen permeability and two different maize silage conservation times on fermentation, microbial quality and aerobic stability. The conservation time affected the pH, lactic and acetic acids, 1,2-propanediol and lactic/acetic acid ratio, with higher pH, lower lactic acid concentration and lactic/acetic acid ratio but higher acetic acid and 1,2-propanediol concentrations being found in silages conserved for 110 days versus silages conserved for 55 days. The plastic film affected the pH, lactic and acetic acids and lactic/acetic acid ratio. The yeast count was lower and aerobic stability higher for silage conserved under the oxygen barrier film for both conservation periods. The positive interaction between length of storage and the increased anaerobiosis of silage during conservation provided by the oxygen barrier compared with polyethylene film helped reduce the yeast count and increase the aerobic stability of maize silage, even when less acetic acid was produced during ensiling. © 2014 Society of Chemical Industry.

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

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.

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.

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.

Trait space of rare plants in a fire-dependent ecosystem.

PubMed

Ames, Gregory M; Wall, Wade A; Hohmann, Matthew G; Wright, Justin P

2017-08-01

The causes of species rarity are of critical concern because of the high extinction risk associated with rarity. Studies examining individual rare species have limited generality, whereas trait-based approaches offer a means to identify functional causes of rarity that can be applied to communities with disparate species pools. Differences in functional traits between rare and common species may be indicative of the functional causes of species rarity and may therefore be useful in crafting species conservation strategies. However, there is a conspicuous lack of studies comparing the functional traits of rare species and co-occurring common species. We measured 18 important functional traits for 19 rare and 134 common understory plant species from North Carolina's Sandhills region and compared their trait distributions to determine whether there are significant functional differences that may explain species rarity. Flowering, fire, and tissue-chemistry traits differed significantly between rare and common, co-occurring species. Differences in specific traits suggest that fire suppression has driven rarity in this system and that changes to the timing and severity of prescribed fire may improve conservation success. Our method provides a useful tool to prioritize conservation efforts in other systems based on the likelihood that rare species are functionally capable of persisting. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Amplified plant turnover in response to climate change forecast by Late Quaternary records

NASA Astrophysics Data System (ADS)

Nogués-Bravo, D.; Veloz, S.; Holt, B. G.; Singarayer, J.; Valdes, P.; Davis, B.; Brewer, S. C.; Williams, J. W.; Rahbek, C.

2016-12-01

Conservation decisions are informed by twenty-first-century climate impact projections that typically predict high extinction risk. Conversely, the palaeorecord shows strong sensitivity of species abundances and distributions to past climate changes, but few clear instances of extinctions attributable to rising temperatures. However, few studies have incorporated palaeoecological data into projections of future distributions. Here we project changes in abundance and conservation status under a climate warming scenario for 187 European and North American plant taxa using niche-based models calibrated against taxa-climate relationships for the past 21,000 years. We find that incorporating long-term data into niche-based models increases the magnitude of projected future changes for plant abundances and community turnover. The larger projected changes in abundances and community turnover translate into different, and often more threatened, projected IUCN conservation status for declining tree taxa, compared with traditional approaches. An average of 18.4% (North America) and 15.5% (Europe) of taxa switch IUCN categories when compared with single-time model results. When taxa categorized as `Least Concern' are excluded, the palaeo-calibrated models increase, on average, the conservation threat status of 33.2% and 56.8% of taxa. Notably, however, few models predict total disappearance of taxa, suggesting resilience for these taxa, if climate were the only extinction driver. Long-term studies linking palaeorecords and forecasting techniques have the potential to improve conservation assessments.

Impact of combinatory growth factor application on rabbit Achilles tendon injury with operative versus conservative treatment: a pilot study.

PubMed

Konerding, Moritz A; Arlt, Friederike; Wellmann, Axel; Li, Vincent; Li, William

2010-02-01

Acute Achilles tendon (AT) rupture is a common injury with a comparatively high complication rate. Presently, surgical treatments compete with nonoperative treatment modalities. The aim of this study was to elucidate the possible beneficial effects of short-term combinatory application of growth factors on tendon healing during operative or conservative treatment. In this controlled laboratory study, the left ATs of 40 adult New Zealand White rabbits were transected and either sutured or treated conservatively. Half of the animals from each treatment modality group repetitively received a mixture of VEGF165, bFGF, and rPDGF which was administered peritendineally. The left legs were immobilized with external fixateurs for 6 weeks. The ATs were harvested 3 months after intervention. Tensile strength tests revealed no significant differences between operative and conservative treatments. Compared to the normal right ATs, 60% of the average breaking strength was reached 3 months after surgery. Growth factor application did not result in significant improvements. Only a tendency towards higher blood vessel densities was noted in the groups treated with the factors. Collagen type I/III ratios also displayed no significant differences. This study indicates that there is no difference in the biomechanical outcome of conservative versus operative AT rupture treatment and only a marginal impact of short-term combinatory growth and angiogenesis factor application.

Genetic approaches refine ex situ lowland tapir (Tapirus terrestris) conservation.

PubMed

Gonçalves da Silva, Anders; Lalonde, Danielle R; Quse, Viviana; Shoemaker, Alan; Russello, Michael A

2010-01-01

Ex situ conservation management remains an important tool in the face of continued habitat loss and global environmental change. Here, we use microsatellite marker variation to evaluate conventional assumptions of pedigree-based ex situ population management and directly inform a captive lowland tapir breeding program within a range country. We found relatively high levels of genetic variation (N(total) = 41; mean H(E) = 0.67 across 10 variable loci) and little evidence for relatedness among founder individuals (N(founders) = 10; mean relatedness = -0.05). Seven of 29 putative parent-offspring relationships were excluded by parentage analysis based on allele sharing, and we identified 2 individuals of high genetic value to the population (mk

Comparative Study on High-Order Positivity-preserving WENO Schemes

NASA Technical Reports Server (NTRS)

Kotov, D. V.; Yee, H. C.; Sjogreen, B.

2013-01-01

In gas dynamics and magnetohydrodynamics flows, physically, the density and the pressure p should both be positive. In a standard conservative numerical scheme, however, the computed internal energy is obtained by subtracting the kinetic energy from the total energy, resulting in a computed p that may be negative. Examples are problems in which the dominant energy is kinetic. Negative may often emerge in computing blast waves. In such situations the computed eigenvalues of the Jacobian will become imaginary. Consequently, the initial value problem for the linearized system will be ill posed. This explains why failure of preserving positivity of density or pressure may cause blow-ups of the numerical algorithm. The adhoc methods in numerical strategy which modify the computed negative density and/or the computed negative pressure to be positive are neither a conservative cure nor a stable solution. Conservative positivity-preserving schemes are more appropriate for such flow problems. The ideas of Zhang & Shu (2012) and Hu et al. (2012) precisely address the aforementioned issue. Zhang & Shu constructed a new conservative positivity-preserving procedure to preserve positive density and pressure for high-order WENO schemes by the Lax-Friedrichs flux (WENO/LLF). In general, WENO/LLF is too dissipative for flows such as turbulence with strong shocks computed in direct numerical simulations (DNS) and large eddy simulations (LES). The new conservative positivity-preserving procedure proposed in Hu et al. (2012) can be used with any high-order shock-capturing scheme, including high-order WENO schemes using the Roe's flux (WENO/Roe). The goal of this study is to compare the results obtained by non-positivity-preserving methods with the recently developed positivity-preserving schemes for representative test cases. In particular the more difficult 3D Noh and Sedov problems are considered. These test cases are chosen because of the negative pressure/density most often exhibited by standard high-order shock-capturing schemes. The simulation of a hypersonic nonequilibrium viscous shock tube that is related to the NASA Electric Arc Shock Tube (EAST) is also included. EAST is a high-temperature and high Mach number viscous nonequilibrium flow consisting of 13 species. In addition, as most common shock-capturing schemes have been developed for problems without source terms, when applied to problems with nonlinear and/or sti source terms these methods can result in spurious solutions, even when solving a conservative system of equations with a conservative scheme. This kind of behavior can be observed even for a scalar case (LeVeque & Yee 1990) as well as for the case consisting of two species and one reaction (Wang et al. 2012). For further information concerning this issue see (LeVeque & Yee 1990; Griffiths et al. 1992; Lafon & Yee 1996; Yee et al. 2012). This EAST example indicated that standard high-order shock-capturing methods exhibit instability of density/pressure in addition to grid-dependent discontinuity locations with insufficient grid points. The evaluation of these test cases is based on the stability of the numerical schemes together with the accuracy of the obtained solutions.

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.

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.

'Conservation Education' and the Foundations of National Prosperity: Comparative Perspectives from Early Twentieth-Century North America and Britain.

ERIC Educational Resources Information Center

Marsden, William E.

1998-01-01

Compares the development of conservation education in North America and Britain. Reports that the focus of British conservation education was on preserving the countryside, while the United States focused on protecting natural resources. Finds that a major difference was that the label of 'conservation education' did not appear in Britain. (CMK)

An international comparison of government expenditures for energy conservation research and development:

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

McDonald, S.C.

1988-03-01

This study provides a comparison of US and foreign government spending for energy conservation research and development (R and D). The countries included in this analysis are: the United States, United Kingdom, France, Sweden, West Germany, and Japan. The approach of this paper was to compare the research program of each country at a high level of aggregation with the US Department of Energy (DOE) program structure. This paper does not allow for differences in the way each country defines or accounts for research.

Effect of resonance decay on conserved number fluctuations in a hadron resonance gas model

NASA Astrophysics Data System (ADS)

Mishra, D. K.; Garg, P.; Netrakanti, P. K.; Mohanty, A. K.

2016-07-01

We study the effect of charged secondaries coming from resonance decay on the net-baryon, net-charge, and net-strangeness fluctuations in high-energy heavy-ion collisions within the hadron resonance gas (HRG) model. We emphasize the importance of including weak decays along with other resonance decays in the HRG, while comparing with the experimental observables. The effect of kinematic cuts on resonances and primordial particles on the conserved number fluctuations are also studied. The HRG model calculations with the inclusion of resonance decays and kinematical cuts are compared with the recent experimental data from STAR and PHENIX experiments. We find good agreement between our model calculations and the experimental measurements for both net-proton and net-charge distributions.

Estimates of effective population size and inbreeding in South African indigenous chicken populations: implications for the conservation of unique genetic resources.

PubMed

Mtileni, Bohani; Dzama, Kennedy; Nephawe, Khathutshelo; Rhode, Clint

2016-06-01

Conservation of locally adapted indigenous livestock breeds has become an important objective in sustainable animal breeding, as these breeds represent a unique genetic resource. Therefore, the Agricultural Research Council of South Africa initiated a conservation programme for four South African indigenous chicken breeds. The evaluation and monitoring of the genetic constitution of these conservation flocks is important for proper management of the conservation programme. Using molecular genetic analyses, the effective population sizes and relatedness of these conservation flocks were compared to village (field) chicken populations from which they were derived. Genetic diversity within and between these populations are further discussed within the context of population size. The conservation flocks for the respective breeds had relatively small effective population sizes (point estimate range 38.6-78.6) in comparison to the field populations (point estimate range 118.9-580.0). Furthermore, evidence supports a transient heterozygous excess, generally associated with the occurrence of a recent population bottleneck. Genetic diversity, as measured by the number of alleles, heterozygosity and information index, was also significantly reduced in the conservation flocks. The average relatedness amongst the conservation flocks was high, whilst it remained low for the field populations. There was also significant evidence for population differentiation between field and conservation populations. F st estimates for conservation flocks were moderate to high with a maximum reached between VD_C and VD_F (0.285). However, F st estimates for field population were excessively low between the NN_C and EC_F (0.007) and between EC_F and OV_F (0.009). The significant population differentiation of the conservation flocks from their geographically correlated field populations of origin is further supported by the analysis of molecular variance (AMOVA), with 10.51 % of genetic diversity ascribed to population differences within groups (F SC = 0.106). The results suggest that significant genetic erosion has occurred within the conservation flocks due to inbreeding, pronounced effects of random drift and selection. It might be necessary to introduce new breeding individuals from the respective field populations in order to increase the effective population sizes of the conservation flocks and counter the effects of genetic erosion.

Maintaining replication origins in the face of genomic change.

PubMed

Di Rienzi, Sara C; Lindstrom, Kimberly C; Mann, Tobias; Noble, William S; Raghuraman, M K; Brewer, Bonita J

2012-10-01

Origins of replication present a paradox to evolutionary biologists. As a collection, they are absolutely essential genomic features, but individually are highly redundant and nonessential. It is therefore difficult to predict to what extent and in what regard origins are conserved over evolutionary time. Here, through a comparative genomic analysis of replication origins and chromosomal replication patterns in the budding yeasts Saccharomyces cerevisiae and Lachancea waltii, we assess to what extent replication origins survived genomic change produced from 150 million years of evolution. We find that L. waltii origins exhibit a core consensus sequence and nucleosome occupancy pattern highly similar to those of S. cerevisiae origins. We further observe that the overall progression of chromosomal replication is similar between L. waltii and S. cerevisiae. Nevertheless, few origins show evidence of being conserved in location between the two species. Among the conserved origins are those surrounding centromeres and adjacent to histone genes, suggesting that proximity to an origin may be important for their regulation. We conclude that, over evolutionary time, origins maintain sequence, structure, and regulation, but are continually being created and destroyed, with the result that their locations are generally not conserved.

Maintaining replication origins in the face of genomic change

PubMed Central

Di Rienzi, Sara C.; Lindstrom, Kimberly C.; Mann, Tobias; Noble, William S.; Raghuraman, M.K.; Brewer, Bonita J.

2012-01-01

Origins of replication present a paradox to evolutionary biologists. As a collection, they are absolutely essential genomic features, but individually are highly redundant and nonessential. It is therefore difficult to predict to what extent and in what regard origins are conserved over evolutionary time. Here, through a comparative genomic analysis of replication origins and chromosomal replication patterns in the budding yeasts Saccharomyces cerevisiae and Lachancea waltii, we assess to what extent replication origins survived genomic change produced from 150 million years of evolution. We find that L. waltii origins exhibit a core consensus sequence and nucleosome occupancy pattern highly similar to those of S. cerevisiae origins. We further observe that the overall progression of chromosomal replication is similar between L. waltii and S. cerevisiae. Nevertheless, few origins show evidence of being conserved in location between the two species. Among the conserved origins are those surrounding centromeres and adjacent to histone genes, suggesting that proximity to an origin may be important for their regulation. We conclude that, over evolutionary time, origins maintain sequence, structure, and regulation, but are continually being created and destroyed, with the result that their locations are generally not conserved. PMID:22665441

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.

Nutrient elements in large Chinese estuaries

NASA Astrophysics Data System (ADS)

Zhang, Jing

1996-07-01

Based on comprehensive observations since 1983, this study summarizes major features of nutrient elements (nitrogen, phosphorus and silicon) in large Chinese river/estuary systems. Elevated nutrient element levels were observed in Chinese rivers, when compared to large and less disturbed aquatic systems (e.g. the Amazon, Zaire and Orinoco). Data from this study are similar to those obtained from the polluted and/or eutrophic rivers in Europe and North America (e.g. the Rhóne and Loire). Nutrient elements may have either conservative or active distributions, or both, in the mixing zone, depending on the element and the estuary. For example, non-conservative behaviors were observed in the upper estuary, where nutrient elements may be remobilized due to the strong desorption and variations of the fresh water end-member, but conservative distributions were found afterwards in the lower estuary. Outside the riverine effluent plumes, nutrient elements may be depleted in surface waters relative to elevated bioproduction, whereas the regeneration with respect to decomposition of organic material and/or nitrification/denitrification offshore, may sustain high levels of nutrient elements in near-bottom waters. Laboratory experiment data generally compares well with field observations. The high fluxes and area] yields of nutrient elements from large Chinese rivers, indicate the extensive use of chemical fertilizers and domestic waste drainage over watersheds in China.

Land Management Restrictions and Options for Change in Perpetual Conservation Easements

NASA Astrophysics Data System (ADS)

Rissman, Adena; Bihari, Menka; Hamilton, Christopher; Locke, Christina; Lowenstein, David; Motew, Melissa; Price, Jessica; Smail, Robert

2013-07-01

Conservation organizations rely on conservation easements for diverse purposes, including protection of species and natural communities, working forests, and open space. This research investigated how perpetual conservation easements incorporated property rights, responsibilities, and options for change over time in land management. We compared 34 conservation easements held by one federal, three state, and four nonprofit organizations in Wisconsin. They incorporated six mechanisms for ongoing land management decision-making: management plans (74 %), modifications to permitted landowner uses with discretionary consent (65 %), amendment clauses (53 %), easement holder rights to conduct land management (50 %), reference to laws or policies as compliance terms (47 %), and conditional use permits (12 %). Easements with purposes to protect species and natural communities had more ecological monitoring rights, organizational control over land management, and mechanisms for change than easements with general open space purposes. Forestry purposes were associated with mechanisms for change but not necessarily with ecological monitoring rights or organizational control over land management. The Natural Resources Conservation Service-Wetland Reserve Program had a particularly consistent approach with high control over land use and some discretion to modify uses through permits. Conservation staff perceived a need to respond to changing social and ecological conditions but were divided on whether climate change was likely to negatively impact their conservation easements. Many conservation easements involved significant constraints on easement holders' options for altering land management to achieve conservation purposes over time. This study suggests the need for greater attention to easement drafting, monitoring, and ongoing decision processes to ensure the public benefits of land conservation in changing landscapes.

Land management restrictions and options for change in perpetual conservation easements.

PubMed

Rissman, Adena; Bihari, Menka; Hamilton, Christopher; Locke, Christina; Lowenstein, David; Motew, Melissa; Price, Jessica; Smail, Robert

2013-07-01

Conservation organizations rely on conservation easements for diverse purposes, including protection of species and natural communities, working forests, and open space. This research investigated how perpetual conservation easements incorporated property rights, responsibilities, and options for change over time in land management. We compared 34 conservation easements held by one federal, three state, and four nonprofit organizations in Wisconsin. They incorporated six mechanisms for ongoing land management decision-making: management plans (74 %), modifications to permitted landowner uses with discretionary consent (65 %), amendment clauses (53 %), easement holder rights to conduct land management (50 %), reference to laws or policies as compliance terms (47 %), and conditional use permits (12 %). Easements with purposes to protect species and natural communities had more ecological monitoring rights, organizational control over land management, and mechanisms for change than easements with general open space purposes. Forestry purposes were associated with mechanisms for change but not necessarily with ecological monitoring rights or organizational control over land management. The Natural Resources Conservation Service-Wetland Reserve Program had a particularly consistent approach with high control over land use and some discretion to modify uses through permits. Conservation staff perceived a need to respond to changing social and ecological conditions but were divided on whether climate change was likely to negatively impact their conservation easements. Many conservation easements involved significant constraints on easement holders' options for altering land management to achieve conservation purposes over time. This study suggests the need for greater attention to easement drafting, monitoring, and ongoing decision processes to ensure the public benefits of land conservation in changing landscapes.

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

Modeling the impact of conservation agriculture on crop production and soil properties in Mediterranean climate

NASA Astrophysics Data System (ADS)

Moussadek, Rachid; Mrabet, Rachid; Dahan, Rachid; Laghrour, Malika; Lembiad, Ibtissam; ElMourid, Mohamed

2015-04-01

In Morocco, rainfed agriculture is practiced in the majority of agricultural land. However, the intensive land use coupled to the irregular rainfall constitutes a serious threat that affect country's food security. Conservation agriculture (CA) represents a promising alternative to produce more and sustainably. In fact, the direct seeding showed high yield in arid regions of Morocco but its extending to other more humid agro-ecological zones (rainfall > 350mm) remains scarce. In order to promote CA in Morocco, differents trials have been installed in central plateau of Morocco, to compare CA to conventional tillage (CT). The yields of the main practiced crops (wheat, lentil and checkpea) under CA and CT were analyzed and compared in the 3 soils types (Vertisol, Cambisol and Calcisol). Also, we studied the effect of CA on soil organic matter (SOM) and soil losses (SL) in the 3 different sites. The APSIM model was used to model the long term impact of CA compared to CT. The results obtained in this research have shown favorable effects of CA on crop production, SOM and soil erosion. Key words: Conservation agriculture, yield, soil properties, modeling, APSIM, Morocco.

Comparative genomic sequence analysis of strawberry and other rosids reveals significant microsynteny

PubMed Central

2010-01-01

Background Fragaria belongs to the Rosaceae, an economically important family that includes a number of important fruit producing genera such as Malus and Prunus. Using genomic sequences from 50 Fragaria fosmids, we have examined the microsynteny between Fragaria and other plant models. Results In more than half of the strawberry fosmids, we found syntenic regions that are conserved in Populus, Vitis, Medicago and/or Arabidopsis with Populus containing the greatest number of syntenic regions with Fragaria. The longest syntenic region was between LG VIII of the poplar genome and the strawberry fosmid 72E18, where seven out of twelve predicted genes were collinear. We also observed an unexpectedly high level of conserved synteny between Fragaria (rosid I) and Vitis (basal rosid). One of the strawberry fosmids, 34E24, contained a cluster of R gene analogs (RGAs) with NBS and LRR domains. We detected clusters of RGAs with high sequence similarity to those in 34E24 in all the genomes compared. In the phylogenetic tree we have generated, all the NBS-LRR genes grouped together with Arabidopsis CNL-A type NBS-LRR genes. The Fragaria RGA grouped together with those of Vitis and Populus in the phylogenetic tree. Conclusions Our analysis shows considerable microsynteny between Fragaria and other plant genomes such as Populus, Medicago, Vitis, and Arabidopsis to a lesser degree. We also detected a cluster of NBS-LRR type genes that are conserved in all the genomes compared. PMID:20565715

Ovarian Conservation and Overall Survival in Young Women With Early-Stage Low-Grade Endometrial Cancer.

PubMed

Matsuo, Koji; Machida, Hiroko; Shoupe, Donna; Melamed, Alexander; Muderspach, Laila I; Roman, Lynda D; Wright, Jason D

2016-10-01

To characterize contributing factors for ovarian conservation during surgical treatment for endometrial cancer and to examine the association of ovarian conservation on survival of young women with early-stage, low-grade tumors. This was a population-based study using the Surveillance, Epidemiology, and End Results program to identify surgically treated stage I type I (grade 1-2 endometrioid histology) endometrial cancer cases diagnosed between 1983 and 2012 (N=86,005). Multivariable models were used to identify independent factors for ovarian conservation. Survival outcomes and cause of death were examined for women aged younger than 50 with stage I type I endometrial cancer who underwent ovarian conservation (1,242 among 12,860 women [9.7%]). On multivariable analysis, age younger than 50 years, grade 1 endometrioid histology, and tumor size 2.0 cm or less were noted to be independent factors for ovarian conservation (all, P<.001). For 9,110 women aged younger than 50 years with stage I grade 1 tumors, cause-specific survival was similar between ovarian conservation and oophorectomy cases (20-year rates 98.9% compared with 97.7%, P=.31), whereas overall survival was significantly higher in ovarian conservation cases than oophorectomy cases (88.8% compared with 82.0%, P=.011). On multivariable analysis, ovarian conservation remained an independent prognostic factor for improved overall survival (adjusted hazard ratio 0.73, 95% confidence interval [CI] 0.54-0.98, P=.036) and was independently associated with a lower cumulative risk of death resulting from cardiovascular disease compared with oophorectomy (20-year rates, 2.3% compared with 3.7%, adjusted hazard ratio 0.40, 95% CI 0.17-0.91, P=.029). Contrary, cause-specific survival (20-year rates 94.6% compared with 96.1%, P=.68) and overall survival (81.0% compared with 80.6%, P=.91) were similar between ovarian conservation and oophorectomy among 3,750 women aged younger than 50 years with stage I grade 2 tumors. Ovarian conservation is performed in less than 10% of young women with stage I type I endometrial cancer. Ovarian conservation is associated with decreased mortality in young women with stage I grade 1 tumors.

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

Lyon, Stuart, E-mail: lyonsey@optusnet.com.au; Mott, Nigel, E-mail: nigelmott76@hotmail.com; Koukounaras, Jim

Chylothorax is an uncommon type of pleural effusion whose etiology may be classified as traumatic or nontraumatic. Low-output chylothoraces usually respond well to conservative management, whereas high-output chylothoraces are more likely to require surgical or interventional treatment. Conservative management focuses on alleviation of symptoms, replacement of fluid and nutrient losses, and reduction of chyle output to facilitate spontaneous healing. Surgical management can be technically difficult due to the high incidence of variant anatomy and the high-risk patient population. Percutaneous treatments have rapidly developed and evolved during the past 14 years to represent a minimally invasive treatment compared with the moremore » invasive nature of surgery. Percutaneous therapies provide a range of treatment options despite difficult or variant anatomy, with a reported high success rate coupled with low morbidity and mortality. This article is a review of etiology, diagnosis, and treatment of chylothorax, with a focus on interventional management techniques.« less

High genetic diversity in the endangered and narrowly distributed amphibian species Leptobrachium leishanense.

PubMed

Zhang, Wei; Luo, Zhenhua; Zhao, Mian; Wu, Hua

2015-09-01

Threatened species typically have a small or declining population size, which make them highly susceptible to loss of genetic diversity through genetic drift and inbreeding. Genetic diversity determines the evolutionary potential of a species; therefore, maintaining the genetic diversity of threatened species is essential for their conservation. In this study, we assessed the genetic diversity of the adaptive major histocompatibility complex (MHC) genes in an endangered and narrowly distributed amphibian species, Leptobrachium leishanense in Southwest China. We compared the genetic variation of MHC class I genes with that observed in neutral markers (5 microsatellite loci and cytochrome b gene) to elucidate the relative roles of genetic drift and natural selection in shaping the current MHC polymorphism in this species. We found a high level of genetic diversity in this population at both MHC and neutral markers compared with other threatened amphibian species. Historical positive selection was evident in the MHC class I genes. The higher allelic richness in MHC markers compared with that of microsatellite loci suggests that selection rather than genetic drift plays a prominent role in shaping the MHC variation pattern, as drift can affect all the genome in a similar way but selection directly targets MHC genes. Although demographic analysis revealed no recent bottleneck events in L. leishanense, additional population decline will accelerate the dangerous status for this species. We suggest that the conservation management of L. leishanense should concentrate on maximizing the retention of genetic diversity through preventing their continuous population decline. Protecting their living habitats and forbidding illegal hunting are the most important measures for conservation of L. leishanense. © 2015 International Society of Zoological Sciences, Institute of Zoology/Chinese Academy of Sciences and Wiley Publishing Asia Pty Ltd.

The Evolution of COP9 Signalosome in Unicellular and Multicellular Organisms.

PubMed

Barth, Emanuel; Hübler, Ron; Baniahmad, Aria; Marz, Manja

2016-05-02

The COP9 signalosome (CSN) is a highly conserved protein complex, recently being crystallized for human. In mammals and plants the COP9 complex consists of nine subunits, CSN 1-8 and CSNAP. The CSN regulates the activity of culling ring E3 ubiquitin and plays central roles in pleiotropy, cell cycle, and defense of pathogens. Despite the interesting and essential functions, a thorough analysis of the CSN subunits in evolutionary comparative perspective is missing. Here we compared 61 eukaryotic genomes including plants, animals, and yeasts genomes and show that the most conserved subunits of eukaryotes among the nine subunits are CSN2 and CSN5. This may indicate a strong evolutionary selection for these two subunits. Despite the strong conservation of the protein sequence, the genomic structures of the intron/exon boundaries indicate no conservation at genomic level. This suggests that the gene structure is exposed to a much less selection compared with the protein sequence. We also show the conservation of important active domains, such as PCI (proteasome lid-CSN-initiation factor) and MPN (MPR1/PAD1 amino-terminal). We identified novel exons and alternative splicing variants for all CSN subunits. This indicates another level of complexity of the CSN. Notably, most COP9-subunits were identified in all multicellular and unicellular eukaryotic organisms analyzed, but not in prokaryotes or archaeas. Thus, genes encoding CSN subunits present in all analyzed eukaryotes indicate the invention of the signalosome at the root of eukaryotes. The identification of alternative splice variants indicates possible "mini-complexes" or COP9 complexes with independent subunits containing potentially novel and not yet identified functions. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The Evolution of COP9 Signalosome in Unicellular and Multicellular Organisms

PubMed Central

Barth, Emanuel; Hübler, Ron; Baniahmad, Aria; Marz, Manja

2016-01-01

The COP9 signalosome (CSN) is a highly conserved protein complex, recently being crystallized for human. In mammals and plants the COP9 complex consists of nine subunits, CSN 1–8 and CSNAP. The CSN regulates the activity of culling ring E3 ubiquitin and plays central roles in pleiotropy, cell cycle, and defense of pathogens. Despite the interesting and essential functions, a thorough analysis of the CSN subunits in evolutionary comparative perspective is missing. Here we compared 61 eukaryotic genomes including plants, animals, and yeasts genomes and show that the most conserved subunits of eukaryotes among the nine subunits are CSN2 and CSN5. This may indicate a strong evolutionary selection for these two subunits. Despite the strong conservation of the protein sequence, the genomic structures of the intron/exon boundaries indicate no conservation at genomic level. This suggests that the gene structure is exposed to a much less selection compared with the protein sequence. We also show the conservation of important active domains, such as PCI (proteasome lid-CSN-initiation factor) and MPN (MPR1/PAD1 amino-terminal). We identified novel exons and alternative splicing variants for all CSN subunits. This indicates another level of complexity of the CSN. Notably, most COP9-subunits were identified in all multicellular and unicellular eukaryotic organisms analyzed, but not in prokaryotes or archaeas. Thus, genes encoding CSN subunits present in all analyzed eukaryotes indicate the invention of the signalosome at the root of eukaryotes. The identification of alternative splice variants indicates possible “mini-complexes” or COP9 complexes with independent subunits containing potentially novel and not yet identified functions. PMID:27044515

Threatened and Endangered Subspecies with Vulnerable Ecological Traits Also Have High Susceptibility to Sea Level Rise and Habitat Fragmentation

PubMed Central

Benscoter, Allison M.; Reece, Joshua S.; Noss, Reed F.; Brandt, Laura A.; Mazzotti, Frank J.; Romañach, Stephanie S.; Watling, James I.

2013-01-01

The presence of multiple interacting threats to biodiversity and the increasing rate of species extinction make it critical to prioritize management efforts on species and communities that maximize conservation success. We implemented a multi-step approach that coupled vulnerability assessments evaluating threats to Florida taxa such as climate change, sea-level rise, and habitat fragmentation with in-depth literature surveys of taxon-specific ecological traits. The vulnerability, adaptive capacity, and ecological traits of 12 threatened and endangered subspecies were compared to non-listed subspecies of the same parent species. Overall, the threatened and endangered subspecies showed high vulnerability and low adaptive capacity, in particular to sea level rise and habitat fragmentation. They also exhibited larger home ranges and greater dispersal limitation compared to non-endangered subspecies, which may inhibit their ability to track changing climate in fragmented landscapes. There was evidence for lower reproductive capacity in some of the threatened or endangered taxa, but not for most. Taxa located in the Florida Keys or in other low coastal areas were most vulnerable to sea level rise, and also showed low levels of adaptive capacity, indicating they may have a lower probability of conservation success. Our analysis of at-risk subspecies and closely related non-endangered subspecies demonstrates that ecological traits help to explain observed differences in vulnerability and adaptive capacity. This study points to the importance of assessing the relative contributions of multiple threats and evaluating conservation value at the species (or subspecies) level when resources are limited and several factors affect conservation success. PMID:23940614

Threatened and endangered subspecies with vulnerable ecological traits also have high susceptibility to sea level rise and habitat fragmentation.

PubMed

Benscoter, Allison M; Reece, Joshua S; Noss, Reed F; Brandt, Laura A; Mazzotti, Frank J; Romañach, Stephanie S; Watling, James I

2013-01-01

The presence of multiple interacting threats to biodiversity and the increasing rate of species extinction make it critical to prioritize management efforts on species and communities that maximize conservation success. We implemented a multi-step approach that coupled vulnerability assessments evaluating threats to Florida taxa such as climate change, sea-level rise, and habitat fragmentation with in-depth literature surveys of taxon-specific ecological traits. The vulnerability, adaptive capacity, and ecological traits of 12 threatened and endangered subspecies were compared to non-listed subspecies of the same parent species. Overall, the threatened and endangered subspecies showed high vulnerability and low adaptive capacity, in particular to sea level rise and habitat fragmentation. They also exhibited larger home ranges and greater dispersal limitation compared to non-endangered subspecies, which may inhibit their ability to track changing climate in fragmented landscapes. There was evidence for lower reproductive capacity in some of the threatened or endangered taxa, but not for most. Taxa located in the Florida Keys or in other low coastal areas were most vulnerable to sea level rise, and also showed low levels of adaptive capacity, indicating they may have a lower probability of conservation success. Our analysis of at-risk subspecies and closely related non-endangered subspecies demonstrates that ecological traits help to explain observed differences in vulnerability and adaptive capacity. This study points to the importance of assessing the relative contributions of multiple threats and evaluating conservation value at the species (or subspecies) level when resources are limited and several factors affect conservation success.

Threatened and endangered subspecies with vulnerable ecological traits Also have high susceptibility to sea level rise and habitat fragmentation

USGS Publications Warehouse

Benscoter, Allison M.; Reece, Joshua S.; Noss, Reed F.; Brandt, Laura B.; Mazzotti, Frank J.; Romañach, Stephanie S.; Watling, James I.

2013-01-01

The presence of multiple interacting threats to biodiversity and the increasing rate of species extinction make it critical to prioritize management efforts on species and communities that maximize conservation success. We implemented a multi-step approach that coupled vulnerability assessments evaluating threats to Florida taxa such as climate change, sea-level rise, and habitat fragmentation with in-depth literature surveys of taxon-specific ecological traits. The vulnerability, adaptive capacity, and ecological traits of 12 threatened and endangered subspecies were compared to non-listed subspecies of the same parent species. Overall, the threatened and endangered subspecies showed high vulnerability and low adaptive capacity, in particular to sea level rise and habitat fragmentation. They also exhibited larger home ranges and greater dispersal limitation compared to non-endangered subspecies, which may inhibit their ability to track changing climate in fragmented landscapes. There was evidence for lower reproductive capacity in some of the threatened or endangered taxa, but not for most. Taxa located in the Florida Keys or in other low coastal areas were most vulnerable to sea level rise, and also showed low levels of adaptive capacity, indicating they may have a lower probability of conservation success. Our analysis of at-risk subspecies and closely related non-endangered subspecies demonstrates that ecological traits help to explain observed differences in vulnerability and adaptive capacity. This study points to the importance of assessing the relative contributions of multiple threats and evaluating conservation value at the species (or subspecies) level when resources are limited and several factors affect conservation success.

Mapping the economic costs and benefits of conservation.

PubMed

Naidoo, Robin; Ricketts, Taylor H

2006-10-01

Resources for biodiversity conservation are severely limited, requiring strategic investment. Understanding both the economic benefits and costs of conserving ecosystems will help to allocate scarce dollars most efficiently. However, although cost-benefit analyses are common in many areas of policy, they are not typically used in conservation planning. We conducted a spatial evaluation of the costs and benefits of conservation for a landscape in the Atlantic forests of Paraguay. We considered five ecosystem services (i.e., sustainable bushmeat harvest, sustainable timber harvest, bioprospecting for pharmaceutical products, existence value, and carbon storage in aboveground biomass) and compared them to estimates of the opportunity costs of conservation. We found a high degree of spatial variability in both costs and benefits over this relatively small (approximately 3,000 km(2)) landscape. Benefits exceeded costs in some areas, with carbon storage dominating the ecosystem service values and swamping opportunity costs. Other benefits associated with conservation were more modest and exceeded costs only in protected areas and indigenous reserves. We used this cost-benefit information to show that one potential corridor between two large forest patches had net benefits that were three times greater than two otherwise similar alternatives. Spatial cost-benefit analysis can powerfully inform conservation planning, even though the availability of relevant data may be limited, as was the case in our study area. It can help us understand the synergies between biodiversity conservation and economic development when the two are indeed aligned and to clearly understand the trade-offs when they are not.

Mapping the Economic Costs and Benefits of Conservation

PubMed Central

Naidoo, Robin; Ricketts, Taylor H

2006-01-01

Resources for biodiversity conservation are severely limited, requiring strategic investment. Understanding both the economic benefits and costs of conserving ecosystems will help to allocate scarce dollars most efficiently. However, although cost-benefit analyses are common in many areas of policy, they are not typically used in conservation planning. We conducted a spatial evaluation of the costs and benefits of conservation for a landscape in the Atlantic forests of Paraguay. We considered five ecosystem services (i.e., sustainable bushmeat harvest, sustainable timber harvest, bioprospecting for pharmaceutical products, existence value, and carbon storage in aboveground biomass) and compared them to estimates of the opportunity costs of conservation. We found a high degree of spatial variability in both costs and benefits over this relatively small (~3,000 km2) landscape. Benefits exceeded costs in some areas, with carbon storage dominating the ecosystem service values and swamping opportunity costs. Other benefits associated with conservation were more modest and exceeded costs only in protected areas and indigenous reserves. We used this cost-benefit information to show that one potential corridor between two large forest patches had net benefits that were three times greater than two otherwise similar alternatives. Spatial cost-benefit analysis can powerfully inform conservation planning, even though the availability of relevant data may be limited, as was the case in our study area. It can help us understand the synergies between biodiversity conservation and economic development when the two are indeed aligned and to clearly understand the trade-offs when they are not. PMID:17076583

Conserved cell cycle regulatory properties within the amino terminal domain of the Epstein-Barr virus nuclear antigen 3C

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

Sharma, Nikhil; Knight, Jason S.; Robertson, Erle S.

The gammaherpesviruses Rhesus lymphocryptovirus (LCV) and Epstein-Barr virus (EBV) are closely related phylogenetically. Rhesus LCV efficiently immortalizes Rhesus B cells in vitro. However, despite a high degree of conservation between the Rhesus LCV and EBV genomes, Rhesus LCV fails to immortalize human B cells in vitro. This species restriction may, at least in part, be linked to the EBV nuclear antigens (EBNAs) and latent membrane proteins (LMPs), known to be essential for B cell transformation. We compared specific properties of EBNA3C, a well-characterized and essential EBV protein, with its Rhesus counterpart to determine whether EBNA3C phenotypes which contribute to cellmore » cycle regulation are conserved in the Rhesus LCV. We show that both EBNA3C and Rhesus EBNA3C bind to a conserved region of mammalian cyclins, regulate pRb stability, and modulate SCF{sup Skp2}-dependent ubiquitination. These results suggest that Rhesus LCV restriction from human B cell immortalization is independent of the conserved cell cycle regulatory functions of the EBNA3C protein.« less

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.

Assessing the Robustness of Complete Bacterial Genome Segmentations

NASA Astrophysics Data System (ADS)

Devillers, Hugo; Chiapello, Hélène; Schbath, Sophie; El Karoui, Meriem

Comparison of closely related bacterial genomes has revealed the presence of highly conserved sequences forming a "backbone" that is interrupted by numerous, less conserved, DNA fragments. Segmentation of bacterial genomes into backbone and variable regions is particularly useful to investigate bacterial genome evolution. Several software tools have been designed to compare complete bacterial chromosomes and a few online databases store pre-computed genome comparisons. However, very few statistical methods are available to evaluate the reliability of these software tools and to compare the results obtained with them. To fill this gap, we have developed two local scores to measure the robustness of bacterial genome segmentations. Our method uses a simulation procedure based on random perturbations of the compared genomes. The scores presented in this paper are simple to implement and our results show that they allow to discriminate easily between robust and non-robust bacterial genome segmentations when using aligners such as MAUVE and MGA.

Local Residents Perception of Benefits and Losses From Protected Areas in India and Nepal

NASA Astrophysics Data System (ADS)

Karanth, Krithi K.; Nepal, Sanjay K.

2012-02-01

High densities of people living around protected areas (PAs) in South Asia require management strategies to balance conservation goals and livelihood needs. Based on a survey of 777 households around five PAs in India and Nepal, this paper provides a comparative perspective of Indian and Nepali households' views of protected area benefits and costs, their attitude toward conservation in general, and attitude toward protected area staff. Results indicate mixed responses towards tourism, varying from very favorable in Nepal to less favorable in India. The majority (81%) held positive attitudes towards the existence and importance of PAs but had negative perceptions of PA staff (69%). Most residents perceived benefits from access to fuel wood, fodder and other PA resources including benefits from tourism, while crop and livestock losses from wildlife were the main costs. Households overall positive attitudes towards the PAs and conservation despite high losses from living around PAs suggests that local residents may support conservation if their livelihood needs are met. Comparisons of household attitudes and perceptions suggest that locally based strategies rather than top-down approaches are likely to be more effective. Extending PA benefits to smaller landholders, households that are highly resource-dependent or experiencing higher income losses from human-wildlife conflicts, and less educated residents are particularly important to balance costs and losses from living around protected areas.

Local residents perception of benefits and losses from protected areas in India and Nepal.

PubMed

Karanth, Krithi K; Nepal, Sanjay K

2012-02-01

High densities of people living around protected areas (PAs) in South Asia require management strategies to balance conservation goals and livelihood needs. Based on a survey of 777 households around five PAs in India and Nepal, this paper provides a comparative perspective of Indian and Nepali households' views of protected area benefits and costs, their attitude toward conservation in general, and attitude toward protected area staff. Results indicate mixed responses towards tourism, varying from very favorable in Nepal to less favorable in India. The majority (81%) held positive attitudes towards the existence and importance of PAs but had negative perceptions of PA staff (69%). Most residents perceived benefits from access to fuel wood, fodder and other PA resources including benefits from tourism, while crop and livestock losses from wildlife were the main costs. Households overall positive attitudes towards the PAs and conservation despite high losses from living around PAs suggests that local residents may support conservation if their livelihood needs are met. Comparisons of household attitudes and perceptions suggest that locally based strategies rather than top-down approaches are likely to be more effective. Extending PA benefits to smaller landholders, households that are highly resource-dependent or experiencing higher income losses from human-wildlife conflicts, and less educated residents are particularly important to balance costs and losses from living around protected areas.

Reciprocal osmotic challenges reveal mechanisms of divergence in phenotypic plasticity in the killifish Fundulus heteroclitus.

PubMed

Brennan, Reid S; Galvez, Fernando; Whitehead, Andrew

2015-04-15

The killifish Fundulus heteroclitus is an estuarine species with broad physiological plasticity, enabling acclimation to diverse stressors. Previous work suggests that freshwater populations expanded their physiology to accommodate low salinity environments; however, it is unknown whether this compromises their tolerance to high salinity. We used a comparative approach to investigate the mechanisms of a derived freshwater phenotype and the fate of an ancestral euryhaline phenotype after invasion of a freshwater environment. We compared physiological and transcriptomic responses to high- and low-salinity stress in fresh and brackish water populations and found an enhanced plasticity to low salinity in the freshwater population coupled with a reduced ability to acclimate to high salinity. Transcriptomic data identified genes with a conserved common response, a conserved salinity-dependent response and responses associated with population divergence. Conserved common acclimation responses revealed stress responses and alterations in cell-cycle regulation as important mechanisms in the general osmotic response. Salinity-specific responses included the regulation of genes involved in ion transport, intracellular calcium, energetic processes and cellular remodeling. Genes diverged between populations were primarily those showing salinity-specific expression and included those regulating polyamine homeostasis and the cell cycle. Additionally, when populations were matched with their native salinity, expression patterns were consistent with the concept of 'transcriptomic resilience', suggesting local adaptation. These findings provide insight into the fate of a plastic phenotype after a shift in environmental salinity and help to reveal mechanisms allowing for euryhalinity. © 2015. Published by The Company of Biologists Ltd.

Developmental plasticity and language: A comparative perspective

PubMed Central

Griebel, Ulrike; Pepperberg, Irene; Oller, D. Kimbrough

2016-01-01

The growing field of evo-devo is increasingly demonstrating the complexity of steps involved in genetic, intracellular regulatory, and extracellular environmental control of the development of phenotypes. A key result of such work is an account for the remarkable plasticity of organismal form in many species based on relatively minor changes in regulation of highly conserved genes and genetic processes. Accounting for behavioral plasticity is of similar potential interest but has received far less attention. Of particular interest is plasticity in communication systems, where human language represents an ultimate target for research. The present paper considers plasticity of language capabilities in a comparative framework, focusing attention on examples of a remarkable fact: Whereas there exist design features of mature human language that have never been observed to occur in nonhumans in the wild, many of these features can be developed to notable extents when nonhumans are enculturated through human training (especially with intensive social interaction). These examples of enculturated developmental plasticity across extremely diverse taxa suggest, consistent with the evo-devo theme of highly conserved processes in evolution, that human language is founded in part on cognitive capabilities that are indeed ancient and that even modern humans show self-organized emergence of many language capabilities in the context of rich enculturation, built on the special social/ecological history of the hominin line. Human culture can thus be seen as a regulatory system encouraging language development in the context of a cognitive background with many highly conserved features. PMID:27003391

Developmental Plasticity and Language: A Comparative Perspective.

PubMed

Griebel, Ulrike; Pepperberg, Irene M; Oller, D Kimbrough

2016-04-01

The growing field of evo-devo is increasingly demonstrating the complexity of steps involved in genetic, intracellular regulatory, and extracellular environmental control of the development of phenotypes. A key result of such work is an account for the remarkable plasticity of organismal form in many species based on relatively minor changes in regulation of highly conserved genes and genetic processes. Accounting for behavioral plasticity is of similar potential interest but has received far less attention. Of particular interest is plasticity in communication systems, where human language represents an ultimate target for research. The present paper considers plasticity of language capabilities in a comparative framework, focusing attention on examples of a remarkable fact: Whereas there exist design features of mature human language that have never been observed to occur in non-humans in the wild, many of these features can be developed to notable extents when non-humans are enculturated through human training (especially with intensive social interaction). These examples of enculturated developmental plasticity across extremely diverse taxa suggest, consistent with the evo-devo theme of highly conserved processes in evolution, that human language is founded in part on cognitive capabilities that are indeed ancient and that even modern humans show self-organized emergence of many language capabilities in the context of rich enculturation, built on the special social/ecological history of the hominin line. Human culture can thus be seen as a regulatory system encouraging language development in the context of a cognitive background with many highly conserved features. Copyright © 2016 Cognitive Science Society, Inc.

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 metabolites produced by Bacillus species are highly conserved, known compounds with important signaling roles in the physiology and development of this bacterium. Additionally, there is significant unique biosynthetic machinery distributed across the genus that might lead to new, unknown metabolites with diverse biological functions. Inspired by the findings of our genomic analysis, we speculate that the highly conserved alkylpyrones might have an important biological activity within this genus. We go on to validate this prediction by demonstrating that these natural products are developmental signals in Bacillus and act by inhibiting sporulation.

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.

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.

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

Characterization of the Role of a Highly Conserved Sequence in ATP Binding Cassette Transporter G (ABCG) Family in ABCG1 Stability, Oligomerization, and Trafficking

PubMed Central

2013-01-01

ATP-binding cassette transporter G1 (ABCG1) mediates cholesterol and oxysterol efflux onto lipidated lipoproteins and plays an important role in macrophage reverse cholesterol transport. Here, we identified a highly conserved sequence present in the five ABCG transporter family members. The conserved sequence is located between the nucleotide binding domain and the transmembrane domain and contains five amino acid residues from Asn at position 316 to Phe at position 320 in ABCG1 (NPADF). We found that cells expressing mutant ABCG1, in which Asn316, Pro317, Asp319, and Phe320 in the conserved sequence were replaced with Ala simultaneously, showed impaired cholesterol efflux activity compared with wild type ABCG1-expressing cells. A more detailed mutagenesis study revealed that mutation of Asn316 or Phe 320 to Ala significantly reduced cellular cholesterol and 7-ketocholesterol efflux conferred by ABCG1, whereas replacement of Pro317 or Asp319 with Ala had no detectable effect. To confirm the important role of Asn316 and Phe320, we mutated Asn316 to Asp (N316D) and Gln (N316Q), and Phe320 to Ile (F320I) and Tyr (F320Y). The mutant F320Y showed the same phenotype as wild type ABCG1. However, the efflux of cholesterol and 7-ketocholesterol was reduced in cells expressing ABCG1 mutant N316D, N316Q, or F320I compared with wild type ABCG1. Further, mutations N316Q and F320I impaired ABCG1 trafficking while having no marked effect on the stability and oligomerization of ABCG1. The mutant N316Q and F320I could not be transported to the cell surface efficiently. Instead, the mutant proteins were mainly localized intracellularly. Thus, these findings indicate that the two highly conserved amino acid residues, Asn and Phe, play an important role in ABCG1-dependent export of cellular cholesterol, mainly through the regulation of ABCG1 trafficking. PMID:24320932

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.

Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities.

PubMed

Mhuantong, Wuttichai; Charoensawan, Varodom; Kanokratana, Pattanop; Tangphatsornruang, Sithichoke; Champreda, Verawat

2015-01-01

As one of the most abundant agricultural wastes, sugarcane bagasse is largely under-exploited, but it possesses a great potential for the biofuel, fermentation, and cellulosic biorefinery industries. It also provides a unique ecological niche, as the microbes in this lignocellulose-rich environment thrive in relatively high temperatures (50°C) with varying microenvironments of aerobic surface to anoxic interior. The microbial community in bagasse thus presents a good resource for the discovery and characterization of new biomass-degrading enzymes; however, it remains largely unexplored. We have constructed a fosmid library of sugarcane bagasse and obtained the largest bagasse metagenome to date. A taxonomic classification of the bagasse metagenome reviews the predominance of Proteobacteria, which are also found in high abundance in other aerobic environments. Based on the functional characterization of biomass-degrading enzymes, we have demonstrated that the bagasse microbial community benefits from a large repertoire of lignocellulolytic enzymes, which allows them to digest different components of lignocelluoses into single molecule sugars. Comparative genomic analyses with other lignocellulolytic and non-lignocellulolytic metagenomes show that microbial communities are taxonomically separable by their aerobic "open" or anoxic "closed" environments. Importantly, a functional analysis of lignocellulose-active genes (based on the CAZy classifications) reveals core enzymes highly conserved within the lignocellulolytic group, regardless of their taxonomic compositions. Cellulases, in particular, are markedly more pronounced compared to the non-lignocellulolytic group. In addition to the core enzymes, the bagasse fosmid library also contains some uniquely enriched glycoside hydrolases, as well as a large repertoire of the newly defined auxiliary activity proteins. Our study demonstrates a conservation and diversification of carbohydrate-active genes among diverse microbial species in different biomass-degrading niches, and signifies the importance of taking a global approach to functionally investigate a microbial community as a whole, as compared to focusing on individual organisms.

Exploring corrections to the Optomechanical Hamiltonian.

PubMed

Sala, Kamila; Tufarelli, Tommaso

2018-06-14

We compare two approaches for deriving corrections to the "linear model" of cavity optomechanics, in order to describe effects that are beyond first order in the radiation pressure coupling. In the regime where the mechanical frequency is much lower than the cavity one, we compare: (I) a widely used phenomenological Hamiltonian conserving the photon number; (II) a two-mode truncation of C. K. Law's microscopic model, which we take as the "true" system Hamiltonian. While these approaches agree at first order, the latter model does not conserve the photon number, resulting in challenging computations. We find that approach (I) allows for several analytical predictions, and significantly outperforms the linear model in our numerical examples. Yet, we also find that the phenomenological Hamiltonian cannot fully capture all high-order corrections arising from the C. K. Law model.

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 change. PMID:18302999

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 proteins contributed to the diversification of animal body organization.

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…

Ovarian Conservation and Overall Survival in Young Women With Early-Stage Cervical Cancer.

PubMed

Matsuo, Koji; Machida, Hiroko; Shoupe, Donna; Melamed, Alexander; Muderspach, Laila I; Roman, Lynda D; Wright, Jason D

2017-01-01

To identify predictors of ovarian conservation at hysterectomy and to examine the association of ovarian conservation and survival of young women with early-stage cervical cancer. This is a retrospective cohort study using the Surveillance, Epidemiology, and End Results Program to identify hysterectomy-based surgically treated patients with stage I cervical cancer diagnosed between 1983 and 2012 (N=16,511). Multivariable models were used to identify independent factors associated with ovarian conservation. Among the subgroup of 9,419 women younger than 50 years of age with stage I disease, survival outcomes and causes of death were examined for 3,908 (41.5%) women who underwent ovarian conservation at hysterectomy without radiotherapy. On multivariable analysis, age younger than 50 years, stage IA disease, and squamous histology were independent factors associated with ovarian conservation (all, P<.001). Among 5,526 women younger than 50 years of age with stage IA disease who underwent hysterectomy without radiotherapy, overall survival was significantly higher in patients undergoing ovarian conservation than in those undergoing oophorectomy (20-year rate, 93.5% compared with 86.8%, P<.001); cervical cancer-specific survival was similar between the patients who underwent ovarian conservation and those who underwent oophorectomy (98.8% compared with 97.8%, P=.12). On multivariable analysis, ovarian conservation remained an independent prognostic factor for improved overall survival (adjusted hazard ratio 0.63, 95% confidence interval [CI] 0.49-0.82, P=.001) and was independently associated with lower cumulative risks of death resulting from cardiovascular disease (20-year cumulative rate, 1.2% compared with 3.3%, adjusted hazard ratio 0.47, 95% CI 0.26-0.86, P=.014) and other chronic disease (0.5% compared with 1.4%, adjusted hazard ratio 0.24, 95% CI 0.09-0.65, P=.005) compared with oophorectomy. Both cervical cancer-specific survival (20-year rate, 93.1% compared with 92.0%, P=.37) and overall survival (86.7% compared with 84.6%, P=.12) were similar between ovarian conservation and oophorectomy among 3,893 women younger than 50 years of age with stage IB disease who underwent hysterectomy without radiotherapy. Among young women with stage IA cervical cancer, ovarian conservation at hysterectomy is associated with decreased all-cause mortality including death resulting from cardiovascular disease and other chronic diseases.

Biodiversity at risk under future cropland expansion and intensification.

PubMed

Kehoe, Laura; Romero-Muñoz, Alfredo; Polaina, Ester; Estes, Lyndon; Kreft, Holger; Kuemmerle, Tobias

2017-08-01

Agriculture is the leading driver of biodiversity loss. However, its future impact on biodiversity remains unclear, especially because agricultural intensification is often neglected, and high path-dependency is assumed when forecasting agricultural development-although the past suggests that shock events leading to considerable agricultural change occur frequently. Here, we investigate the possible impacts on biodiversity of pathways of expansion and intensification. Our pathways are not built to reach equivalent production targets, and therefore they should not be directly compared; they instead highlight areas at risk of high biodiversity loss across the entire option space of possible agricultural change. Based on an extensive database of biodiversity responses to agriculture, we find 30% of species richness and 31% of species abundances potentially lost because of agricultural expansion across the Amazon and Afrotropics. Only 21% of high-risk expansion areas in the Afrotropics overlap with protected areas (compared with 43% of the Neotropics). Areas at risk of biodiversity loss from intensification are found in India, Eastern Europe and the Afromontane region (7% species richness, 13% abundance loss). Many high-risk regions are not adequately covered by conservation prioritization schemes, and have low national conservation spending and high agricultural growth. Considering rising agricultural demand, we highlight areas where timely land-use planning may proactively mitigate biodiversity loss.

Multiplexed microsatellite recovery using massively parallel sequencing

Treesearch

T.N. Jennings; B.J. Knaus; T.D. Mullins; S.M. Haig; R.C. Cronn

2011-01-01

Conservation and management of natural populations requires accurate and inexpensive genotyping methods. Traditional microsatellite, or simple sequence repeat (SSR), marker analysis remains a popular genotyping method because of the comparatively low cost of marker development, ease of analysis and high power of genotype discrimination. With the availability of...

Restoration of degraded arid farmland at Project Wadi Attir: Impact of conservation on biological productivity and soil organic matter

NASA Astrophysics Data System (ADS)

Mor-Mussery, Amir; Helman, David; Ben Eli, Michael; Leu, Stefan

2017-04-01

The Israeli Negev Desert, as most Mediterranean drylands, is profoundly degraded. We have been documenting degradation and successful rehabilitation approaches in recent research, aiming at maximizing environmental and economic benefits while restoring healthy dryland soils and perennial vegetation to act as carbon sinks. These methods have been implemented for rehabilitation of Project Wadi Attir's. 50 hectares of heavily degraded farmland suffering from intensive soil erosion (expressed in dense gullies net and massive overland flow). Project Wadi Attir is a groundbreaking initiative of the Bedouin community in the Negev, for establishing a model sustainable agricultural operation. The project was initiated by the US-based Sustainability Laboratory and the Hura Municipal Council. The project is designed to demonstrate implementation of holistic sustainability principles developed by The Lab. The project's ecosystem restoration component involves site development, erosion control, soil conservation and improvement, planting of native and agroforestry trees, together with conservation and protection of biodiversity hotspots and avoiding grazing have, within three years, revealed the high biodiversity and productivity potential of this arid/semi-arid landscape. A number of shrublands and loess plots were subject to strict conservation, avoiding tilling and grazing. Soil fertility, productivity and biodiversity of these conserved plots inside the farm boundaries was compared to similar unprotected plots outside the farm fences by sampling in the field and by using satellite imaging. Our findings indicate a gradual improvement of SOM content specifically in the conserved shrubland area. Water infiltration, herbaceous biomass productivity and ants' activity of the protected plots also significantly increased within 3 years compared to the unprotected control areas. Starting from similar soil organic matter content in 2013 (3.3%) in the rocky slopes, in 2016 1% higher SOM was measured inside the farm vs. outside (4.5% compared to 3.5%, respectively). In spring 2014 herbaceous biomass production was similar in both areas (0.05 Kg per m2), while in spring 2016 0.25 Kg per m2 were measured in the pedestal inside the farm compared to 0.06 Kg per m2 outside were observed. Consistent but less dramatic, changes were observed in the loess areas inside the farm with a productivity difference of 1.1 inside compared to 0.19 Kg per m2 outside in 2016 as compared to 0.05 Kg per m2 observed in both areas in 2013. Our results indicate that soil conservation together with proper land management and protection of biodiversity hotspots will enable sustainable agricultural management in degraded drylands all over the globe under significant gains in productivity, biodiversity and carbon sequestration.

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

PubMed

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

2016-01-19

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

PDB-wide identification of biological assemblies from conserved quaternary structure geometry.

PubMed

Dey, Sucharita; Ritchie, David W; Levy, Emmanuel D

2018-01-01

Protein structures are key to understanding biomolecular mechanisms and diseases, yet their interpretation is hampered by limited knowledge of their biologically relevant quaternary structure (QS). A critical challenge in inferring QS information from crystallographic data is distinguishing biological interfaces from fortuitous crystal-packing contacts. Here, we tackled this problem by developing strategies for aligning and comparing QS states across both homologs and data repositories. QS conservation across homologs proved remarkably strong at predicting biological relevance and is implemented in two methods, QSalign and anti-QSalign, for annotating homo-oligomers and monomers, respectively. QS conservation across repositories is implemented in QSbio (http://www.QSbio.org), which approaches the accuracy of manual curation and allowed us to predict >100,000 QS states across the Protein Data Bank. Based on this high-quality data set, we analyzed pairs of structurally conserved interfaces, and this analysis revealed a striking plasticity whereby evolutionary distant interfaces maintain similar interaction geometries through widely divergent chemical properties.

A comprehensive analysis of three Asiatic black bear mitochondrial genomes (subspecies ussuricus, formosanus and mupinensis), with emphasis on the complete mtDNA sequence of Ursus thibetanus ussuricus (Ursidae).

PubMed

Hwang, Dae-Sik; Ki, Jang-Seu; Jeong, Dong-Hyuk; Kim, Bo-Hyun; Lee, Bae-Keun; Han, Sang-Hoon; Lee, Jae-Seong

2008-08-01

In the present paper, we describe the mitochondrial genome sequence of the Asiatic black bear (Ursus thibetanus ussuricus) with particular emphasis on the control region (CR), and compared with mitochondrial genomes on molecular relationships among the bears. The mitochondrial genome sequence of U. thibetanus ussuricus was 16,700 bp in size with mostly conserved structures (e.g. 13 protein-coding, two rRNA genes, 22 tRNA genes). The CR consisted of several typical conserved domains such as F, E, D, and C boxes, and a conserved sequence block. Nucleotide sequences and the repeated motifs in the CR were different among the bear species, and their copy numbers were also variable according to populations, even within F1 generations of U. thibetanus ussuricus. Comparative analyses showed that the CR D1 region was highly informative for the discrimination of the bear family. These findings suggest that nucleotide sequences of both repeated motifs and CR D1 in the bear family are good markers for species discriminations.

Obtaining accurate glucose measurements from wild animals under field conditions: comparing a hand held glucometer with a standard laboratory technique in grey seals

PubMed Central

Turner, Lucy M.; Millward, Sebastian; Moss, Simon E. W.; Hall, Ailsa J.

2017-01-01

Abstract Glucose is an important metabolic fuel and circulating levels are tightly regulated in most mammals, but can drop when body fuel reserves become critically low. Glucose is mobilized rapidly from liver and muscle during stress in response to increased circulating cortisol. Blood glucose levels can thus be of value in conservation as an indicator of nutritional status and may be a useful, rapid assessment marker for acute or chronic stress. However, seals show unusual glucose regulation: circulating levels are high and insulin sensitivity is limited. Accurate blood glucose measurement is therefore vital to enable meaningful health and physiological assessments in captive, wild or rehabilitated seals and to explore its utility as a marker of conservation relevance in these animals. Point-of-care devices are simple, portable, relatively cheap and use less blood compared with traditional sampling approaches, making them useful in conservation-related monitoring. We investigated the accuracy of a hand-held glucometer for ‘instant’ field measurement of blood glucose, compared with blood drawing followed by laboratory testing, in wild grey seals (Halichoerus grypus), a species used as an indicator for Good Environmental Status in European waters. The glucometer showed high precision, but low accuracy, relative to laboratory measurements, and was least accurate at extreme values. It did not provide a reliable alternative to plasma analysis. Poor correlation between methods may be due to suboptimal field conditions, greater and more variable haematocrit, faster erythrocyte settling rate and/or lipaemia in seals. Glucometers must therefore be rigorously tested before use in new species and demographic groups. Sampling, processing and glucose determination methods have major implications for conclusions regarding glucose regulation, and health assessment in seals generally, which is important in species of conservation concern and in development of circulating glucose as a marker of stress or nutritional state for use in management and monitoring. PMID:28413683

A Comparative Transcriptomic Analysis Reveals Conserved Features of Stem Cell Pluripotency in Planarians and Mammals

PubMed Central

Labbé, Roselyne M.; Irimia, Manuel; Currie, Ko W.; Lin, Alexander; Zhu, Shu Jun; Brown, David D.R.; Ross, Eric J.; Voisin, Veronique; Bader, Gary D.; Blencowe, Benjamin J.; Pearson, Bret J.

2014-01-01

Many long-lived species of animals require the function of adult stem cells throughout their lives. However, the transcriptomes of stem cells in invertebrates and vertebrates have not been compared, and consequently, ancestral regulatory circuits that control stem cell populations remain poorly defined. In this study, we have used data from high-throughput RNA sequencing to compare the transcriptomes of pluripotent adult stem cells from planarians with the transcriptomes of human and mouse pluripotent embryonic stem cells. From a stringently defined set of 4,432 orthologs shared between planarians, mice and humans, we identified 123 conserved genes that are ≥5-fold differentially expressed in stem cells from all three species. Guided by this gene set, we used RNAi screening in adult planarians to discover novel stem cell regulators, which we found to affect the stem cell-associated functions of tissue homeostasis, regeneration, and stem cell maintenance. Examples of genes that disrupted these processes included the orthologs of TBL3, PSD12, TTC27, and RACK1. From these analyses, we concluded that by comparing stem cell transcriptomes from diverse species, it is possible to uncover conserved factors that function in stem cell biology. These results provide insights into which genes comprised the ancestral circuitry underlying the control of stem cell self-renewal and pluripotency. PMID:22696458

Optimization in the utility maximization framework for conservation planning: a comparison of solution procedures in a study of multifunctional agriculture

PubMed Central

Stoms, David M.; Davis, Frank W.

2014-01-01

Quantitative methods of spatial conservation prioritization have traditionally been applied to issues in conservation biology and reserve design, though their use in other types of natural resource management is growing. The utility maximization problem is one form of a covering problem where multiple criteria can represent the expected social benefits of conservation action. This approach allows flexibility with a problem formulation that is more general than typical reserve design problems, though the solution methods are very similar. However, few studies have addressed optimization in utility maximization problems for conservation planning, and the effect of solution procedure is largely unquantified. Therefore, this study mapped five criteria describing elements of multifunctional agriculture to determine a hypothetical conservation resource allocation plan for agricultural land conservation in the Central Valley of CA, USA. We compared solution procedures within the utility maximization framework to determine the difference between an open source integer programming approach and a greedy heuristic, and find gains from optimization of up to 12%. We also model land availability for conservation action as a stochastic process and determine the decline in total utility compared to the globally optimal set using both solution algorithms. Our results are comparable to other studies illustrating the benefits of optimization for different conservation planning problems, and highlight the importance of maximizing the effectiveness of limited funding for conservation and natural resource management. PMID:25538868

Optimization in the utility maximization framework for conservation planning: a comparison of solution procedures in a study of multifunctional agriculture

USGS Publications Warehouse

Kreitler, Jason R.; Stoms, David M.; Davis, Frank W.

2014-01-01

Quantitative methods of spatial conservation prioritization have traditionally been applied to issues in conservation biology and reserve design, though their use in other types of natural resource management is growing. The utility maximization problem is one form of a covering problem where multiple criteria can represent the expected social benefits of conservation action. This approach allows flexibility with a problem formulation that is more general than typical reserve design problems, though the solution methods are very similar. However, few studies have addressed optimization in utility maximization problems for conservation planning, and the effect of solution procedure is largely unquantified. Therefore, this study mapped five criteria describing elements of multifunctional agriculture to determine a hypothetical conservation resource allocation plan for agricultural land conservation in the Central Valley of CA, USA. We compared solution procedures within the utility maximization framework to determine the difference between an open source integer programming approach and a greedy heuristic, and find gains from optimization of up to 12%. We also model land availability for conservation action as a stochastic process and determine the decline in total utility compared to the globally optimal set using both solution algorithms. Our results are comparable to other studies illustrating the benefits of optimization for different conservation planning problems, and highlight the importance of maximizing the effectiveness of limited funding for conservation and natural resource management.

Comparing impacts between formal and informal recreational trails.

PubMed

Pickering, Catherine Marina; Norman, Patrick

2017-05-15

Globally there are hundreds of thousands of kilometres of recreational trails traversing natural areas of high conservation value: but what are their impacts and do impacts differ among trails? We compared the effects of four common types of recreational trails [(1) narrow and (2) medium width informal bare earth trails and (3) gravel and (4) tarmac/concrete formal trails] on vegetation adjacent to trails in a high conservation value plant community that is popular for mountain biking and hiking in Australia. Plant species composition was recorded in quadrats along the edge of the four types of trails and in control sites away from trails. Vegetation cover, the cover of individual growth forms, and species richness along the edges of all four types of trails were similar to the controls, although the wider trails affected plant composition, with the tarmac and gravel trails favouring different species. With very few comparative studies, more research is required to allow managers and researchers to directly compare differences in the severity and types of impacts on vegetation among trails. In the meantime, limiting damage to vegetation on the edge of hardened trails during construction, use and maintenance is important, and hardening trails may not always be appropriate. Copyright © 2016. Published by Elsevier Ltd.

Mapping the ecological dimensions and potential distributions of endangered relic shrubs in western Ordos biodiversity center

PubMed Central

Zhu, Geng-Ping; Li, Hui-Qi; Zhao, Li; Man, Liang; Liu, Qiang

2016-01-01

Potential distributions of endemic relic shrubs in western Ordos were poorly mapped, which hindered our implementation of proper conservation. Here we investigated the applicability of ecological niche modeling for endangered relic shrubs to detect areas of priority for biodiversity conservation and analyze differences in ecological niche spaces used by relic shrubs. We applied ordination and niche modeling techniques to assess main environmental drivers of five endemic relic shrubs in western Ordos, namely, Ammopiptanthus mongolicus, Amygdalus mongolica, Helianthemum songaricum, Potaninia mongolica, and Tetraena mongolica. We calculated niche overlap metrics in gridded environmental spaces and compared geographical projections of ecological niches to determine similarities and differences of niches occupied by relic shrubs. All studied taxa presented different responses to environmental factors, which resulted in a unique combination of niche conditions. Precipitation availability and soil quality characteristics play important roles in the distributions of most shrubs. Each relic shrub is constrained by a unique set of environmental conditions, the distribution of one species cannot be implied by the distribution of another, highlighting the inadequacy of one-fits-all type of conservation measure. Our stacked habitat suitability maps revealed regions around Yellow River, which are highly suitable for most species, thereby providing high conservation value. PMID:27199260

Mapping the ecological dimensions and potential distributions of endangered relic shrubs in western Ordos biodiversity center.

PubMed

Zhu, Geng-Ping; Li, Hui-Qi; Zhao, Li; Man, Liang; Liu, Qiang

2016-05-20

Potential distributions of endemic relic shrubs in western Ordos were poorly mapped, which hindered our implementation of proper conservation. Here we investigated the applicability of ecological niche modeling for endangered relic shrubs to detect areas of priority for biodiversity conservation and analyze differences in ecological niche spaces used by relic shrubs. We applied ordination and niche modeling techniques to assess main environmental drivers of five endemic relic shrubs in western Ordos, namely, Ammopiptanthus mongolicus, Amygdalus mongolica, Helianthemum songaricum, Potaninia mongolica, and Tetraena mongolica. We calculated niche overlap metrics in gridded environmental spaces and compared geographical projections of ecological niches to determine similarities and differences of niches occupied by relic shrubs. All studied taxa presented different responses to environmental factors, which resulted in a unique combination of niche conditions. Precipitation availability and soil quality characteristics play important roles in the distributions of most shrubs. Each relic shrub is constrained by a unique set of environmental conditions, the distribution of one species cannot be implied by the distribution of another, highlighting the inadequacy of one-fits-all type of conservation measure. Our stacked habitat suitability maps revealed regions around Yellow River, which are highly suitable for most species, thereby providing high conservation value.

The High Priests of the Black Academic Right.

ERIC Educational Resources Information Center

Megalli, Mark

1995-01-01

Examines and compares the new black conservative thinkers who are leading the opposition to affirmative action and other government interventions designed to advance the educational position of blacks. The author reviews such major figures as Shelby Steele, Glenn C. Loury, Walter E. Williams, William Julius Wilson, and Thomas Sowell. (GR)

Nucleotide sequence of a complementary DNA encoding pea cytosolic copper/zinc superoxide dismutase. [Pisum sativum L

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

White, D.A.; Zilinskas, B.A.

1991-08-01

The authors now report the nucleotide sequence of the cytosolic Cu/Zn SOD cloned from a {lambda}gt11 cDNA library constructed from mRNA extracted from leaves of 7- to 10-d pea seedlings (Pisum sativum L.). The clone was isolated using a 22-base synthetic oligonucleotide complementary to the amino acid sequence CGIIGLQG. This sequence, found at the protein's carboxy terminus, is highly conserved among plant cytosolic Cu/Zn SODs but not chloroplastic Cu/Zn SODs. The 738-base pair sequence contains an open reading frame specifying 152 codons and a predicted M{sub r} of 18,024 D. The deduced amino acid sequence is highly homologous (79-82% identity)more » with the sequences of other known plant cytosolic Cu/Zn SODs but less highly conserved (63-65%) when compared with several chloroplastic Cu/Zn SODs including pea (10).« less

Does the evolutionary conservation of microsatellite loci imply function?

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

Shriver, M.D.; Deka, R.; Ferrell, R.E.

Microsatellites are highly polymorphic tandem arrays of short (1-6 bp) sequence motifs which have been found widely distributed in the genomes of all eukaryotes. We have analyzed allele frequency data on 16 microsatellite loci typed in the great apes (human, chimp, orangutan, and gorilla). The majority of these loci (13) were isolated from human genomic libraries; three were cloned from chimpanzee genomic DNA. Most of these loci are not only present in all apes species, but are polymorphic with comparable levels of heterozygosity and have alleles which overlap in size. The extent of divergence of allele frequencies among these fourmore » species were studies using the stepwise-weighted genetic distance (Dsw), which was previously shown to conform to linearity with evolutionary time since divergence for loci where mutations exist in a stepwise fashion. The phylogenetic tree of the great apes constructed from this distance matrix was consistent with the expected topology, with a high bootstrap confidence (82%) for the human/chimp clade. However, the allele frequency distributions of these species are 10 times more similar to each other than expected when they were calibrated with a conservative estimate of the time since separation of humans and the apes. These results are in agreement with sequence-based surveys of microsatellites which have demonstrated that they are highly (90%) conserved over short periods of evolutionary time (< 10 million years) and moderately (30%) conserved over long periods of evolutionary time (> 60-80 million years). This evolutionary conservation has prompted some authors to speculate that there are functional constraints on microsatellite loci. In contrast, the presence of directional bias of mutations with constraints and/or selection against aberrant sized alleles can explain these results.« less

Comparative analysis of the small RNA transcriptomes of Pinus contorta and Oryza sativa

PubMed Central

Morin, Ryan D.; Aksay, Gozde; Dolgosheina, Elena; Ebhardt, H. Alexander; Magrini, Vincent; Mardis, Elaine R.; Sahinalp, S. Cenk; Unrau, Peter J.

2008-01-01

The diversity of microRNAs and small-interfering RNAs has been extensively explored within angiosperms by focusing on a few key organisms such as Oryza sativa and Arabidopsis thaliana. A deeper division of the plants is defined by the radiation of the angiosperms and gymnosperms, with the latter comprising the commercially important conifers. The conifers are expected to provide important information regarding the evolution of highly conserved small regulatory RNAs. Deep sequencing provides the means to characterize and quantitatively profile small RNAs in understudied organisms such as these. Pyrosequencing of small RNAs from O. sativa revealed, as expected, ∼21- and ∼24-nt RNAs. The former contained known microRNAs, and the latter largely comprised intergenic-derived sequences likely representing heterochromatin siRNAs. In contrast, sequences from Pinus contorta were dominated by 21-nt small RNAs. Using a novel sequence-based clustering algorithm, we identified sequences belonging to 18 highly conserved microRNA families in P. contorta as well as numerous clusters of conserved small RNAs of unknown function. Using multiple methods, including expressed sequence folding and machine learning algorithms, we found a further 53 candidate novel microRNA families, 51 appearing specific to the P. contorta library. In addition, alignment of small RNA sequences to the O. sativa genome revealed six perfectly conserved classes of small RNA that included chloroplast transcripts and specific types of genomic repeats. The conservation of microRNAs and other small RNAs between the conifers and the angiosperms indicates that important RNA silencing processes were highly developed in the earliest spermatophytes. Genomic mapping of all sequences to the O. sativa genome can be viewed at http://microrna.bcgsc.ca/cgi-bin/gbrowse/rice_build_3/. PMID:18323537

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 development. Our results offer critical insights for current conservation and strategic land-use planning in China. The approach is transferable and easy to implement by end-users, and applicable for national- and local-scale systematic conservation prioritization practices.

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 development. Our results offer critical insights for current conservation and strategic land-use planning in China. The approach is transferable and easy to implement by end-users, and applicable for national- and local-scale systematic conservation prioritization practices. PMID:25072933

Social Network Analysis Identifies Key Participants in Conservation Development.

PubMed

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

2018-05-01

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

Non-oscillatory central differencing for hyperbolic conservation laws

NASA Technical Reports Server (NTRS)

Nessyahu, Haim; Tadmor, Eitan

1988-01-01

Many of the recently developed high resolution schemes for hyperbolic conservation laws are based on upwind differencing. The building block for these schemes is the averaging of an appropriate Godunov solver; its time consuming part involves the field-by-field decomposition which is required in order to identify the direction of the wind. Instead, the use of the more robust Lax-Friedrichs (LxF) solver is proposed. The main advantage is simplicity: no Riemann problems are solved and hence field-by-field decompositions are avoided. The main disadvantage is the excessive numerical viscosity typical to the LxF solver. This is compensated for by using high-resolution MUSCL-type interpolants. Numerical experiments show that the quality of results obtained by such convenient central differencing is comparable with those of the upwind schemes.

The conservation value of South East Asia's highly degraded forests: evidence from leaf-litter ants

PubMed Central

Woodcock, Paul; Edwards, David P.; Fayle, Tom M.; Newton, Rob J.; Khen, Chey Vun; Bottrell, Simon H.; Hamer, Keith C.

2011-01-01

South East Asia is widely regarded as a centre of threatened biodiversity owing to extensive logging and forest conversion to agriculture. In particular, forests degraded by repeated rounds of intensive logging are viewed as having little conservation value and are afforded meagre protection from conversion to oil palm. Here, we determine the biological value of such heavily degraded forests by comparing leaf-litter ant communities in unlogged (natural) and twice-logged forests in Sabah, Borneo. We accounted for impacts of logging on habitat heterogeneity by comparing species richness and composition at four nested spatial scales, and examining how species richness was partitioned across the landscape in each habitat. We found that twice-logged forest had fewer species occurrences, lower species richness at small spatial scales and altered species composition compared with natural forests. However, over 80 per cent of species found in unlogged forest were detected within twice-logged forest. Moreover, greater species turnover among sites in twice-logged forest resulted in identical species richness between habitats at the largest spatial scale. While two intensive logging cycles have negative impacts on ant communities, these degraded forests clearly provide important habitat for numerous species and preventing their conversion to oil palm and other crops should be a conservation priority. PMID:22006966

Ants as a measure of effectiveness of habitat conservation planning in southern California

USGS Publications Warehouse

Mitrovich, Milan J.; Matsuda, Tritia; Pease, Krista H.; Fisher, Robert N.

2010-01-01

In the United States multispecies habitat conservation plans were meant to be the solution to conflicts between economic development and protection of biological diversity. Although now widely applied, questions exist concerning the scientific credibility of the conservation planning process and effectiveness of the plans. We used ants to assess performance of one of the first regional conservation plans developed in the United States, the Orange County Central-Coastal Natural Community Conservation Plan (NCCP), in meeting its broader conservation objectives of biodiversity and ecosystem-level protection. We collected pitfall data on ants for over 3 years on 172 sites established across a network of conservation lands in coastal southern California. Although recovered native ant diversity for the study area was high, site-occupancy models indicated the invasive and ecologically disruptive Argentine ant ( Linepithema humile) was present at 29% of sites, and sites located within 200 m of urban and agricultural areas were more likely to have been invaded. Within invaded sites, native ants were largely displaced, and their median species richness declined by more than 60% compared with uninvaded sites. At the time of planning, 24% of the 15,133-ha reserve system established by Orange County NCCP fell within 200 m of an urban or agricultural edge. With complete build out of lands surrounding the reserve, the proportion of the reserve system vulnerable to invasion will grow to 44%. Our data indicate that simply protecting designated areas from development is not enough. If habitat conservation plans are to fulfill their conservation promise of ecosystem-level protection, a more-integrated and systematic approach to the process of habitat conservation planning is needed.

Characterization and Comparative Profiling of MiRNA Transcriptomes in Bighead Carp and Silver Carp

PubMed Central

Chi, Wei; Tong, Chaobo; Gan, Xiaoni; He, Shunping

2011-01-01

MicroRNAs (miRNAs) are small non-coding RNA molecules that are processed from large ‘hairpin’ precursors and function as post-transcriptional regulators of target genes. Although many individual miRNAs have recently been extensively studied, there has been very little research on miRNA transcriptomes in teleost fishes. By using high throughput sequencing technology, we have identified 167 and 166 conserved miRNAs (belonging to 108 families) in bighead carp (Hypophthalmichthys nobilis) and silver carp (Hypophthalmichthys molitrix), respectively. We compared the expression patterns of conserved miRNAs by means of hierarchical clustering analysis and log2 ratio. Results indicated that there is not a strong correlation between sequence conservation and expression conservation, most of these miRNAs have similar expression patterns. However, high expression differences were also identified for several individual miRNAs. Several miRNA* sequences were also found in our dataset and some of them may have regulatory functions. Two computational strategies were used to identify novel miRNAs from un-annotated data in the two carps. A first strategy based on zebrafish genome, identified 8 and 22 novel miRNAs in bighead carp and silver carp, respectively. We postulate that these miRNAs should also exist in the zebrafish, but the methodologies used have not allowed for their detection. In the second strategy we obtained several carp-specific miRNAs, 31 in bighead carp and 32 in silver carp, which showed low expression. Gain and loss of family members were observed in several miRNA families, which suggests that duplication of animal miRNA genes may occur through evolutionary processes which are similar to the protein-coding genes. PMID:21858165

Exposing ecological and economic costs of the research-implementation gap and compromises in decision making.

PubMed

Kareksela, Santtu; Moilanen, Atte; Ristaniemi, Olli; Välivaara, Reima; Kotiaho, Janne S

2018-02-01

The frequently discussed gap between conservation science and practice is manifest in the gap between spatial conservation prioritization plans and their implementation. We analyzed the research-implementation gap of one zoning case by comparing results of a spatial prioritization analysis aimed at avoiding ecological impact of peat mining in a regional zoning process with the final zoning plan. We examined the relatively complex planning process to determine the gaps among research, zoning, and decision making. We quantified the ecological costs of the differing trade-offs between ecological and socioeconomic factors included in the different zoning suggestions by comparing the landscape-level loss of ecological features (species occurrences, habitat area, etc.) between the different solutions for spatial allocation of peat mining. We also discussed with the scientists and planners the reasons for differing zoning suggestions. The implemented plan differed from the scientists suggestion in that its focus was individual ecological features rather than all the ecological features for which there were data; planners and decision makers considered effects of peat mining on areas not included in the prioritization analysis; zoning was not truly seen as a resource-allocation process and not emphasized in general minimizing ecological losses while satisfying economic needs (peat-mining potential); and decision makers based their prioritization of sites on site-level information showing high ecological value and on single legislative factors instead of finding a cost-effective landscape-level solution. We believe that if the zoning and decision-making processes are very complex, then the usefulness of science-based prioritization tools is likely to be reduced. Nevertheless, we found that high-end tools were useful in clearly exposing trade-offs between conservation and resource utilization. © 2017 Society for Conservation Biology.

Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens

PubMed Central

Naz, Sadia; Ngo, Tony; Farooq, Umar

2017-01-01

Background The rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for Disease Prevention and Control have been considered a major threat due to the rise in nosocomial infections. Here, we compared putative drug binding pockets of twelve essential and mostly conserved metabolic enzymes in numerous bacterial pathogens including those of the ESKAPE group and Mycobacterium tuberculosis. The comparative analysis will provide guidelines for the likelihood of transferability of the inhibitors from one species to another. Methods Nine bacterial species including six ESKAPE pathogens, Mycobacterium tuberculosis along with Mycobacterium smegmatis and Eschershia coli, two non-pathogenic bacteria, have been selected for drug binding pocket analysis of twelve essential enzymes. The amino acid sequences were obtained from Uniprot, aligned using ICM v3.8-4a and matched against the Pocketome encyclopedia. We used known co-crystal structures of selected target enzyme orthologs to evaluate the location of their active sites and binding pockets and to calculate a matrix of pairwise sequence identities across each target enzyme across the different species. This was used to generate sequence maps. Results High sequence identity of enzyme binding pockets, derived from experimentally determined co-crystallized structures, was observed among various species. Comparison at both full sequence level and for drug binding pockets of key metabolic enzymes showed that binding pockets are highly conserved (sequence similarity up to 100%) among various ESKAPE pathogens as well as Mycobacterium tuberculosis. Enzymes orthologs having conserved binding sites may have potential to interact with inhibitors in similar way and might be helpful for design of similar class of inhibitors for a particular species. The derived pocket alignments and distance-based maps provide guidelines for drug discovery and repurposing. In addition they also provide recommendations for the relevant model bacteria that may be used for initial drug testing. Discussion Comparing ligand binding sites through sequence identity calculation could be an effective approach to identify conserved orthologs as drug binding pockets have shown higher level of conservation among various species. By using this approach we could avoid the problems associated with full sequence comparison. We identified essential metabolic enzymes among ESKAPE pathogens that share high sequence identity in their putative drug binding pockets (up to 100%), of which known inhibitors can potentially antagonize these identical pockets in the various species in a similar manner. PMID:28948099

Analysis of drug binding pockets and repurposing opportunities for twelve essential enzymes of ESKAPE pathogens.

PubMed

Naz, Sadia; Ngo, Tony; Farooq, Umar; Abagyan, Ruben

2017-01-01

The rapid increase in antibiotic resistance by various bacterial pathogens underlies the significance of developing new therapies and exploring different drug targets. A fraction of bacterial pathogens abbreviated as ESKAPE by the European Center for Disease Prevention and Control have been considered a major threat due to the rise in nosocomial infections. Here, we compared putative drug binding pockets of twelve essential and mostly conserved metabolic enzymes in numerous bacterial pathogens including those of the ESKAPE group and Mycobacterium tuberculosis . The comparative analysis will provide guidelines for the likelihood of transferability of the inhibitors from one species to another. Nine bacterial species including six ESKAPE pathogens, Mycobacterium tuberculosis along with Mycobacterium smegmatis and Eschershia coli , two non-pathogenic bacteria, have been selected for drug binding pocket analysis of twelve essential enzymes. The amino acid sequences were obtained from Uniprot, aligned using ICM v3.8-4a and matched against the Pocketome encyclopedia. We used known co-crystal structures of selected target enzyme orthologs to evaluate the location of their active sites and binding pockets and to calculate a matrix of pairwise sequence identities across each target enzyme across the different species. This was used to generate sequence maps. High sequence identity of enzyme binding pockets, derived from experimentally determined co-crystallized structures, was observed among various species. Comparison at both full sequence level and for drug binding pockets of key metabolic enzymes showed that binding pockets are highly conserved (sequence similarity up to 100%) among various ESKAPE pathogens as well as Mycobacterium tuberculosis . Enzymes orthologs having conserved binding sites may have potential to interact with inhibitors in similar way and might be helpful for design of similar class of inhibitors for a particular species. The derived pocket alignments and distance-based maps provide guidelines for drug discovery and repurposing. In addition they also provide recommendations for the relevant model bacteria that may be used for initial drug testing. Comparing ligand binding sites through sequence identity calculation could be an effective approach to identify conserved orthologs as drug binding pockets have shown higher level of conservation among various species. By using this approach we could avoid the problems associated with full sequence comparison. We identified essential metabolic enzymes among ESKAPE pathogens that share high sequence identity in their putative drug binding pockets (up to 100%), of which known inhibitors can potentially antagonize these identical pockets in the various species in a similar manner.

Using environmental heterogeneity to plan for sea-level rise.

PubMed

Hunter, Elizabeth A; Nibbelink, Nathan P

2017-12-01

Environmental heterogeneity is increasingly being used to select conservation areas that will provide for future biodiversity under a variety of climate scenarios. This approach, termed conserving nature's stage (CNS), assumes environmental features respond to climate change more slowly than biological communities, but will CNS be effective if the stage were to change as rapidly as the climate? We tested the effectiveness of using CNS to select sites in salt marshes for conservation in coastal Georgia (U.S.A.), where environmental features will change rapidly as sea level rises. We calculated species diversity based on distributions of 7 bird species with a variety of niches in Georgia salt marshes. Environmental heterogeneity was assessed across six landscape gradients (e.g., elevation, salinity, and patch area). We used 2 approaches to select sites with high environmental heterogeneity: site complementarity (environmental diversity [ED]) and local environmental heterogeneity (environmental richness [ER]). Sites selected based on ER predicted present-day species diversity better than randomly selected sites (up to an 8.1% improvement), were resilient to areal loss from SLR (1.0% average areal loss by 2050 compared with 0.9% loss of randomly selected sites), and provided habitat to a threatened species (0.63 average occupancy compared with 0.6 average occupancy of randomly selected sites). Sites selected based on ED predicted species diversity no better or worse than random and were not resilient to SLR (2.9% average areal loss by 2050). Despite the discrepancy between the 2 approaches, CNS is a viable strategy for conservation site selection in salt marshes because the ER approach was successful. It has potential for application in other coastal areas where SLR will affect environmental features, but its performance may depend on the magnitude of geological changes caused by SLR. Our results indicate that conservation planners that had heretofore excluded low-lying coasts from CNS planning could include coastal ecosystems in regional conservation strategies. © 2017 Society for Conservation Biology.

Genomic cloning and promoter functional analysis of myostatin-2 in shi drum, Umbrina cirrosa: conservation of muscle-specific promoter activity.

PubMed

Nadjar-Boger, Elisabeth; Maccatrozzo, Lisa; Radaelli, Giuseppe; Funkenstein, Bruria

2013-02-01

Myostatin (MSTN) is a member of the transforming growth factor-ß superfamily, known as a negative regulator of skeletal muscle development and growth in mammals. In contrast to mammals, fish possess at least two paralogs of MSTN: MSTN-1 and MSTN-2. Here we describe the cloning and sequence analysis of spliced and precursor (unspliced) transcripts as well as the 5' flanking region of MSTN-2 from the marine fish Umbrina cirrosa (ucMSTN-2). In silico analysis revealed numerous putative cis regulatory elements including several E-boxes known as binding sites to myogenic transcription factors. Transient transfection experiments using non-muscle and muscle cell lines showed high transcriptional activity in muscle cells and in differentiated neural cells, in accordance with our previous findings in MSTN-2 promoter from Sparus aurata. Comparative informatics analysis of MSTN-2 from several fish species revealed high conservation of the predicted amino acid sequence as well as the gene structure (exon length) although intron length varied between species. The proximal promoter of MSTN-2 gene was found to be conserved among Perciforms. In conclusion, this study reinforces our conclusion that MSTN-2 promoter is a very strong promoter, especially in muscle cells. In addition, we show that the MSTN-2 gene structure is highly conserved among fishes as is the predicted amino acid sequence of the peptide. Copyright © 2012 Elsevier Inc. All rights reserved.

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...

Effective comparative analysis of protein-protein interaction networks by measuring the steady-state network flow using a Markov model.

PubMed

Jeong, Hyundoo; Qian, Xiaoning; Yoon, Byung-Jun

2016-10-06

Comparative analysis of protein-protein interaction (PPI) networks provides an effective means of detecting conserved functional network modules across different species. Such modules typically consist of orthologous proteins with conserved interactions, which can be exploited to computationally predict the modules through network comparison. In this work, we propose a novel probabilistic framework for comparing PPI networks and effectively predicting the correspondence between proteins, represented as network nodes, that belong to conserved functional modules across the given PPI networks. The basic idea is to estimate the steady-state network flow between nodes that belong to different PPI networks based on a Markov random walk model. The random walker is designed to make random moves to adjacent nodes within a PPI network as well as cross-network moves between potential orthologous nodes with high sequence similarity. Based on this Markov random walk model, we estimate the steady-state network flow - or the long-term relative frequency of the transitions that the random walker makes - between nodes in different PPI networks, which can be used as a probabilistic score measuring their potential correspondence. Subsequently, the estimated scores can be used for detecting orthologous proteins in conserved functional modules through network alignment. Through evaluations based on multiple real PPI networks, we demonstrate that the proposed scheme leads to improved alignment results that are biologically more meaningful at reduced computational cost, outperforming the current state-of-the-art algorithms. The source code and datasets can be downloaded from http://www.ece.tamu.edu/~bjyoon/CUFID .

Algal subsidies enhance invertebrate prey for threatened shorebirds: A novel conservation tool on ocean beaches?

NASA Astrophysics Data System (ADS)

Schlacher, Thomas A.; Hutton, Briony M.; Gilby, Ben L.; Porch, Nicholaus; Maguire, Grainne S.; Maslo, Brooke; Connolly, Rod M.; Olds, Andrew D.; Weston, Michael A.

2017-05-01

Birds breeding on ocean beaches are threatened globally, often requiring significant investments in species conservation and habitat management. Conservation actions typically encompass spatial and temporal threat reductions and protection of eggs and broods. Still, populations decline or recover only slowly, calling for fresh approaches in beach-bird conservation. Because energetic demands are critically high during the nesting and chick rearing phases, and chick survival is particularly low, supplementing prey to breeding birds and their offspring is theoretically attractive as a means to complement more traditional conservation measures. Prey for plovers and similar species on ocean beaches consists of invertebrates (e.g. small crustaceans, insects) many of which feed on stranded masses of plant material (e.g. kelp and seagrass) and use this 'wrack' as habitat. We added wrack to the upper beach where plovers nest and their chicks forage to test whether algal subsidies promote the abundance and diversity of their invertebrate prey. Adding wrack to the upper beach significantly increased the abundance and diversity of invertebrate prey items. At wrack subsidies greater than 50% of surface cover invertebrate assemblages became highly distinct compared with those that received smaller additions of wrack. Substantial (2-4 fold) increases in the abundance amphipods and isopods that are principal prey items for plovers drove these shifts. This proof-of-concept study demonstrates the feasibility of food provisioning for birds on ocean shores. Whilst novel, it is practicable, inexpensive and does not introduce further restrictions or man-made structures. Thus, it can meaningfully add to the broader arsenal of conservation tools for threatened species that are wholly reliant on sandy beaches as breeding and foraging habitats.

Kyphoplasty vs conservative treatment: a case-control study in 110 post-menopausal women population. Is kyphoplasty better than conservative treatment?

PubMed

Colangelo, D; Nasto, L A; Genitiempo, M; Formica, V M; Autore, G; Pambianco, V; Tamburrelli, F C; Cerulli, G; Pola, E

2015-11-01

Osteoporosis is a highly prevalent disease worldwide. Consequences of vertebral osteoporotic fractures include pain and progressive vertebral collapse resulting in spinal kyphosis, decreased quality of life, disability and mortality. Minimally invasive procedures represent an advance to the treatment of osteoporotic VCFs. Despite encouraging results reported by many authors, surgical intervention in an osteoporotic spine is fraught with difficulties. Advanced patients age and comorbidities are of great concern. We designed a retrospective case-control study on 110 post-menopausal women consecutively visited at our institution. Study population was split in a surgical and a conservative cohort, according to the provided treatment. Kyphoplasty treated patients had lower back pain VAS scores at 1 month as compared with conservatively treated patients (p < 0.05). EQ5D validated questionnaire also showed a better quality of life at 1 month for surgically treated patients (p < 0.05). SF-12 scores showed greater improvements at 1 month and 3 months with statistically significant difference between the two groups just at 3 months (p < 0.05). At 12 months, scores from all scales were not statistically different between the two cohorts, although surgically treated patients showed better trends than conservatively treated patients in pain and quality of life. Kyphoplasty was able to restore more than 54.55% of the original segmental kyphosis, whereas patients in conservative cohort lost 6.67% of the original segmental kyphosis on average. Kyphoplasty is a modern minimal invasive surgery, allowing faster recovery than bracing treatment. It can avoid the deformity in kyphosis due to VCF. In fact, the risk to develop a new vertebral fracture after the first one is very high.

Multispecies benefits of wetland conservation for marsh birds, frogs, and species at risk.

PubMed

Tozer, Douglas C; Steele, Owen; Gloutney, Mark

2018-04-15

Wetlands conserved using water level manipulation, cattle exclusion, naturalization of uplands, and other techniques under the North American Waterfowl Management Plan ("conservation project wetlands") are important for ducks, geese, and swans ("waterfowl"). However, the assumption that conservation actions for waterfowl also benefit other wildlife is rarely quantified. We modeled detection and occupancy of species at sites within 42 conservation project wetlands compared to sites within 52 similar nearby unmanaged wetlands throughout southern Ontario, Canada, and small portions of the adjacent U.S., using citizen science data collected by Bird Studies Canada's Great Lakes Marsh Monitoring Program, including 2 waterfowl and 13 non-waterfowl marsh-breeding bird species (n = 413 sites) and 7 marsh-breeding frog species (n = 191 sites). Occupancy was significantly greater at conservation project sites compared to unmanaged sites in 7 of 15 (47%) bird species and 3 of 7 (43%) frog species, with occupancy being higher by a difference of 0.12-0.38 across species. Notably, occupancy of priority conservation concern or at-risk Black Tern (Chlidonias niger), Common Gallinule (Gallinula galeata), Least Bittern (Ixobrychus exilis), Sora (Porzana carolina), and Western Chorus Frog (Pseudacris triseriata) was significantly higher at conservation project sites compared to unmanaged sites. The results demonstrate the utility of citizen science to inform wetland conservation, and suggest that actions under the North American Waterfowl Management Plan are effective for conserving non-waterfowl species. Copyright © 2018 Elsevier Ltd. All rights reserved.

Different realizations of Cooper-Frye sampling with conservation laws

NASA Astrophysics Data System (ADS)

Schwarz, C.; Oliinychenko, D.; Pang, L.-G.; Ryu, S.; Petersen, H.

2018-01-01

Approaches based on viscous hydrodynamics for the hot and dense stage and hadronic transport for the final dilute rescattering stage are successfully applied to the dynamic description of heavy ion reactions at high beam energies. One crucial step in such hybrid approaches is the so-called particlization, which is the transition between the hydrodynamic description and the microscopic degrees of freedom. For this purpose, individual particles are sampled on the Cooper-Frye hypersurface. In this work, four different realizations of the sampling algorithms are compared, with three of them incorporating the global conservation laws of quantum numbers in each event. The algorithms are compared within two types of scenarios: a simple ‘box’ hypersurface consisting of only one static cell and a typical particlization hypersurface for Au+Au collisions at \\sqrt{{s}{NN}}=200 {GeV}. For all algorithms the mean multiplicities (or particle spectra) remain unaffected by global conservation laws in the case of large volumes. In contrast, the fluctuations of the particle numbers are affected considerably. The fluctuations of the newly developed SPREW algorithm based on the exponential weight, and the recently suggested SER algorithm based on ensemble rejection, are smaller than those without conservation laws and agree with the expectation from the canonical ensemble. The previously applied mode sampling algorithm produces dramatically larger fluctuations than expected in the corresponding microcanonical ensemble, and therefore should be avoided in fluctuation studies. This study might be of interest for the investigation of particle fluctuations and correlations, e.g. the suggested signatures for a phase transition or a critical endpoint, in hybrid approaches that are affected by global conservation laws.

Computational identification of developmental enhancers:conservation and function of transcription factor binding-site clustersin drosophila melanogaster and drosophila psedoobscura

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

Berman, Benjamin P.; Pfeiffer, Barret D.; Laverty, Todd R.

2004-08-06

The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene, and assayedmore » embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. Measuring conservation of sequence features closely linked to function--such as binding-site clustering--makes better use of comparative sequence data than commonly used methods that examine only sequence identity.« less

Canonical Genetic Signatures of the Adult Human Brain

PubMed Central

Hawrylycz, Michael; Miller, Jeremy A.; Menon, Vilas; Feng, David; Dolbeare, Tim; Guillozet-Bongaarts, Angela L.; Jegga, Anil G.; Aronow, Bruce J.; Lee, Chang-Kyu; Bernard, Amy; Glasser, Matthew F.; Dierker, Donna L.; Menche, Jörge; Szafer, Aaron; Collman, Forrest; Grange, Pascal; Berman, Kenneth A.; Mihalas, Stefan; Yao, Zizhen; Stewart, Lance; Barabási, Albert-László; Schulkin, Jay; Phillips, John; Ng, Lydia; Dang, Chinh; Haynor, David R.; Jones, Allan; Van Essen, David C.; Koch, Christof; Lein, Ed

2015-01-01

The structure and function of the human brain are highly stereotyped, implying a conserved molecular program responsible for its development, cellular structure, and function. We applied a correlation-based metric of “differential stability” (DS) to assess reproducibility of gene expression patterning across 132 structures in six individual brains, revealing meso-scale genetic organization. The highest DS genes are highly biologically relevant, with enrichment for brain-related biological annotations, disease associations, drug targets, and literature citations. Using high DS genes we identified 32 anatomically diverse and reproducible gene expression signatures, which represent distinct cell types, intracellular components, and/or associations with neurodevelopmental and neurodegenerative disorders. Genes in neuron-associated compared to non-neuronal networks showed higher preservation between human and mouse; however, many diversely-patterned genes displayed dramatic shifts in regulation between species. Finally, highly consistent transcriptional architecture in neocortex is correlated with resting state functional connectivity, suggesting a link between conserved gene expression and functionally relevant circuitry. PMID:26571460

Applicability of a Conservative Margin Approach for Assessing NDE Flaw Detectability

NASA Technical Reports Server (NTRS)

Koshti, ajay M.

2007-01-01

Nondestructive Evaluation (NDE) procedures are required to detect flaws in structures with a high percentage detectability and high confidence. Conventional Probability of Detection (POD) methods are statistical in nature and require detection data from a relatively large number of flaw specimens. In many circumstances, due to the high cost and long lead time, it is impractical to build the large set of flaw specimens that is required by the conventional POD methodology. Therefore, in such situations it is desirable to have a flaw detectability estimation approach that allows for a reduced number of flaw specimens but provides a high degree of confidence in establishing the flaw detectability size. This paper presents an alternative approach called the conservative margin approach (CMA). To investigate the applicability of the CMA approach, flaw detectability sizes determined by the CMA and POD approaches have been compared on actual datasets. The results of these comparisons are presented and the applicability of the CMA approach is discussed.

Structural Investigation of Disordered Stress Proteins. Comparison of Full-Length Dehydrins with Isolated Peptides of Their Conserved Segments1

PubMed Central

Mouillon, Jean-Marie; Gustafsson, Petter; Harryson, Pia

2006-01-01

Dehydrins constitute a class of intrinsically disordered proteins that are expressed under conditions of water-related stress. Characteristic of the dehydrins are some highly conserved stretches of seven to 17 residues that are repetitively scattered in their sequences, the K-, S-, Y-, and Lys-rich segments. In this study, we investigate the putative role of these segments in promoting structure. The analysis is based on comparative analysis of four full-length dehydrins from Arabidopsis (Arabidopsis thaliana; Cor47, Lti29, Lti30, and Rab18) and isolated peptide mimics of the K-, Y-, and Lys-rich segments. In physiological buffer, the circular dichroism spectra of the full-length dehydrins reveal overall disordered structures with a variable content of poly-Pro helices, a type of elongated secondary structure relying on bridging water molecules. Similar disordered structures are observed for the isolated peptides of the conserved segments. Interestingly, neither the full-length dehydrins nor their conserved segments are able to adopt specific structure in response to altered temperature, one of the factors that regulate their expression in vivo. There is also no structural response to the addition of metal ions, increased protein concentration, or the protein-stabilizing salt Na2SO4. Taken together, these observations indicate that the dehydrins are not in equilibrium with high-energy folded structures. The result suggests that the dehydrins are highly evolved proteins, selected to maintain high configurational flexibility and to resist unspecific collapse and aggregation. The role of the conserved segments is thus not to promote tertiary structure, but to exert their biological function more locally upon interaction with specific biological targets, for example, by acting as beads on a string for specific recognition, interaction with membranes, or intermolecular scaffolding. In this perspective, it is notable that the Lys-rich segment in Cor47 and Lti29 shows sequence similarity with the animal chaperone HSP90. PMID:16565295

Evolution of DNA-Binding Sites of a Floral Master Regulatory Transcription Factor

PubMed Central

Muiño, Jose M.; de Bruijn, Suzanne; Pajoro, Alice; Geuten, Koen; Vingron, Martin; Angenent, Gerco C.; Kaufmann, Kerstin

2016-01-01

Flower development is controlled by the action of key regulatory transcription factors of the MADS-domain family. The function of these factors appears to be highly conserved among species based on mutant phenotypes. However, the conservation of their downstream processes is much less well understood, mostly because the evolutionary turnover and variation of their DNA-binding sites (BSs) among plant species have not yet been experimentally determined. Here, we performed comparative ChIP (chromatin immunoprecipitation)-seq experiments of the MADS-domain transcription factor SEPALLATA3 (SEP3) in two closely related Arabidopsis species: Arabidopsis thaliana and A. lyrata which have very similar floral organ morphology. We found that BS conservation is associated with DNA sequence conservation, the presence of the CArG-box BS motif and on the relative position of the BS to its potential target gene. Differences in genome size and structure can explain that SEP3 BSs in A. lyrata can be located more distantly to their potential target genes than their counterparts in A. thaliana. In A. lyrata, we identified transposition as a mechanism to generate novel SEP3 binding locations in the genome. Comparative gene expression analysis shows that the loss/gain of BSs is associated with a change in gene expression. In summary, this study investigates the evolutionary dynamics of DNA BSs of a floral key-regulatory transcription factor and explores factors affecting this phenomenon. PMID:26429922

Inequity in ecosystem service delivery: Socioeconomic gaps in the public-private conservation network

USGS Publications Warehouse

Villamagna, Amy M.; Mogollón, Beatriz; Angermeier, Paul L.

2017-01-01

Conservation areas, both public and private, are critical tools to protect biodiversity and deliver important ecosystem services (ES) to society. Although societal benefits from such ES are increasingly used to promote public support of conservation, the number of beneficiaries, their identity, and the magnitude of benefits are largely unknown for the vast majority of conservation areas in the United States public-private conservation network. The location of conservation areas in relation to people strongly influences the direction and magnitude of ES flows as well as the identity of beneficiaries. We analyzed benefit zones, the areas to which selected ES could be conveyed to beneficiaries, to assess who benefits from a typical conservation network. Better knowledge of ES flows and beneficiaries will help land conservationists make a stronger case for the broad collateral benefits of conservation and help to address issues of social-environmental justice. To evaluate who benefits the most from the current public-private conservation network, we delineated the benefit zones for local ES (within 16 km) that are conveyed along hydrological paths from public (federal and state) and private (easements) conservation lands in the states of North Carolina and Virginia, USA. We also discuss the challenges and demonstrate an approach for delineating nonhydrological benefits that are passively conveyed to beneficiaries. We mapped and compared the geographic distribution of benefit zones within and among conservation area types. We further compared beneficiary demographics across benefit zones of the conservation area types and found that hydrological benefit zones of federal protected areas encompass disproportionately fewer minority beneficiaries compared to statewide demographic patterns. In contrast, benefit zones of state protected areas and private easements encompassed a much greater proportion of minority beneficiaries (~22–25%). Benefit zones associated with private conservation lands included beneficiaries of significantly greater household income than benefit zones of other types of conservation areas. Our analysis of ES flows revealed significant socioeconomic gaps in how the current public-private conservation network benefits the public. These gaps warrant consideration in regional conservation plans and suggest that private conservation initiatives may be best suited for responding to the equity challenge. Enhancing the ecosystem benefits and the equity of benefit delivery from private conservation networks could build public and political support for long-term conservation strategies and ultimately enhance conservation efficacy.

Comparison of Fully-Compressible Equation Sets for Atmospheric Dynamics

NASA Technical Reports Server (NTRS)

Ahmad, Nashat N.

2016-01-01

Traditionally, the equation for the conservation of energy used in atmospheric models is based on potential temperature and is used in place of the total energy conservation. This paper compares the application of the two equations sets for both the Euler and the Navier-Stokes solutions using several benchmark test cases. A high-resolution wave-propagation method which accurately takes into account the source term due to gravity is used for computing the non-hydrostatic atmospheric flows. It is demonstrated that there is little to no difference between the results obtained using the two different equation sets for Euler as well as Navier-Stokes solutions.

Comparative Analysis of Immune Checkpoint Molecules and Their Potential Role in the Transmissible Tasmanian Devil Facial Tumor Disease

PubMed Central

Flies, Andrew S.; Blackburn, Nicholas B.; Lyons, Alan Bruce; Hayball, John D.; Woods, Gregory M.

2017-01-01

Immune checkpoint molecules function as a system of checks and balances that enhance or inhibit immune responses to infectious agents, foreign tissues, and cancerous cells. Immunotherapies that target immune checkpoint molecules, particularly the inhibitory molecules programmed cell death 1 and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4), have revolutionized human oncology in recent years, yet little is known about these key immune signaling molecules in species other than primates and rodents. The Tasmanian devil facial tumor disease is caused by transmissible cancers that have resulted in a massive decline in the wild Tasmanian devil population. We have recently demonstrated that the inhibitory checkpoint molecule PD-L1 is upregulated on Tasmanian devil (Sarcophilus harrisii) facial tumor cells in response to the interferon-gamma cytokine. As this could play a role in immune evasion by tumor cells, we performed a thorough comparative analysis of checkpoint molecule protein sequences among Tasmanian devils and eight other species. We report that many of the key signaling motifs and ligand-binding sites in the checkpoint molecules are highly conserved across the estimated 162 million years of evolution since the last common ancestor of placental and non-placental mammals. Specifically, we discovered that the CTLA-4 (MYPPPY) ligand-binding motif and the CTLA-4 (GVYVKM) inhibitory domain are completely conserved across all nine species used in our comparative analysis, suggesting that the function of CTLA-4 is likely conserved in these species. We also found that cysteine residues for intra- and intermolecular disulfide bonds were also highly conserved. For instance, all 20 cysteine residues involved in disulfide bonds in the human 4-1BB molecule were also present in devil 4-1BB. Although many key sequences were conserved, we have also identified immunoreceptor tyrosine-based inhibitory motifs (ITIMs) and immunoreceptor tyrosine-based switch motifs (ITSMs) in genes and protein domains that have not been previously reported in any species. This checkpoint molecule analysis and review of salient features for each of the molecules presented here can serve as road map for the development of a Tasmanian devil facial tumor disease immunotherapy. Finally, the strategies can be used as a guide for veterinarians, ecologists, and other researchers willing to venture into the nascent field of wild immunology. PMID:28515726

Validation of an advanced practice physiotherapy model of care in an orthopaedic outpatient clinic

PubMed Central

2013-01-01

Background In Canada, new models of orthopaedic care involving advanced practice physiotherapists (APP) are being implemented. In these new models, aimed at improving the efficiency of care for patients with musculoskeletal disorders, APPs diagnose, triage and conservatively treat patients. Formal validation of the efficiency and appropriateness of these emerging models is scarce. The purpose of this study is to assess the diagnostic agreement of an APP compared to orthopaedic surgeons as well as to assess treatment concordance, healthcare resource use, and patient satisfaction in this new model. Methods 120 patients presenting for an initial consult for hip or knee complaints in an outpatient orthopaedic hospital clinic in Montreal, Canada, were independently assessed by an APP and by one of three participating orthopaedic surgeons. Each health care provider independently diagnosed the patients and provided triage recommendations (conservative or surgical management). Proportion of raw agreement and Cohen’s kappa were used to assess inter-rater agreement for diagnosis, triage, treatment recommendations and imaging tests ordered. Chi-Square tests were done in order to compare the type of conservative treatment recommendations made by the APP and the surgeons and Student t-tests to compare patient satisfaction between the two types of care. Results The majority of patients assessed were female (54%), mean age was 54.1 years and 91% consulted for a knee complaint. The raw agreement proportion for diagnosis was 88% and diagnostic inter-rater agreement was very high (κ=0.86; 95% CI: 0.80-0.93). The triage recommendations (conservative or surgical management) raw agreement proportion was found to be 88% and inter-rater agreement for triage recommendation was high (κ=0.77; 95% CI: 0.65-0.88). No differences were found between providers with respect to imaging tests ordered (p≥0.05). In terms of conservative treatment recommendations made, the APP gave significantly more education and prescribed more NSAIDs, joint injections, exercises and supervised physiotherapy (p<0.05). Patient satisfaction was significantly higher for APP care than for the surgeons care (p<0.05). Conclusion The diagnoses and triage recommendations for patients with hip and knee disorders made by the APP were similar to the orthopaedic surgeons. These results provide evidence supporting the APP model for orthopaedic care. PMID:23656928

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

USDA-ARS?s Scientific Manuscript database

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

Students' Progression of Understanding the Matter Concept from Elementary to High School

ERIC Educational Resources Information Center

Liu, Xiufeng; Lesniak, Kathleen M.

2005-01-01

Using the US national sample from the Third International Mathematics and Science Study (TIMSS) and the Rasch modeling method, this study identified the conceptual progression sequence of various matter concept aspects, and compared students' latent abilities against the sequence. We found that the four matter aspects, i.e. conservation, physical…

Development and application of a PCR assay to detect chicken and turkey parvoviruses in commercial poultry flocks in the United States.

USDA-ARS?s Scientific Manuscript database

Comparative sequence analysis of six independent chicken and turkey parvovirus nonstructural (NS) genes revealed specific genomic regions with 100% nucleotide sequence identity. A PCR assay with primers targeting these conserved genome sequences proved to be highly specific and sensitive to detect p...

Comparative costs of programmes to conserve chicken genetic variation based on maintaining living populations or storing cryopreserved material

USDA-ARS?s Scientific Manuscript database

Consolidations in the poultry breeding industry and academic poultry departments have resulted in the loss of avian populations. The cost of maintaining living populations is high, but ex-situ alternatives are now available. Semen can be cryopreserved and lines can be recovered by backcrossing, or...

A Comprehensive Comparison of Relativistic Particle Integrators

NASA Astrophysics Data System (ADS)

Ripperda, B.; Bacchini, F.; Teunissen, J.; Xia, C.; Porth, O.; Sironi, L.; Lapenta, G.; Keppens, R.

2018-03-01

We compare relativistic particle integrators commonly used in plasma physics, showing several test cases relevant for astrophysics. Three explicit particle pushers are considered, namely, the Boris, Vay, and Higuera–Cary schemes. We also present a new relativistic fully implicit particle integrator that is energy conserving. Furthermore, a method based on the relativistic guiding center approximation is included. The algorithms are described such that they can be readily implemented in magnetohydrodynamics codes or Particle-in-Cell codes. Our comparison focuses on the strengths and key features of the particle integrators. We test the conservation of invariants of motion and the accuracy of particle drift dynamics in highly relativistic, mildly relativistic, and non-relativistic settings. The methods are compared in idealized test cases, i.e., without considering feedback onto the electrodynamic fields, collisions, pair creation, or radiation. The test cases include uniform electric and magnetic fields, {\\boldsymbol{E}}× {\\boldsymbol{B}} fields, force-free fields, and setups relevant for high-energy astrophysics, e.g., a magnetic mirror, a magnetic dipole, and a magnetic null. These tests have direct relevance for particle acceleration in shocks and in magnetic reconnection.

An intertebrate ecosystem engineer likely covered under the umbrella of sage-grouse conservation

USGS Publications Warehouse

Carlisle, Jason D.; Stewart, David R.; Chalfoun, Anna D.

2017-01-01

Conservation practitioners often rely on areas designed to protect species of greatest conservation priority to also conserve co-occurring species (i.e., the umbrella species concept). The extent to which vertebrate species may serve as suitable umbrellas for invertebrate species, however, has rarely been explored. Sage-grouse (Centrocercus spp.) have high conservation priority throughout much of the rangelands of western North America and are considered an umbrella species through which the conservation of entire rangeland ecosystems can be accomplished. Harvester ants are ecosystem engineers and play important roles in the maintenance and function of rangeland ecosystems. We compared indices of the abundance of western harvester ants (Pogonomyrmex occidentalis) and Greater Sage-Grouse (Centrocercus urophasianus) at 72 sites in central Wyoming, USA, in 2012. The abundance of harvester ant mounds was best predicted by a regression model that included a combination of local habitat characteristics and the abundance of sage-grouse. When controlling for habitat-related factors, areas with higher abundances of sage-grouse pellets (an index of sage-grouse abundance and/or habitat use) had higher abundances of ant mounds than areas with lower abundances of sage-grouse pellets. The causal mechanism underlying this positive relationship between sage-grouse and ant mound abundance at the fine scale could be indirect (e.g., both species prefer similar environmental conditions) or direct (e.g., sage-grouse prefer areas with a high abundance of ant mounds because ants are an important prey item during certain life stages). We observed no relationship between a broad-scale index of breeding sage-grouse density and the abundance of ant mounds. We suspect that consideration of the nonbreeding habitat of sage-grouse and finer-scale measures of sagegrouse abundance are critical to the utility of sage-grouse as an umbrella species for the conservation of harvester ants and their important role in rangeland ecosystems.

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.

High Intensity Laser Therapy (HILT) versus TENS and NSAIDs in low back pain: clinical study

NASA Astrophysics Data System (ADS)

Zati, Allesandro; Fortuna, Damiano; Valent, A.; Filippi, M. V.; Bilotta, Teresa W.

2004-09-01

Low back pain, caused by lumbar disc herniation, is prevalently treated with a conservative approach. In this study we valued the efficacy of High Intensity Laser Therapy (HILT), compared with accepted therapies such as TENS and NSAIDs. Laser therapy obtained similar results in the short term, but better clinical effect over time than TENS and NSAIDs. In conclusion high intensity laser therapy appears to be a interesting new treatment, worthy of further research.

A High-Resolution Comparative Chromosome Map of Cricetus cricetus and Peromyscus eremicus Reveals the Involvement of Constitutive Heterochromatin in Breakpoint Regions.

PubMed

Vieira-da-Silva, Ana; Louzada, Sandra; Adega, Filomena; Chaves, Raquel

2015-01-01

Compared to humans and other mammals, rodent genomes, specifically Muroidea species, underwent intense chromosome reshuffling in which many complex structural rearrangements occurred. This fact makes them preferential animal models for studying the process of karyotype evolution. Here, we present the first combined chromosome comparative maps between 2 Cricetidae species, Cricetus cricetus and Peromyscus eremicus, and the index species Mus musculus and Rattus norvegicus. Comparative chromosome painting was done using mouse and rat paint probes together with in silico analysis from the Ensembl genome browser database. Hereby, evolutionary events (inter- and intrachromosomal rearrangements) that occurred in C. cricetus and P. eremicus since the putative ancestral Muroidea genome could be inferred, and evolutionary breakpoint regions could be detected. A colocalization of constitutive heterochromatin and evolutionary breakpoint regions in each genome was observed. Our results suggest the involvement of constitutive heterochromatin in karyotype restructuring of these species, despite the different levels of conservation of the C. cricetus (derivative) and P. eremicus (conserved) genomes. © 2015 S. Karger AG, Basel.

The distribution, diversity, and conservation status of Cycas in China.

PubMed

Zheng, Ying; Liu, Jian; Feng, Xiuyan; Gong, Xun

2017-05-01

As ancient gymnosperm and woody plants, cycads have survived through dramatic tectonic activities, climate fluctuation, and environmental variations making them of great significance in studying the origin and evolution of flora biodiversity. However, they are among the most threatened plant groups in the world. The principal aim of this review is to outline the distribution, diversity, and conservation status of Cycas in China and provide suggestions for conservation practices. In this review, we describe the taxonomy, distribution, and conservation status of Cycas in China. By comparing Chinese Cycas species with its relatives worldwide, we then discuss the current genetic diversity, genetic differentiation of Cycas, and try to disentangle the potential effects of Quaternary climate changes and topographical events on Cycas . We review conservation practices from both researchers and practitioners for these rare and endangered species. High genetic diversity at the species level and strong genetic differentiation within Cycas have been observed. Most Cycas species in southwest China have experienced population retreats in contrast to the coastal Cycas 's expansion during the Quaternary glaciation. Additionally, human activities and habitat fragmentation have pushed these endangered taxa to the brink of extinction. Although numerous efforts have been made to mitigate threats to Cycas survival, implementation and compliance monitoring in protection zones are currently inadequate. We outline six proposals to strengthen conservation measures for Cycas in China and anticipate that these measures will provide guidelines for further research on population genetics as well as conservation biology of not only cycads but also other endangered species worldwide.

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 regulate cellular, physiological or developmental processes specific to the taxa that produce them, as appears likely to be the case for those miRNAs that have only been observed in Populus. Non-conserved and conserved miRNAs seem to target genes with similar biological functions indicating that similar selection pressures are acting on both types of miRNAs. The expansion in the number of most conserved miRNAs in Populus relative to Arabidopsis, may be linked to the recent genome duplication in Populus, the slow evolution of the Populus genome, or to differences in the selection pressure on duplicated miRNAs in these species. PMID:18166134

Dugong dugon feeding in tropical Australian seagrass meadows: implications for conservation planning.

PubMed

Tol, Samantha J; Coles, Rob G; Congdon, Bradley C

2016-01-01

Dugongs (Dugong dugon) are listed as vulnerable to extinction due to rapid population reductions caused in part by loss of seagrass feeding meadows. Understanding dugong feeding behaviour in tropical Australia, where the majority of dugongs live, will assist conservation strategies. We examined whether feeding patterns in intertidal seagrass meadows in tropical north-eastern Australia were related to seagrass biomass, species composition and/or nitrogen content. The total biomass of each seagrass species removed by feeding dugongs was measured and compared to its relative availability. Nitrogen concentrations were also determined for each seagrass species present at the sites. Dugongs consumed seagrass species in proportion to their availability, with biomass being the primary determining factor. Species composition and/or nitrogen content influenced consumption to a lesser degree. Conservation plans focused on protecting high biomass intertidal seagrass meadows are likely to be most effective at ensuring the survival of dugong in tropical north-eastern Australia.

Conservative management of tendinopathy: an evidence-based approach

PubMed Central

Loppini, Mattia; Maffulli, Nicola

2011-01-01

Summary Tendinopathy is one of the most frequent overuse injuries associated with sport. It is a failure of a chronic healing response associated with both chronic overloaded and unloaded states. Although several conservative therapeutic options have been proposed, very few of them are supported by randomized controlled trials. Eccentric exercises provide excellent clinical results both in athletic and sedentary patients, with no reported adverse effects. Combining eccentric loading and low-energy shock wave therapy produces higher success rates compared with eccentric training alone or shock wave therapy alone. High-volume injection of normal saline solution, corticosteroids, or anesthetics can reduce pain and improve long-term function in patients with Achilles or patellar tendinopathy. The use of injectable substances such as platelet-rich plasma, autologous blood, polidocanol, and corticosteroids in and around tendons is not support by strong clinical evidence. Further randomized controlled trials are necessary to define the best conservative management of tendinopathy. PMID:23738261

Outcomes with invasive vs conservative management of cardiogenic shock complicating acute myocardial infarction.

PubMed

Bangalore, Sripal; Gupta, Navdeep; Guo, Yu; Lala, Anuradha; Balsam, Leora; Roswell, Robert O; Reyentovich, Alex; Hochman, Judith S

2015-06-01

In the SHOCK trial, an invasive strategy of early revascularization was associated with a significant mortality benefit at 6 months when compared with initial stabilization in patients with cardiogenic shock complicating acute myocardial infarction. Our objectives were to evaluate the data on real-world practice and outcomes of invasive vs conservative management in patients with cardiogenic shock. We analyzed data from the Nationwide Inpatient Sample from 2002 to 2011 with primary discharge diagnosis of acute myocardial infarction and secondary diagnosis of cardiogenic shock. Propensity score matching was used to assemble a cohort of patients managed invasively (with cardiac catheterization, percutaneous coronary intervention, or coronary artery bypass graft surgery) vs conservatively with similar baseline characteristics. The primary outcome was in-hospital mortality. We identified 60,833 patients with cardiogenic shock, of which 20,644 patients (10,322 in each group) with similar propensity scores, including 11,004 elderly patients (≥75 years), were in the final analysis. Patients who underwent invasive management had 59% lower odds of in-hospital mortality (37.7% vs 59.7%; odds ratio [OR] 0.41; 95% confidence interval [CI], 0.39-0.43; P < .0001) when compared with those managed conservatively. This lower mortality was consistently seen across all tested subgroups; specifically in the elderly (≥75 years) (44.0% vs 63.6%; OR 0.45; 95% CI, 0.42-0.49; P < .0001) and those younger than 75 years (30.6% vs 55.1%; OR 0.36; 95% CI, 0.33-0.39; P < .0001), although the magnitude of risk reduction differed (Pinteraction < .0001). In this largest cohort of patients with cardiogenic shock complicating acute myocardial infarction, patients managed invasively had significantly lower mortality when compared with those managed conservatively, even in the elderly. Our results emphasize the need for aggressive management in this high-risk subgroup. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparing pseudo-absences generation techniques in Boosted Regression Trees models for conservation purposes: A case study on amphibians in a protected area.

PubMed

Cerasoli, Francesco; Iannella, Mattia; D'Alessandro, Paola; Biondi, Maurizio

2017-01-01

Boosted Regression Trees (BRT) is one of the modelling techniques most recently applied to biodiversity conservation and it can be implemented with presence-only data through the generation of artificial absences (pseudo-absences). In this paper, three pseudo-absences generation techniques are compared, namely the generation of pseudo-absences within target-group background (TGB), testing both the weighted (WTGB) and unweighted (UTGB) scheme, and the generation at random (RDM), evaluating their performance and applicability in distribution modelling and species conservation. The choice of the target group fell on amphibians, because of their rapid decline worldwide and the frequent lack of guidelines for conservation strategies and regional-scale planning, which instead could be provided through an appropriate implementation of SDMs. Bufo bufo, Salamandrina perspicillata and Triturus carnifex were considered as target species, in order to perform our analysis with species having different ecological and distributional characteristics. The study area is the "Gran Sasso-Monti della Laga" National Park, which hosts 15 Natura 2000 sites and represents one of the most important biodiversity hotspots in Europe. Our results show that the model calibration ameliorates when using the target-group based pseudo-absences compared to the random ones, especially when applying the WTGB. Contrarily, model discrimination did not significantly vary in a consistent way among the three approaches with respect to the tree target species. Both WTGB and RDM clearly isolate the highly contributing variables, supplying many relevant indications for species conservation actions. Moreover, the assessment of pairwise variable interactions and their three-dimensional visualization further increase the amount of useful information for protected areas' managers. Finally, we suggest the use of RDM as an admissible alternative when it is not possible to individuate a suitable set of species as a representative target-group from which the pseudo-absences can be generated.

The complete mitochondrial genome of the medicinal fungus Ganoderma applanatum (Polyporales, Basidiomycota).

PubMed

Wang, Xin-Cun; Shao, Junjie; Liu, Chang

2016-07-01

We have determined the complete nucleotide sequence of the mitochondrial genome of the medicinal fungus Ganoderma applanatum (Pers.) Pat. using the next-generation sequencing technology. The circular molecule is 119,803 bp long with a GC content of 26.66%. Gene prediction revealed genes encoding 15 conserved proteins, 25 tRNAs, the large and small ribosomal RNAs, all genes are located on the same strand except trnW-CCA. Compared with previously sequenced genomes of G. lucidum, G. meredithiae and G. sinense, the order of the protein and rRNA genes is highly conserved; however, the types of tRNA genes are slightly different. The mitochondrial genome of G. applanatum will contribute to the understanding of the phylogeny and evolution of Ganoderma and Ganodermataceae, the group containing many species with high medicinal values.

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...

Efficiency of a Protected-Area Network in a Mediterranean Region: A Multispecies Assessment with Raptors

NASA Astrophysics Data System (ADS)

Abellán, María D.; Martínez, José E.; Palazón, José A.; Esteve, Miguel Á.; Calvo, José F.

2011-05-01

Three different systems of designating protected areas in a Mediterranean region in southeastern Spain were studied, referring to their effectiveness and efficiency for protecting both the breeding territories and the suitable habitat of a set of ten raptor species. Taking into consideration the varying degrees of endangerment of these species, a map of multispecies conservation values was also drawn up and superimposed on the three protected-area systems studied. In order to compare the levels of protection afforded by the three systems, we considered two indices that measured their relative effectiveness and efficiency. The effectiveness estimated the proportion of territories or optimal habitat protected by the networks while efficiency implicitly considered the area of each system (percentage of breeding territories or optimal habitat protected per 1% of land protected). Overall, our results showed that the most efficient system was that formed by the set of regional parks and reserves (17 protected breeding territories per 100 km2), although, given its small total area, it was by far the least effective (only protecting the 21% of the breeding territories of all species and 17% of the area of high conservation value). The systems formed by the Special Protection Areas (designated under the EU "Birds Directive") and by the Special Conservation Areas (designated under the EU "Habitats Directive") notably increased the percentages of protected territories of all species (61%) and area of high conservation value (57%), but their efficiency was not as high as expected in most cases. The overall level of protection was high for all species except for the Lesser Kestrel ( Falco naumanni), an endangered falcon that inhabits pseudo-steppe and traditional agricultural habitats, which are clearly underrepresented in the protected-area network of the study region.

The effect of entrapped nonaqueous phase liquids on tracer transport in heterogeneous porous media: Laboratory experiments at the intermediate scale

USGS Publications Warehouse

Barth, Gilbert R.; Illangasekare, T.H.; Rajaram, H.

2003-01-01

This work considers the applicability of conservative tracers for detecting high-saturation nonaqueous-phase liquid (NAPL) entrapment in heterogeneous systems. For this purpose, a series of experiments and simulations was performed using a two-dimensional heterogeneous system (10??1.2 m), which represents an intermediate scale between laboratory and field scales. Tracer tests performed prior to injecting the NAPL provide the baseline response of the heterogeneous porous medium. Two NAPL spill experiments were performed and the entrapped-NAPL saturation distribution measured in detail using a gamma-ray attenuation system. Tracer tests following each of the NAPL spills produced breakthrough curves (BTCs) reflecting the impact of entrapped NAPL on conservative transport. To evaluate significance, the impact of NAPL entrapment on the conservative-tracer breakthrough curves was compared to simulated breakthrough curve variability for different realizations of the heterogeneous distribution. Analysis of the results reveals that the NAPL entrapment has a significant impact on the temporal moments of conservative-tracer breakthrough curves. ?? 2003 Elsevier B.V. All rights reserved.

Between-country collaboration and consideration of costs increase conservation planning efficiency in the Mediterranean Basin.

PubMed

Kark, Salit; Levin, Noam; Grantham, Hedley S; Possingham, Hugh P

2009-09-08

The importance of global and regional coordination in conservation is growing, although currently, the majority of conservation programs are applied at national and subnational scales. Nevertheless, multinational programs incur transaction costs and resources beyond what is required in national programs. Given the need to maximize returns on investment within limited conservation budgets, it is crucial to quantify how much more biodiversity can be protected by coordinating multinational conservation efforts when resources are fungible. Previous studies that compared different scales of conservation decision-making mostly ignored spatial variability in biodiversity threats and the cost of actions. Here, we developed a simple integrating metric, taking into account both the cost of conservation and threats to biodiversity. We examined the Mediterranean Basin biodiversity hotspot, which encompasses over 20 countries. We discovered that for vertebrates to achieve similar conservation benefits, one would need substantially more money and area if each country were to act independently as compared to fully coordinated action across the Basin. A fully coordinated conservation plan is expected to save approximately US$67 billion, 45% of total cost, compared with the uncoordinated plan; and if implemented over a 10-year period, the plan would cost approximately 0.1% of the gross national income of all European Union (EU) countries annually. The initiative declared in the recent Paris Summit for the Mediterranean provides a political basis for such complex coordination. Surprisingly, because many conservation priority areas selected are located in EU countries, a partly coordinated solution incorporating only EU-Mediterranean countries is almost as efficient as the fully coordinated scenario.

Between-country collaboration and consideration of costs increase conservation planning efficiency in the Mediterranean Basin

PubMed Central

Kark, Salit; Levin, Noam; Grantham, Hedley S.; Possingham, Hugh P.

2009-01-01

The importance of global and regional coordination in conservation is growing, although currently, the majority of conservation programs are applied at national and subnational scales. Nevertheless, multinational programs incur transaction costs and resources beyond what is required in national programs. Given the need to maximize returns on investment within limited conservation budgets, it is crucial to quantify how much more biodiversity can be protected by coordinating multinational conservation efforts when resources are fungible. Previous studies that compared different scales of conservation decision-making mostly ignored spatial variability in biodiversity threats and the cost of actions. Here, we developed a simple integrating metric, taking into account both the cost of conservation and threats to biodiversity. We examined the Mediterranean Basin biodiversity hotspot, which encompasses over 20 countries. We discovered that for vertebrates to achieve similar conservation benefits, one would need substantially more money and area if each country were to act independently as compared to fully coordinated action across the Basin. A fully coordinated conservation plan is expected to save approximately US$67 billion, 45% of total cost, compared with the uncoordinated plan; and if implemented over a 10-year period, the plan would cost ≈0.1% of the gross national income of all European Union (EU) countries annually. The initiative declared in the recent Paris Summit for the Mediterranean provides a political basis for such complex coordination. Surprisingly, because many conservation priority areas selected are located in EU countries, a partly coordinated solution incorporating only EU-Mediterranean countries is almost as efficient as the fully coordinated scenario. PMID:19717457

Individual perception of bees: Between perceived danger and willingness to protect.

PubMed

Schönfelder, Mona Lisa; Bogner, Franz Xaver

2017-01-01

The current loss of biodiversity has found its way into the media. Especially the loss of bees as pollinators has recently received much attention aiming to increase public awareness about the consequence of pollinator loss and strategies for protection. However, pollinating insects like bees often prompt considerable anxiety. Negative emotions such as fear and disgust often lead to lack of support for conservation and appropriate initiatives for protection. Our study monitored perceptions of bees in the contexts of conservation and danger bees possibly represent by applying a semantic differential using contrasting adjectives under the heading "I think bees are…". Additionally, open questions were applied to examine individual perceptions of danger and conservation of bees. Respondents were students from primary school, secondary school and university. We compared these novices (n = 499) to experts (beekeepers, n = 153). An exploratory factor analysis of the semantic differential responses yielded three major oblique factors: Interest, Danger and Conservation & Usefulness. The inter-correlations of these factors were significant. Although all subgroups showed an overall high willingness to protect bees, the perception of danger scored medium. The individual experience of bee stings was the most prevalent reason for expressing fear. Educational programs focusing on pollinator conservation may reduce the perceived danger through removing misinformation, and supporting interest in the species. Based on the overall positive attitude toward bees, we suggest introducing bees (e.g., Apis mellifera) as a flagship species for pollinator conservation.

Neuromolecular responses to social challenge: common mechanisms across mouse, stickleback fish, and honey bee.

PubMed

Rittschof, Clare C; Bukhari, Syed Abbas; Sloofman, Laura G; Troy, Joseph M; Caetano-Anollés, Derek; Cash-Ahmed, Amy; Kent, Molly; Lu, Xiaochen; Sanogo, Yibayiri O; Weisner, Patricia A; Zhang, Huimin; Bell, Alison M; Ma, Jian; Sinha, Saurabh; Robinson, Gene E; Stubbs, Lisa

2014-12-16

Certain complex phenotypes appear repeatedly across diverse species due to processes of evolutionary conservation and convergence. In some contexts like developmental body patterning, there is increased appreciation that common molecular mechanisms underlie common phenotypes; these molecular mechanisms include highly conserved genes and networks that may be modified by lineage-specific mutations. However, the existence of deeply conserved mechanisms for social behaviors has not yet been demonstrated. We used a comparative genomics approach to determine whether shared neuromolecular mechanisms could underlie behavioral response to territory intrusion across species spanning a broad phylogenetic range: house mouse (Mus musculus), stickleback fish (Gasterosteus aculeatus), and honey bee (Apis mellifera). Territory intrusion modulated similar brain functional processes in each species, including those associated with hormone-mediated signal transduction and neurodevelopment. Changes in chromosome organization and energy metabolism appear to be core, conserved processes involved in the response to territory intrusion. We also found that several homologous transcription factors that are typically associated with neural development were modulated across all three species, suggesting that shared neuronal effects may involve transcriptional cascades of evolutionarily conserved genes. Furthermore, immunohistochemical analyses of a subset of these transcription factors in mouse again implicated modulation of energy metabolism in the behavioral response. These results provide support for conserved genetic "toolkits" that are used in independent evolutions of the response to social challenge in diverse taxa.

Spatial and temporal dimensions of landscape fragmentation across the Brazilian Amazon.

PubMed

Rosa, Isabel M D; Gabriel, Cristina; Carreiras, Joāo M B

2017-01-01

The Brazilian Amazon in the past decades has been suffering severe landscape alteration, mainly due to anthropogenic activities, such as road building and land clearing for agriculture. Using a high-resolution time series of land cover maps (classified as mature forest, non-forest, secondary forest) spanning from 1984 through 2011, and four uncorrelated fragmentation metrics (edge density, clumpiness index, area-weighted mean patch size and shape index), we examined the temporal and spatial dynamics of forest fragmentation in three study areas across the Brazilian Amazon (Manaus, Santarém and Machadinho d'Oeste), inside and outside conservation units. Moreover, we compared the impacts on the landscape of: (1) different land uses (e.g. cattle ranching, crop production), (2) occupation processes (spontaneous vs. planned settlements) and (3) implementation of conservation units. By 2010/2011, municipalities located along the Arc of Deforestation had more than 55% of the remaining mature forest strictly confined to conservation units. Further, the planned settlement showed a higher rate of forest loss, a more persistent increase in deforested areas and a higher relative incidence of deforestation inside conservation units. Distinct agricultural activities did not lead to significantly different landscape structures; the accessibility of the municipality showed greater influence in the degree of degradation of the landscapes. Even with a high proportion of the landscapes covered by conservation units, which showed a strong inhibitory effect on forest fragmentation, we show that dynamic agriculturally driven economic activities, in municipalities with extensive road development, led to more regularly shaped, heavily fragmented landscapes, with higher densities of forest edge.

Remarkable sequence conservation of the last intron in the PKD1 gene.

PubMed

Rodova, Marianna; Islam, M Rafiq; Peterson, Kenneth R; Calvet, James P

2003-10-01

The last intron of the PKD1 gene (intron 45) was found to have exceptionally high sequence conservation across four mammalian species: human, mouse, rat, and dog. This conservation did not extend to the comparable intron in pufferfish. Pairwise comparisons for intron 45 showed 91% identity (human vs. dog) to 100% identity (mouse vs. rat) for an average for all four species of 94% identity. In contrast, introns 43 and 44 of the PKD1 gene had average pairwise identities of 57% and 54%, and exons 43, 44, and 45 and the coding region of exon 46 had average pairwise identities of 80%, 84%, 82%, and 80%. Intron 45 is 90 to 95 bp in length, with the major region of sequence divergence being in a central 4-bp to 9-bp variable region. RNA secondary structure analysis of intron 45 predicts a branching stem-loop structure in which the central variable region lies in one loop and the putative branch point sequence lies in another loop, suggesting that the intron adopts a specific stem-loop structure that may be important for its removal. Although intron 45 appears to conform to the class of small, G-triplet-containing introns that are spliced by a mechanism utilizing intron definition, its high sequence conservation may be a reflection of constraints imposed by a unique mechanism that coordinates splicing of this last PKD1 intron with polyadenylation.

Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size.

PubMed

Medugorac, Ivica; Medugorac, Ana; Russ, Ingolf; Veit-Kensch, Claudia E; Taberlet, Pierre; Luntz, Bernhard; Mix, Henry M; Förster, Martin

2009-08-01

In times of rapid global and unforeseeable environmental changes, there is an urgent need for a sustainable cattle breeding policy, based on a global view. Most of the indigenous breeds are specialized in a particular habitat or production system but are rapidly disappearing. Thus, they represent an important resource to meet present and future breeding objectives. Based on 105 microsatellites, we obtained thorough information on genetic diversity and population structure of 16 cattle breeds that cover a geographical area from the domestication centre near Anatolia, through the Balkan and alpine regions, to the North-West of Europe. Breeds under strict artificial selection and indigenous breeds under traditional breeding schemes were included. The overall results showed that the genetic diversity is widespread in Busa breeds in the Anatolian and Balkan areas, when compared with the alpine and north-western European breeds. Our results reflect long-term evolutionary and short-term breeding events very well. The regular pattern of allele frequency distribution in the entire cattle population studied clearly suggests conservation of rare alleles by conservation of preferably unselected traditional breeds with large effective population sizes. From a global and long-term conservation genetics point of view, the native and highly variable breeds closer to the domestication centre could serve as valuable sources of genes for future needs, not only for cattle but also for other farm animals.

Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution

PubMed Central

2012-01-01

Background Staphylococcus aureus Repeat (STAR) elements are a type of interspersed intergenic direct repeat. In this study the conservation and variation in these elements was explored by bioinformatic analyses of published staphylococcal genome sequences and through sequencing of specific STAR element loci from a large set of S. aureus isolates. Results Using bioinformatic analyses, we found that the STAR elements were located in different genomic loci within each staphylococcal species. There was no correlation between the number of STAR elements in each genome and the evolutionary relatedness of staphylococcal species, however higher levels of repeats were observed in both S. aureus and S. lugdunensis compared to other staphylococcal species. Unexpectedly, sequencing of the internal spacer sequences of individual repeat elements from multiple isolates showed conservation at the sequence level within deep evolutionary lineages of S. aureus. Whilst individual STAR element loci were demonstrated to expand and contract, the sequences associated with each locus were stable and distinct from one another. Conclusions The high degree of lineage and locus-specific conservation of these intergenic repeat regions suggests that STAR elements are maintained due to selective or molecular forces with some of these elements having an important role in cell physiology. The high prevalence in two of the more virulent staphylococcal species is indicative of a potential role for STAR elements in pathogenesis. PMID:23020678

Comparitive Study of High-Order Positivity-Preserving WENO Schemes

NASA Technical Reports Server (NTRS)

Kotov, D. V.; Yee, H. C.; Sjogreen, B.

2014-01-01

In gas dynamics and magnetohydrodynamics flows, physically, the density ? and the pressure p should both be positive. In a standard conservative numerical scheme, however, the computed internal energy is The ideas of Zhang & Shu (2012) and Hu et al. (2012) precisely address the aforementioned issue. Zhang & Shu constructed a new conservative positivity-preserving procedure to preserve positive density and pressure for high-order Weighted Essentially Non-Oscillatory (WENO) schemes by the Lax-Friedrichs flux (WENO/LLF). In general, WENO/LLF is obtained by subtracting the kinetic energy from the total energy, resulting in a computed p that may be negative. Examples are problems in which the dominant energy is kinetic. Negative ? may often emerge in computing blast waves. In such situations the computed eigenvalues of the Jacobian will become imaginary. Consequently, the initial value problem for the linearized system will be ill posed. This explains why failure of preserving positivity of density or pressure may cause blow-ups of the numerical algorithm. The adhoc methods in numerical strategy which modify the computed negative density and/or the computed negative pressure to be positive are neither a conservative cure nor a stable solution. Conservative positivity-preserving schemes are more appropriate for such flow problems. too dissipative for flows such as turbulence with strong shocks computed in direct numerical simulations (DNS) and large eddy simulations (LES). The new conservative positivity-preserving procedure proposed in Hu et al. (2012) can be used with any high-order shock-capturing scheme, including high-order WENO schemes using the Roe's flux (WENO/Roe). The goal of this study is to compare the results obtained by non-positivity-preserving methods with the recently developed positivity-preserving schemes for representative test cases. In particular the more di cult 3D Noh and Sedov problems are considered. These test cases are chosen because of the negative pressure/density most often exhibited by standard high-order shock-capturing schemes. The simulation of a hypersonic nonequilibrium viscous shock tube that is related to the NASA Electric Arc Shock Tube (EAST) is also included. EAST is a high-temperature and high Mach number viscous nonequilibrium ow consisting of 13 species. In addition, as most common shock-capturing schemes have been developed for problems without source terms, when applied to problems with nonlinear and/or sti source terms these methods can result in spurious solutions, even when solving a conservative system of equations with a conservative scheme. This kind of behavior can be observed even for a scalar case as well as for the case consisting of two species and one reaction.. This EAST example indicated that standard high-order shock-capturing methods exhibit instability of density/pressure in addition to grid-dependent discontinuity locations with insufficient grid points. The evaluation of these test cases is based on the stability of the numerical schemes together with the accuracy of the obtained solutions.

Surgical and nonsurgical treatment of total rupture of the pectoralis major muscle in athletes: update and critical appraisal.

PubMed

Kircher, Jörn; Ziskoven, Christoph; Patzer, Thilo; Zaps, Daniela; Bittersohl, Bernd; Krauspe, Rüdiger

2010-10-11

The complete rupture of the pectoralis major tendon is an uncommon injury but has become increasingly common among athletes in recent years. This may be due to a higher number of individuals taking part in high-impact sports and weightlifting as well as the use of anabolic substances, which can make muscles and tendons vulnerable to injury. In recent literature, there are only few recommendations to rely on conservative treatment alone, but there are a number of reports and case series recommending early surgical intervention. Comparing the results of the two treatment regimens, there is clear evidence for a superior outcome after surgical repair with better cosmesis, better functional results, regaining of muscle power, and return to sports compared with the conservative treatment. In summary, anatomic surgical repair is the treatment of choice for complete acute ruptures of the pectoralis major tendon or muscle in athletes.

Conservative versus invasive stable ischemic heart disease management strategies: what do we plan to learn from the ISCHEMIA trial?

PubMed

Cheng-Torres, Kathleen A; Desai, Karan P; Sidhu, Mandeep S; Maron, David J; Boden, William E

2016-01-01

Over the past decade, landmark randomized clinical trials comparing initial management strategies in stable ischemic heart disease (SIHD) have demonstrated no significant reduction in 'hard' end points (all-cause mortality, cardiac death or myocardial infarction) with one strategy versus another. The main advantage derived from early revascularization is improved short-term quality of life. Nonetheless, questions remain regarding how best to manage SIHD patients, such as whether a high-risk subgroup can be identified that may experience a survival or myocardial infarction benefit from early revascularization, and if not, when should diagnostic catheterization and revascularization be performed. The International Study of Comparative Health Effectiveness with Medical and Invasive Approaches trial is designed to address these questions by randomizing SIHD patients with at least moderate ischemia to an initial conservative strategy of optimal medical therapy or an initial invasive strategy of optimal medical therapy plus cardiac catheterization and revascularization.

Rich stochastic dynamics of co-doped Er:Yb fluorescence upconversion nanoparticles in the presence of thermal, non-conservative, harmonic and optical forces

NASA Astrophysics Data System (ADS)

Nome, Rene A.; Sorbello, Cecilia; Jobbágy, Matías; Barja, Beatriz C.; Sanches, Vitor; Cruz, Joyce S.; Aguiar, Vinicius F.

2017-03-01

The stochastic dynamics of individual co-doped Er:Yb upconversion nanoparticles (UCNP) were investigated from experiments and simulations. The UCNP were characterized by high-resolution scanning electron microscopy, dynamic light scattering, and zeta potential measurements. Single UCNP measurements were performed by fluorescence upconversion micro-spectroscopy and optical trapping. The mean-square displacement (MSD) from single UCNP exhibited a time-dependent diffusion coefficient which was compared with Brownian dynamics simulations of a viscoelastic model of harmonically bound spheres. Experimental time-dependent two-dimensional trajectories of individual UCNP revealed correlated two-dimensional nanoparticle motion. The measurements were compared with stochastic trajectories calculated in the presence of a non-conservative rotational force field. Overall, the complex interplay of UCNP adhesion, thermal fluctuations and optical forces led to a rich stochastic behavior of these nanoparticles.

Large poroelastic deformation of a soft material

NASA Astrophysics Data System (ADS)

MacMinn, Christopher W.; Dufresne, Eric R.; Wettlaufer, John S.

2014-11-01

Flow through a porous material will drive mechanical deformation when the fluid pressure becomes comparable to the stiffness of the solid skeleton. This has applications ranging from hydraulic fracture for recovery of shale gas, where fluid is injected at high pressure, to the mechanics of biological cells and tissues, where the solid skeleton is very soft. The traditional linear theory of poroelasticity captures this fluid-solid coupling by combining Darcy's law with linear elasticity. However, linear elasticity is only volume-conservative to first order in the strain, which can become problematic when damage, plasticity, or extreme softness lead to large deformations. Here, we compare the predictions of linear poroelasticity with those of a large-deformation framework in the context of two model problems. We show that errors in volume conservation are compounded and amplified by coupling with the fluid flow, and can become important even when the deformation is small. We also illustrate these results with a laboratory experiment.

There is no highly conserved embryonic stage in the vertebrates: implications for current theories of evolution and development.

PubMed

Richardson, M K; Hanken, J; Gooneratne, M L; Pieau, C; Raynaud, A; Selwood, L; Wright, G M

1997-08-01

Embryos of different species of vertebrate share a common organisation and often look similar. Adult differences among species become more apparent through divergence at later stages. Some authors have suggested that members of most or all vertebrate clades pass through a virtually identical, conserved stage. This idea was promoted by Haeckel, and has recently been revived in the context of claims regarding the universality of developmental mechanisms. Thus embryonic resemblance at the tailbud stage has been linked with a conserved pattern of developmental gene expression - the zootype. Haeckel's drawings of the external morphology of various vertebrates remain the most comprehensive comparative data purporting to show a conserved stage. However, their accuracy has been questioned and only a narrow range of species was illustrated. In view of the current widespread interest in evolutionary developmental biology, and especially in the conservation of developmental mechanisms, re-examination of the extent of variation in vertebrate embryos is long overdue. We present here the first review of the external morphology of tailbud embryos, illustrated with original specimens from a wide range of vertebrate groups. We find that embryos at the tailbud stage - thought to correspond to a conserved stage - show variations in form due to allometry, heterochrony, and differences in body plan and somite number. These variations foreshadow important differences in adult body form. Contrary to recent claims that all vertebrate embryos pass through a stage when they are the same size, we find a greater than 10-fold variation in greatest length at the tailbud stage. Our survey seriously undermines the credibility of Haeckel's drawings, which depict not a conserved stage for vertebrates, but a stylised amniote embryo. In fact, the taxonomic level of greatest resemblance among vertebrate embryos is below the subphylum. The wide variation in morphology among vertebrate embryos is difficult to reconcile with the idea of a phyogenetically-conserved tailbud stage, and suggests that at least some developmental mechanisms are not highly constrained by the zootype. Our study also highlights the dangers of drawing general conclusions about vertebrate development from studies of gene expression in a small number of laboratory species.

Conservation of a domestic metapopulation structured into related and partly admixed strains.

PubMed

Ramljak, Jelena; Bunevski, Gjoko; Bytyqi, Hysen; Marković, Božidarka; Brka, Muhamed; Ivanković, Ante; Kume, Kristaq; Stojanović, Srđan; Nikolov, Vasil; Simčič, Mojca; Sölkner, Johann; Kunz, Elisabeth; Rothammer, Sophie; Seichter, Doris; Grünenfelder, Hans-Peter; Broxham, Elli T; Kugler, Waltraud; Medugorac, Ivica

2018-04-01

Preservation of genetic diversity is one of the most pressing challenges in the planetary boundaries concept. Within this context, we focused on genetic diversity in a native, unselected and highly admixed domesticated metapopulation. A set of 1,828 individuals from 60 different cattle breeds was analysed using a medium density SNP chip. Among these breeds, 14 Buša strains formed a metapopulation represented by 350 individuals, while the remaining 46 breeds represented the global cattle population. Genetic analyses showed that the scarcely selected and less differentiated Buša metapopulation contributed a substantial proportion (52.6%) of the neutral allelic diversity to this global taurine population. Consequently, there is an urgent need for synchronized maintenance of this highly fragmented domestic metapopulation, which is distributed over several countries without sophisticated infrastructure and highly endangered by continuous replacement crossing as part of the global genetic homogenization process. This study collected and evaluated samples, data and genomewide information and developed genome-assisted cross-border conservation concepts. To detect and maintain genetic integrity of the metapopulation strains, we designed and applied a composite test that combines six metrics based on additive genetic relationships, a nearest neighbour graph and the distribution of semiprivate alleles. Each metric provides distinct information components about past admixture events and offers an objective and powerful tool for the detection of admixed outliers. The here developed conservation methods and presented experiences could easily be adapted to comparable conservation programmes of domesticated or other metapopulations bred and kept in captivity or under some other sort of human control. © 2018 John Wiley & Sons Ltd.

Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia.

PubMed

Tapio, Miika; Ozerov, Mikhail; Tapio, Ilma; Toro, Miguel A; Marzanov, Nurbiy; Cinkulov, Mirjana; Goncharenko, Galina; Kiselyova, Tatyana; Murawski, Maziek; Kantanen, Juha

2010-08-10

Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.

Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia

PubMed Central

2010-01-01

Background Identification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation. Results Bayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity. Conclusions During initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success. PMID:20698974

Comparative sequence analysis of the X-inactivation center region in mouse, human, and bovine.

PubMed

Chureau, Corinne; Prissette, Marine; Bourdet, Agnès; Barbe, Valérie; Cattolico, Laurence; Jones, Louis; Eggen, André; Avner, Philip; Duret, Laurent

2002-06-01

We have sequenced to high levels of accuracy 714-kb and 233-kb regions of the mouse and bovine X-inactivation centers (Xic), respectively, centered on the Xist gene. This has provided the basis for a fully annotated comparative analysis of the mouse Xic with the 2.3-Mb orthologous region in human and has allowed a three-way species comparison of the core central region, including the Xist gene. These comparisons have revealed conserved genes, both coding and noncoding, conserved CpG islands and, more surprisingly, conserved pseudogenes. The distribution of repeated elements, especially LINE repeats, in the mouse Xic region when compared to the rest of the genome does not support the hypothesis of a role for these repeat elements in the spreading of X inactivation. Interestingly, an asymmetric distribution of LINE elements on the two DNA strands was observed in the three species, not only within introns but also in intergenic regions. This feature is suggestive of important transcriptional activity within these intergenic regions. In silico prediction followed by experimental analysis has allowed four new genes, Cnbp2, Ftx, Jpx, and Ppnx, to be identified and novel, widespread, complex, and apparently noncoding transcriptional activity to be characterized in a region 5' of Xist that was recently shown to attract histone modification early after the onset of X inactivation.

Effectiveness of telerehabilitation programme following surgery in shoulder impingement syndrome (SIS): study protocol for a randomized controlled non-inferiority trial.

PubMed

Pastora-Bernal, Jose-Manuel; Martín-Valero, Rocío; Barón-López, Francisco Javier; García-Gómez, Oscar

2017-02-23

Shoulder pain is common in society, with high prevalence in the general population. Shoulder impingement syndrome (SIS) is the most frequent cause. Patients suffer pain, muscle weakness and loss of movement in the affected joint. Initial treatment is predominantly conservative. The surgical option has high success rates and is often used when conservative strategy fails. Traditional physiotherapy and post-operative exercises are needed for the recovery of joint range, muscle strength, stability and functionality. Telerehabilitation programmes have shown positive results in some orthopaedic conditions after surgery. Customized telerehabilitation intervention programmes should be developed to recover shoulder function after SIS surgery. The objective of this study is to evaluate the feasibility and effectiveness of a telerehabilitation intervention compared with usual care in patients after subacromial decompression surgery. We will compare an intervention group receiving videoconferences and a telerehabilitation programme to a control group receiving traditional physiotherapy intervention in a single-blind, randomized controlled non-inferiority trial study design. Through this study, we will further develop our preliminary data set and practical experience with the telerehabilitation programmes to evaluate their effectiveness and compare this with traditional intervention. We will also explore patient satisfaction and cost-effectiveness. Patient enrolment is ongoing. ClinicalTrials.gov, NCT02909920 . 14 September 2016.

Functional analysis and transcriptional output of the Göttingen minipig genome.

PubMed

Heckel, Tobias; Schmucki, Roland; Berrera, Marco; Ringshandl, Stephan; Badi, Laura; Steiner, Guido; Ravon, Morgane; Küng, Erich; Kuhn, Bernd; Kratochwil, Nicole A; Schmitt, Georg; Kiialainen, Anna; Nowaczyk, Corinne; Daff, Hamina; Khan, Azinwi Phina; Lekolool, Isaac; Pelle, Roger; Okoth, Edward; Bishop, Richard; Daubenberger, Claudia; Ebeling, Martin; Certa, Ulrich

2015-11-14

In the past decade the Göttingen minipig has gained increasing recognition as animal model in pharmaceutical and safety research because it recapitulates many aspects of human physiology and metabolism. Genome-based comparison of drug targets together with quantitative tissue expression analysis allows rational prediction of pharmacology and cross-reactivity of human drugs in animal models thereby improving drug attrition which is an important challenge in the process of drug development. Here we present a new chromosome level based version of the Göttingen minipig genome together with a comparative transcriptional analysis of tissues with pharmaceutical relevance as basis for translational research. We relied on mapping and assembly of WGS (whole-genome-shotgun sequencing) derived reads to the reference genome of the Duroc pig and predict 19,228 human orthologous protein-coding genes. Genome-based prediction of the sequence of human drug targets enables the prediction of drug cross-reactivity based on conservation of binding sites. We further support the finding that the genome of Sus scrofa contains about ten-times less pseudogenized genes compared to other vertebrates. Among the functional human orthologs of these minipig pseudogenes we found HEPN1, a putative tumor suppressor gene. The genomes of Sus scrofa, the Tibetan boar, the African Bushpig, and the Warthog show sequence conservation of all inactivating HEPN1 mutations suggesting disruption before the evolutionary split of these pig species. We identify 133 Sus scrofa specific, conserved long non-coding RNAs (lncRNAs) in the minipig genome and show that these transcripts are highly conserved in the African pigs and the Tibetan boar suggesting functional significance. Using a new minipig specific microarray we show high conservation of gene expression signatures in 13 tissues with biomedical relevance between humans and adult minipigs. We underline this relationship for minipig and human liver where we could demonstrate similar expression levels for most phase I drug-metabolizing enzymes. Higher expression levels and metabolic activities were found for FMO1, AKR/CRs and for phase II drug metabolizing enzymes in minipig as compared to human. The variability of gene expression in equivalent human and minipig tissues is considerably higher in minipig organs, which is important for study design in case a human target belongs to this variable category in the minipig. The first analysis of gene expression in multiple tissues during development from young to adult shows that the majority of transcriptional programs are concluded four weeks after birth. This finding is in line with the advanced state of human postnatal organ development at comparative age categories and further supports the minipig as model for pediatric drug safety studies. Genome based assessment of sequence conservation combined with gene expression data in several tissues improves the translational value of the minipig for human drug development. The genome and gene expression data presented here are important resources for researchers using the minipig as model for biomedical research or commercial breeding. Potential impact of our data for comparative genomics, translational research, and experimental medicine are discussed.

Framing conservation on private lands: conserving oak in Oregon's Willamette Valley

Treesearch

A. Paige Fischer; John C. Bliss

2009-01-01

Conserving threatened habitats on private lands requires policies that advance the interests of landowners and natural resource professionals alike. Through qualitative analysis of individual and focus-group interviews, we compared how family forest owners and natural resource professionals frame conservation of threatened habitat: the oak woodlands and savanna in...

Efficient conservative ADER schemes based on WENO reconstruction and space-time predictor in primitive variables

NASA Astrophysics Data System (ADS)

Zanotti, Olindo; Dumbser, Michael

2016-01-01

We present a new version of conservative ADER-WENO finite volume schemes, in which both the high order spatial reconstruction as well as the time evolution of the reconstruction polynomials in the local space-time predictor stage are performed in primitive variables, rather than in conserved ones. To obtain a conservative method, the underlying finite volume scheme is still written in terms of the cell averages of the conserved quantities. Therefore, our new approach performs the spatial WENO reconstruction twice: the first WENO reconstruction is carried out on the known cell averages of the conservative variables. The WENO polynomials are then used at the cell centers to compute point values of the conserved variables, which are subsequently converted into point values of the primitive variables. This is the only place where the conversion from conservative to primitive variables is needed in the new scheme. Then, a second WENO reconstruction is performed on the point values of the primitive variables to obtain piecewise high order reconstruction polynomials of the primitive variables. The reconstruction polynomials are subsequently evolved in time with a novel space-time finite element predictor that is directly applied to the governing PDE written in primitive form. The resulting space-time polynomials of the primitive variables can then be directly used as input for the numerical fluxes at the cell boundaries in the underlying conservative finite volume scheme. Hence, the number of necessary conversions from the conserved to the primitive variables is reduced to just one single conversion at each cell center. We have verified the validity of the new approach over a wide range of hyperbolic systems, including the classical Euler equations of gas dynamics, the special relativistic hydrodynamics (RHD) and ideal magnetohydrodynamics (RMHD) equations, as well as the Baer-Nunziato model for compressible two-phase flows. In all cases we have noticed that the new ADER schemes provide less oscillatory solutions when compared to ADER finite volume schemes based on the reconstruction in conserved variables, especially for the RMHD and the Baer-Nunziato equations. For the RHD and RMHD equations, the overall accuracy is improved and the CPU time is reduced by about 25 %. Because of its increased accuracy and due to the reduced computational cost, we recommend to use this version of ADER as the standard one in the relativistic framework. At the end of the paper, the new approach has also been extended to ADER-DG schemes on space-time adaptive grids (AMR).

Comparing Methods for Prioritising Protected Areas for Investment: A Case Study Using Madagascar’s Dry Forest Reptiles

PubMed Central

Gardner, Charlie J.; Raxworthy, Christopher J.; Metcalfe, Kristian; Raselimanana, Achille P.; Smith, Robert J.; Davies, Zoe G.

2015-01-01

There are insufficient resources available to manage the world’s existing protected area portfolio effectively, so the most important sites should be prioritised in investment decision-making. Sophisticated conservation planning and assessment tools developed to identify locations for new protected areas can provide an evidence base for such prioritisations, yet decision-makers in many countries lack the institutional support and necessary capacity to use the associated software. As such, simple heuristic approaches such as species richness or number of threatened species are generally adopted to inform prioritisation decisions. However, their performance has never been tested. Using the reptile fauna of Madagascar’s dry forests as a case study, we evaluate the performance of four site prioritisation protocols used to rank the conservation value of 22 established and candidate protected areas. We compare the results to a benchmark produced by the widely-used systematic conservation planning software Zonation. The four indices scored sites on the basis of: i) species richness; ii) an index based on species’ Red List status; iii) irreplaceability (a key metric in systematic conservation planning); and, iv) a novel Conservation Value Index (CVI), which incorporates species-level information on endemism, representation in the protected area system, tolerance of habitat degradation and hunting/collection pressure. Rankings produced by the four protocols were positively correlated to the results of Zonation, particularly amongst high-scoring sites, but CVI and Irreplaceability performed better than Species Richness and the Red List Index. Given the technological capacity constraints experienced by decision-makers in the developing world, our findings suggest that heuristic metrics can represent a useful alternative to more sophisticated analyses, especially when they integrate species-specific information related to extinction risk. However, this can require access to, and understanding of, more complex species data. PMID:26162073

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 multiple scales. © 2017 The Authors. Global Change Biology Published by John Wiley & Sons Ltd.

Computational identification of developmental enhancers:conservation and function of transcription factor binding-site clustersin drosophila melanogaster and drosophila psedoobscura

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

Berman, Benjamin P.; Pfeiffer, Barret D.; Laverty, Todd R.

2004-08-06

Background The identification of sequences that control transcription in metazoans is a major goal of genome analysis. In a previous study, we demonstrated that searching for clusters of predicted transcription factor binding sites could discover active regulatory sequences, and identified 37 regions of the Drosophila melanogaster genome with high densities of predicted binding sites for five transcription factors involved in anterior-posterior embryonic patterning. Nine of these clusters overlapped known enhancers. Here, we report the results of in vivo functional analysis of 27 remaining clusters. Results We generated transgenic flies carrying each cluster attached to a basal promoter and reporter gene,more » and assayed embryos for reporter gene expression. Six clusters are enhancers of adjacent genes: giant, fushi tarazu, odd-skipped, nubbin, squeeze and pdm2; three drive expression in patterns unrelated to those of neighboring genes; the remaining 18 do not appear to have enhancer activity. We used the Drosophila pseudoobscura genome to compare patterns of evolution in and around the 15 positive and 18 false-positive predictions. Although conservation of primary sequence cannot distinguish true from false positives, conservation of binding-site clustering accurately discriminates functional binding-site clusters from those with no function. We incorporated conservation of binding-site clustering into a new genome-wide enhancer screen, and predict several hundred new regulatory sequences, including 85 adjacent to genes with embryonic patterns. Conclusions Measuring conservation of sequence features closely linked to function - such as binding-site clustering - makes better use of comparative sequence data than commonly used methods that examine only sequence identity.« less

Vegetation types on acid soils of Micronesia

Treesearch

Marjorie C. Falanruw; Thomas G.. Cole; Craig D. Whitesell

1987-01-01

The soils and vegetation of the Caroline high islands, Federated States of Micronesia, are being mapped by the U.S. Department of Agriculture's Forest Service and Soil Conservation Service. By the end of 1987, vegetation maps and reports on Kosrae, Pohnpei, Yap, four Truk Islands, and Palau are expected to be available. To compare soil types with vegetation types...

50 CFR 660.399 - EFH Conservation Areas off the Coast of California.

Code of Federal Regulations, 2010 CFR

2010-10-01

.... The boundary of the Harris Point EFH Conservation Area is defined by the mean high water line and... commercial and recreational take of living marine resources is allowed, exists between the mean high water... Scorpion EFH Conservation Area is defined by the mean high water line and a straight line connecting all of...

50 CFR 660.79 - EFH Conservation Areas off the Coast of California.

Code of Federal Regulations, 2011 CFR

2011-10-01

.... The boundary of the Harris Point EFH Conservation Area is defined by the mean high water line and... commercial and recreational take of living marine resources is allowed, exists between the mean high water... Scorpion EFH Conservation Area is defined by the mean high water line and a straight line connecting all of...

Identifying key areas of ecosystem services potential to improve ecological management in Chongqing City, southwest China.

PubMed

Xiao, Yang; Xiao, Qiang

2018-03-29

Because natural ecosystems and ecosystem services (ES) are both critical to the well-being of humankind, it is important to understand their relationships and congruence for conservation planning. Spatial conservation planning is required to set focused preservation priorities and to assess future ecological implications. This study uses the combined measures of ES models and ES potential to estimate and analyze all four groups of ecosystem services to generate opportunities to maximize ecosystem services. Subsequently, we identify the key areas of conservation priorities as future forestation and conservation hotspot zones to improve the ecological management in Chongqing City, located in the upper reaches of the Three Gorges Reservoir Area, China. Results show that ecosystem services potential is extremely obvious. Compared to ecosystem services from 2000, we determined that soil conservation could be increased by 59.11%, carbon sequestration by 129.51%, water flow regulation by 83.42%, and water purification by 84.42%. According to our prioritization results, approximately 48% of area converted to forests exhibited high improvements in all ecosystem services (categorized as hotspot-1, hotspot-2, and hotspot-3). The hotspots identified in this study can be used as an excellent surrogate for evaluation ecological engineering benefits and can be effectively applied in improving ecological management planning.

Role of lifestyle modifications for patients with laryngeal granuloma caused by gastro-esophageal reflux: comparison between conservative treatment and the surgical approach.

PubMed

Kobayashi, Rika; Tsunoda, Koichi; Ueha, Rumi; Fujimaki, Yoko; Nito, Takaharu; Yamasoba, Tatsuya

2017-03-01

It is considered that a regimen combining pharmacologic management and lifestyle modifications is the most effective treatment for laryngeal granulomas caused by GER. This study compared the results of the combination therapy and surgery to determine the best treatment of laryngeal granuloma caused by gastro-esophageal reflux in 51 patients. Prospective study. In the conservative treatment group, the CR rate was 89.7% and recurrence rate was 2.6%, while the lesions remained in patients (7.7%). This study compared the CR and recurrence rates between conservative treatment and surgery for granuloma. The results showed that the laryngeal granuloma recurrence rate was significantly lower with the conservative treatment regimen compared with surgery (p = .0016).

Local participation in biodiversity conservation initiatives: a comparative analysis of different models in South East Mexico.

PubMed

Méndez-López, María Elena; García-Frapolli, Eduardo; Pritchard, Diana J; Sánchez González, María Consuelo; Ruiz-Mallén, Isabel; Porter-Bolland, Luciana; Reyes-Garcia, Victoria

2014-12-01

In Mexico, biodiversity conservation is primarily implemented through three schemes: 1) protected areas, 2) payment-based schemes for environmental services, and 3) community-based conservation, officially recognized in some cases as Indigenous and Community Conserved Areas. In this paper we compare levels of local participation across conservation schemes. Through a survey applied to 670 households across six communities in Southeast Mexico, we document local participation during the creation, design, and implementation of the management plan of different conservation schemes. To analyze the data, we first calculated the frequency of participation at the three different stages mentioned, then created a participation index that characterizes the presence and relative intensity of local participation for each conservation scheme. Results showed that there is a low level of local participation across all the conservation schemes explored in this study. Nonetheless, the payment for environmental services had the highest local participation while the protected areas had the least. Our findings suggest that local participation in biodiversity conservation schemes is not a predictable outcome of a specific (community-based) model, thus implying that other factors might be important in determining local participation. This has implications on future strategies that seek to encourage local involvement in conservation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Multispecies genetic objectives in spatial conservation planning.

PubMed

Nielsen, Erica S; Beger, Maria; Henriques, Romina; Selkoe, Kimberly A; von der Heyden, Sophie

2017-08-01

Growing threats to biodiversity and global alteration of habitats and species distributions make it increasingly necessary to consider evolutionary patterns in conservation decision making. Yet, there is no clear-cut guidance on how genetic features can be incorporated into conservation-planning processes, despite multiple molecular markers and several genetic metrics for each marker type to choose from. Genetic patterns differ between species, but the potential tradeoffs among genetic objectives for multiple species in conservation planning are currently understudied. We compared spatial conservation prioritizations derived from 2 metrics of genetic diversity (nucleotide and haplotype diversity) and 2 metrics of genetic isolation (private haplotypes and local genetic differentiation) in mitochondrial DNA of 5 marine species. We compared outcomes of conservation plans based only on habitat representation with plans based on genetic data and habitat representation. Fewer priority areas were selected for conservation plans based solely on habitat representation than on plans that included habitat and genetic data. All 4 genetic metrics selected approximately similar conservation-priority areas, which is likely a result of prioritizing genetic patterns across a genetically diverse array of species. Largely, our results suggest that multispecies genetic conservation objectives are vital to creating protected-area networks that appropriately preserve community-level evolutionary patterns. © 2016 Society for Conservation Biology.

Adapting environmental function analysis for management of protected areas in small islands--case of Pico Island (the Azores).

PubMed

Calado, Helena; Bragagnolo, Chiara; Silva, Susana; Vergílio, Marta

2016-04-15

Protected areas (PAs) are considered key priorities for ensuring long-term sustainability of small islands. The traditional approach of conservation versus development is currently being replaced by an approach of "win-win" relationships. During the last decades PAs have been increasingly requested to simultaneously ensure biodiversity conservation, mainstream ecosystem services into main development policies, and accounting for leisure-related revenues to sustain local and regional economies. Following this new paradigm, the Smartparks project (Planning and Management System for Small Islands Protected Areas), encompassing this study, aimed at an innovative approach for supporting the management of PAs in small islands. In this study, we propose a methodology based on Environmental Functional Analyses (EFA) to compare the potential for conservation and the potential for use of PAs that can be used not only on small islands but also in other territories. For this purpose, a set of environmental and socio-economic components was defined and selected indicators describing each component to calculate conservation and use/development functions of PAs were established. Pico Island, in the Azores archipelago (Portugal), was selected as the case study for testing the methodology. The EFA for all PAs of Pico Island was performed identifying those with more potential for conservation or for development of human activities, and also those with high levels of conflict. A total of 34 indicators was applied (assigning a value from 1 to 3) to the 22 PAs composing the INP of Pico Island: 44% were scored with a value of 1, in both ecological and social components; 22% and 29% were scored 3 in ecological and social components respectively. Social indicators were generally considered less important than environmental ones. In general, PAs presented higher values for conservation. The results further show that the potential for conservation and/or development was consistent with the IUCN category and the objectives assigned to each PA at the time of its classification. However, most PAs are located in the conflict zone of the EFA matrix, revealing a high interaction between PAs conservation objectives and human activities, which brings concern to decision makers and PAs managers. Despite several limitations, the method allowed the performances of PAs to be compared, providing a suitable tool to support rapid assessments and monitoring of PA networks in small islands. The adaptation of the EFA to the PA domain traces a new path for estimating the multiple values of PAs and it may contribute to improve PA management and decision-making. The method could be further included as part of scenario exercise and adaptive management, supporting the prediction of the future evolution of PAs and assessing their potential for conservation in the future throughout the proposed indicators. Thus, the methodology is not exclusive for small islands contexts and, with necessary adaptations and rescaling, it could be a powerful tool in PAs network management worldwide. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comparative Mitogenomics of the Assassin Bug Genus Peirates (Hemiptera: Reduviidae: Peiratinae) Reveal Conserved Mitochondrial Genome Organization of P. atromaculatus, P. fulvescens and P. turpis

PubMed Central

Zhao, Guangyu; Li, Hu; Zhao, Ping; Cai, Wanzhi

2015-01-01

In this study, we sequenced four new mitochondrial genomes and presented comparative mitogenomic analyses of five species in the genus Peirates (Hemiptera: Reduviidae). Mitochondrial genomes of these five assassin bugs had a typical set of 37 genes and retained the ancestral gene arrangement of insects. The A+T content, AT- and GC-skews were similar to the common base composition biases of insect mtDNA. Genomic size ranges from 15,702 bp to 16,314 bp and most of the size variation was due to length and copy number of the repeat unit in the putative control region. All of the control region sequences included large tandem repeats present in two or more copies. Our result revealed similarity in mitochondrial genomes of P. atromaculatus, P. fulvescens and P. turpis, as well as the highly conserved genomic-level characteristics of these three species, e.g., the same start and stop codons of protein-coding genes, conserved secondary structure of tRNAs, identical location and length of non-coding and overlapping regions, and conservation of structural elements and tandem repeat unit in control region. Phylogenetic analyses also supported a close relationship between P. atromaculatus, P. fulvescens and P. turpis, which might be recently diverged species. The present study indicates that mitochondrial genome has important implications on phylogenetics, population genetics and speciation in the genus Peirates. PMID:25689825

Measuring the effectiveness of conservation: a novel framework to quantify the benefits of sage-grouse conservation policy and easements in Wyoming.

PubMed

Copeland, Holly E; Pocewicz, Amy; Naugle, David E; Griffiths, Tim; Keinath, Doug; Evans, Jeffrey; Platt, James

2013-01-01

Increasing energy and housing demands are impacting wildlife populations throughout western North America. Greater sage-grouse (Centrocercus urophasianus), a species known for its sensitivity to landscape-scale disturbance, inhabits the same low elevation sage-steppe in which much of this development is occurring. Wyoming has committed to maintain sage-grouse populations through conservation easements and policy changes that conserves high bird abundance "core" habitat and encourages development in less sensitive landscapes. In this study, we built new predictive models of oil and gas, wind, and residential development and applied build-out scenarios to simulate future development and measure the efficacy of conservation actions for maintaining sage-grouse populations. Our approach predicts sage-grouse population losses averted through conservation action and quantifies return on investment for different conservation strategies. We estimate that without conservation, sage-grouse populations in Wyoming will decrease under our long-term scenario by 14-29% (95% CI: 4-46%). However, a conservation strategy that includes the "core area" policy and $250 million in targeted easements could reduce these losses to 9-15% (95% CI: 3-32%), cutting anticipated losses by roughly half statewide and nearly two-thirds within sage-grouse core breeding areas. Core area policy is the single most important component, and targeted easements are complementary to the overall strategy. There is considerable uncertainty around the magnitude of our estimates; however, the relative benefit of different conservation scenarios remains comparable because potential biases and assumptions are consistently applied regardless of the strategy. There is early evidence based on a 40% reduction in leased hectares inside core areas that Wyoming policy is reducing potential for future fragmentation inside core areas. Our framework using build-out scenarios to anticipate species declines provides estimates that could be used by decision makers to determine if expected population losses warrant ESA listing.

Measuring the Effectiveness of Conservation: A Novel Framework to Quantify the Benefits of Sage-Grouse Conservation Policy and Easements in Wyoming

PubMed Central

Copeland, Holly E.; Pocewicz, Amy; Naugle, David E.; Griffiths, Tim; Keinath, Doug; Evans, Jeffrey; Platt, James

2013-01-01

Increasing energy and housing demands are impacting wildlife populations throughout western North America. Greater sage-grouse (Centrocercus urophasianus), a species known for its sensitivity to landscape-scale disturbance, inhabits the same low elevation sage-steppe in which much of this development is occurring. Wyoming has committed to maintain sage-grouse populations through conservation easements and policy changes that conserves high bird abundance “core” habitat and encourages development in less sensitive landscapes. In this study, we built new predictive models of oil and gas, wind, and residential development and applied build-out scenarios to simulate future development and measure the efficacy of conservation actions for maintaining sage-grouse populations. Our approach predicts sage-grouse population losses averted through conservation action and quantifies return on investment for different conservation strategies. We estimate that without conservation, sage-grouse populations in Wyoming will decrease under our long-term scenario by 14–29% (95% CI: 4–46%). However, a conservation strategy that includes the “core area” policy and $250 million in targeted easements could reduce these losses to 9–15% (95% CI: 3–32%), cutting anticipated losses by roughly half statewide and nearly two-thirds within sage-grouse core breeding areas. Core area policy is the single most important component, and targeted easements are complementary to the overall strategy. There is considerable uncertainty around the magnitude of our estimates; however, the relative benefit of different conservation scenarios remains comparable because potential biases and assumptions are consistently applied regardless of the strategy. There is early evidence based on a 40% reduction in leased hectares inside core areas that Wyoming policy is reducing potential for future fragmentation inside core areas. Our framework using build-out scenarios to anticipate species declines provides estimates that could be used by decision makers to determine if expected population losses warrant ESA listing. PMID:23826250

Pan-genome analysis of human gastric pathogen H. pylori: comparative genomics and pathogenomics approaches to identify regions associated with pathogenicity and prediction of potential core therapeutic targets.

PubMed

Ali, Amjad; Naz, Anam; Soares, Siomar C; Bakhtiar, Marriam; Tiwari, Sandeep; Hassan, Syed S; Hanan, Fazal; Ramos, Rommel; Pereira, Ulisses; Barh, Debmalya; Figueiredo, Henrique César Pereira; Ussery, David W; Miyoshi, Anderson; Silva, Artur; Azevedo, Vasco

2015-01-01

Helicobacter pylori is a human gastric pathogen implicated as the major cause of peptic ulcer and second leading cause of gastric cancer (~70%) around the world. Conversely, an increased resistance to antibiotics and hindrances in the development of vaccines against H. pylori are observed. Pan-genome analyses of the global representative H. pylori isolates consisting of 39 complete genomes are presented in this paper. Phylogenetic analyses have revealed close relationships among geographically diverse strains of H. pylori. The conservation among these genomes was further analyzed by pan-genome approach; the predicted conserved gene families (1,193) constitute ~77% of the average H. pylori genome and 45% of the global gene repertoire of the species. Reverse vaccinology strategies have been adopted to identify and narrow down the potential core-immunogenic candidates. Total of 28 nonhost homolog proteins were characterized as universal therapeutic targets against H. pylori based on their functional annotation and protein-protein interaction. Finally, pathogenomics and genome plasticity analysis revealed 3 highly conserved and 2 highly variable putative pathogenicity islands in all of the H. pylori genomes been analyzed.

Social influences on adaptive criterion learning.

PubMed

Cassidy, Brittany S; Dubé, Chad; Gutchess, Angela H

2015-07-01

People adaptively shift decision criteria when given biased feedback encouraging specific types of errors. Given that work on this topic has been conducted in nonsocial contexts, we extended the literature by examining adaptive criterion learning in both social and nonsocial contexts. Specifically, we compared potential differences in criterion shifting given performance feedback from social sources varying in reliability and from a nonsocial source. Participants became lax when given false positive feedback for false alarms, and became conservative when given false positive feedback for misses, replicating prior work. In terms of a social influence on adaptive criterion learning, people became more lax in response style over time if feedback was provided by a nonsocial source or by a social source meant to be perceived as unreliable and low-achieving. In contrast, people adopted a more conservative response style over time if performance feedback came from a high-achieving and reliable source. Awareness that a reliable and high-achieving person had not provided their feedback reduced the tendency to become more conservative, relative to those unaware of the source manipulation. Because teaching and learning often occur in a social context, these findings may have important implications for many scenarios in which people fine-tune their behaviors, given cues from others.

Interpreting Mammalian Evolution using Fugu Genome Comparisons

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

Stubbs, L; Ovcharenko, I; Loots, G G

2004-04-02

Comparative sequence analysis of the human and the pufferfish Fugu rubripes (fugu) genomes has revealed several novel functional coding and noncoding regions in the human genome. In particular, the fugu genome has been extremely valuable for identifying transcriptional regulatory elements in human loci harboring unusually high levels of evolutionary conservation to rodent genomes. In such regions, the large evolutionary distance between human and fishes provides an additional filter through which functional noncoding elements can be detected with high efficiency.

Optimal dynamic control of invasions: applying a systematic conservation approach.

PubMed

Adams, Vanessa M; Setterfield, Samantha A

2015-06-01

The social, economic, and environmental impacts of invasive plants are well recognized. However, these variable impacts are rarely accounted for in the spatial prioritization of funding for weed management. We examine how current spatially explicit prioritization methods can be extended to identify optimal budget allocations to both eradication and control measures of invasive species to minimize the costs and likelihood of invasion. Our framework extends recent approaches to systematic prioritization of weed management to account for multiple values that are threatened by weed invasions with a multi-year dynamic prioritization approach. We apply our method to the northern portion of the Daly catchment in the Northern Territory, which has significant conservation values that are threatened by gamba grass (Andropogon gayanus), a highly invasive species recognized by the Australian government as a Weed of National Significance (WONS). We interface Marxan, a widely applied conservation planning tool, with a dynamic biophysical model of gamba grass to optimally allocate funds to eradication and control programs under two budget scenarios comparing maximizing gain (MaxGain) and minimizing loss (MinLoss) optimization approaches. The prioritizations support previous findings that a MinLoss approach is a better strategy when threats are more spatially variable than conservation values. Over a 10-year simulation period, we find that a MinLoss approach reduces future infestations by ~8% compared to MaxGain in the constrained budget scenarios and ~12% in the unlimited budget scenarios. We find that due to the extensive current invasion and rapid rate of spread, allocating the annual budget to control efforts is more efficient than funding eradication efforts when there is a constrained budget. Under a constrained budget, applying the most efficient optimization scenario (control, minloss) reduces spread by ~27% compared to no control. Conversely, if the budget is unlimited it is more efficient to fund eradication efforts and reduces spread by ~65% compared to no control.

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.

Assessing High School Students’ Pro-Environmental Behaviour

NASA Astrophysics Data System (ADS)

Hidayah, N.; Agustin, R. R.

2017-09-01

This paper aims to reveal students’ pro-environmental behavior in a High School. Self-reported behavior assessment was administered in this study involving students with age range 15 to 18 years. Pro-environmental behavior in this study comprises six domains. Those are recycling, waste avoidance, consumerism, energy conservation, mobility and transportation, and vicarious conservation behavior. Pro-environmental behavior (PEB) of science class students was compared to behavior of non-science class students. Effect of students’ grade level and extracurricular activity on the behavior was evaluated. Study revealed that science could improve students’ PEB. It is because environmental topics are covered in science class. Student’s involvement in extracurricular activity may enhance PEB as well. In conclusion, students’ PEB is influenced by class program (science or non-science) but it is not influenced by time length in learning science. This finding could be consider by science educator in choosing strategy to enhance student’s pro-environmental behaviour.

Comparative Evolution of Morphological Regulatory Functions in Candida Species

PubMed Central

Lackey, Erika; Vipulanandan, Geethanjali; Childers, Delma S.

2013-01-01

Morphological transitions play an important role in virulence and virulence-related processes in a wide variety of pathogenic fungi, including the most commonly isolated human fungal pathogen Candida albicans. While environmental signals, transcriptional regulators, and target genes associated with C. albicans morphogenesis are well-characterized, considerably little is known about morphological regulatory mechanisms and the extent to which they are evolutionarily conserved in less pathogenic and less filamentous non-albicans Candida species (NACS). We have identified specific optimal filament-inducing conditions for three NACS (C. tropicalis, C. parapsilosis, and C. guilliermondii), which are very limited, suggesting that these species may be adapted for niche-specific filamentation in the host. Only a subset of evolutionarily conserved C. albicans filament-specific target genes were induced upon filamentation in C. tropicalis, C. parapsilosis, and C. guilliermondii. One of the genes showing conserved expression was UME6, a key filament-specific regulator of C. albicans hyphal development. Constitutive high-level expression of UME6 was sufficient to drive increased filamentation as well as biofilm formation and partly restore conserved filament-specific gene expression in both C. tropicalis and C. parapsilosis, suggesting that evolutionary differences in filamentation ability among pathogenic Candida species may be partially attributed to alterations in the expression level of a conserved filamentous growth machinery. In contrast to UME6, NRG1, an important repressor of C. albicans filamentation, showed only a partly conserved role in controlling NACS filamentation. Overall, our results suggest that C. albicans morphological regulatory functions are partially conserved in NACS and have evolved to respond to more specific sets of host environmental cues. PMID:23913541

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

NASA Astrophysics Data System (ADS)

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

2017-07-01

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

The rise of novelty in ecosystems.

PubMed

Radeloff, Volker C; Williams, John W; Bateman, Brooke L; Burke, Kevin D; Carter, Sarah K; Childress, Evan S; Cromwell, Kara J; Gratton, Claudio; Hasley, Andrew O; Kraemer, Benjamin M; Latzka, Alexander W; Marin-Spiotta, Erika; Meine, Curt D; Munoz, Samuel E; Neeson, Thomas M; Pidgeon, Anna M; Rissman, Adena R; Rivera, Ricardo J; Szymanski, Laura M; Usinowicz, Jacob

2015-12-01

Rapid and ongoing change creates novelty in ecosystems everywhere, both when comparing contemporary systems to their historical baselines, and predicted future systems to the present. However, the level of novelty varies greatly among places. Here we propose a formal and quantifiable definition of abiotic and biotic novelty in ecosystems, map abiotic novelty globally, and discuss the implications of novelty for the science of ecology and for biodiversity conservation. We define novelty as the degree of dissimilarity of a system, measured in one or more dimensions relative to a reference baseline, usually defined as either the present or a time window in the past. In this conceptualization, novelty varies in degree, it is multidimensional, can be measured, and requires a temporal and spatial reference. This definition moves beyond prior categorical definitions of novel ecosystems, and does not include human agency, self-perpetuation, or irreversibility as criteria. Our global assessment of novelty was based on abiotic factors (temperature, precipitation, and nitrogen deposition) plus human population, and shows that there are already large areas with high novelty today relative to the early 20th century, and that there will even be more such areas by 2050. Interestingly, the places that are most novel are often not the places where absolute changes are largest; highlighting that novelty is inherently different from change. For the ecological sciences, highly novel ecosystems present new opportunities to test ecological theories, but also challenge the predictive ability of ecological models and their validation. For biodiversity conservation, increasing novelty presents some opportunities, but largely challenges. Conservation action is necessary along the entire continuum of novelty, by redoubling efforts to protect areas where novelty is low, identifying conservation opportunities where novelty is high, developing flexible yet strong regulations and policies, and establishing long-term experiments to test management approaches. Meeting the challenge of novelty will require advances in the science of ecology, and new and creative. conservation approaches.

Comparative Study on High-Order Positivity-preserving WENO Schemes

NASA Technical Reports Server (NTRS)

Kotov, Dmitry V.; Yee, Helen M.; Sjogreen, Bjorn Axel

2013-01-01

The goal of this study is to compare the results obtained by non-positivity-preserving methods with the recently developed positivity-preserving schemes for representative test cases. In particular the more di cult 3D Noh and Sedov problems are considered. These test cases are chosen because of the negative pressure/density most often exhibited by standard high-order shock-capturing schemes. The simulation of a hypersonic nonequilibrium viscous shock tube that is related to the NASA Electric Arc Shock Tube (EAST) is also included. EAST is a high-temperature and high Mach number viscous nonequilibrium ow consisting of 13 species. In addition, as most common shock-capturing schemes have been developed for problems without source terms, when applied to problems with nonlinear and/or sti source terms these methods can result in spurious solutions, even when solving a conservative system of equations with a conservative scheme. This kind of behavior can be observed even for a scalar case (LeVeque & Yee 1990) as well as for the case consisting of two species and one reaction (Wang et al. 2012). For further information concerning this issue see (LeVeque & Yee 1990; Griffiths et al. 1992; Lafon & Yee 1996; Yee et al. 2012). This EAST example indicated that standard high-order shock-capturing methods exhibit instability of density/pressure in addition to grid-dependent discontinuity locations with insufficient grid points. The evaluation of these test cases is based on the stability of the numerical schemes together with the accuracy of the obtained solutions.

Comparative Efficacy of Hemagglutinin, Nucleoprotein, and Matrix 2 Protein Gene-Based Vaccination against H5N1 Influenza in Mouse and Ferret

PubMed Central

Rao, Srinivas S.; Kong, Wing-Pui; Wei, Chih-Jen; Van Hoeven, Neal; Gorres, J. Patrick; Nason, Martha; Andersen, Hanne; Tumpey, Terrence M.; Nabel, Gary J.

2010-01-01

Efforts to develop a broadly protective vaccine against the highly pathogenic avian influenza A (HPAI) H5N1 virus have focused on highly conserved influenza gene products. The viral nucleoprotein (NP) and ion channel matrix protein (M2) are highly conserved among different strains and various influenza A subtypes. Here, we investigate the relative efficacy of NP and M2 compared to HA in protecting against HPAI H5N1 virus. In mice, previous studies have shown that vaccination with NP and M2 in recombinant DNA and/or adenovirus vectors or with adjuvants confers protection against lethal challenge in the absence of HA. However, we find that the protective efficacy of NP and M2 diminishes as the virulence and dose of the challenge virus are increased. To explore this question in a model relevant to human disease, ferrets were immunized with DNA/rAd5 vaccines encoding NP, M2, HA, NP+M2 or HA+NP+M2. Only HA or HA+NP+M2 vaccination conferred protection against a stringent virus challenge. Therefore, while gene-based vaccination with NP and M2 may provide moderate levels of protection against low challenge doses, it is insufficient to confer protective immunity against high challenge doses of H5N1 in ferrets. These immunogens may require combinatorial vaccination with HA, which confers protection even against very high doses of lethal viral challenge. PMID:20352112

Multi-Action Planning for Threat Management: A Novel Approach for the Spatial Prioritization of Conservation Actions

PubMed Central

Cattarino, Lorenzo; Hermoso, Virgilio; Carwardine, Josie; Kennard, Mark J.; Linke, Simon

2015-01-01

Planning for the remediation of multiple threats is crucial to ensure the long term persistence of biodiversity. Limited conservation budgets require prioritizing which management actions to implement and where. Systematic conservation planning traditionally assumes that all the threats in priority sites are abated (fixed prioritization approach). However, abating only the threats affecting the species of conservation concerns may be more cost-effective. This requires prioritizing individual actions independently within the same site (independent prioritization approach), which has received limited attention so far. We developed an action prioritization algorithm that prioritizes multiple alternative actions within the same site. We used simulated annealing to find the combination of actions that remediate threats to species at the minimum cost. Our algorithm also accounts for the importance of selecting actions in sites connected through the river network (i.e., connectivity). We applied our algorithm to prioritize actions to address threats to freshwater fish species in the Mitchell River catchment, northern Australia. We compared how the efficiency of the independent and fixed prioritization approach varied as the importance of connectivity increased. Our independent prioritization approach delivered more efficient solutions than the fixed prioritization approach, particularly when the importance of achieving connectivity was high. By spatially prioritizing the specific actions necessary to remediate the threats affecting the target species, our approach can aid cost-effective habitat restoration and land-use planning. It is also particularly suited to solving resource allocation problems, where consideration of spatial design is important, such as prioritizing conservation efforts for highly mobile species, species facing climate change-driven range shifts, or minimizing the risk of threats spreading across different realms. PMID:26020794

Multi-action planning for threat management: a novel approach for the spatial prioritization of conservation actions.

PubMed

Cattarino, Lorenzo; Hermoso, Virgilio; Carwardine, Josie; Kennard, Mark J; Linke, Simon

2015-01-01

Planning for the remediation of multiple threats is crucial to ensure the long term persistence of biodiversity. Limited conservation budgets require prioritizing which management actions to implement and where. Systematic conservation planning traditionally assumes that all the threats in priority sites are abated (fixed prioritization approach). However, abating only the threats affecting the species of conservation concerns may be more cost-effective. This requires prioritizing individual actions independently within the same site (independent prioritization approach), which has received limited attention so far. We developed an action prioritization algorithm that prioritizes multiple alternative actions within the same site. We used simulated annealing to find the combination of actions that remediate threats to species at the minimum cost. Our algorithm also accounts for the importance of selecting actions in sites connected through the river network (i.e., connectivity). We applied our algorithm to prioritize actions to address threats to freshwater fish species in the Mitchell River catchment, northern Australia. We compared how the efficiency of the independent and fixed prioritization approach varied as the importance of connectivity increased. Our independent prioritization approach delivered more efficient solutions than the fixed prioritization approach, particularly when the importance of achieving connectivity was high. By spatially prioritizing the specific actions necessary to remediate the threats affecting the target species, our approach can aid cost-effective habitat restoration and land-use planning. It is also particularly suited to solving resource allocation problems, where consideration of spatial design is important, such as prioritizing conservation efforts for highly mobile species, species facing climate change-driven range shifts, or minimizing the risk of threats spreading across different realms.

Distributional dynamics of a vulnerable species in response to past and future climate change: a window for conservation prospects

PubMed Central

Bai, Yunjun; Wei, Xueping

2018-01-01

Background The ongoing change in climate is predicted to exert unprecedented effects on Earth’s biodiversity at all levels of organization. Biological conservation is important to prevent biodiversity loss, especially for species facing a high risk of extinction. Understanding the past responses of species to climate change is helpful for revealing response mechanisms, which will contribute to the development of effective conservation strategies in the future. Methods In this study, we modelled the distributional dynamics of a ‘Vulnerable’ species, Pseudolarix amabilis, in response to late Quaternary glacial-interglacial cycles and future 2080 climate change using an ecological niche model (MaxEnt). We also performed migration vector analysis to reveal the potential migration of the population over time. Results Historical modelling indicates that the range dynamics of P. amabilis is highly sensitive to climate change and that its long-distance dispersal ability and potential for evolutionary adaption are limited. Compared to the current climatically suitable areas for this species, future modelling showed significant migration northward towards future potential climatically suitable areas. Discussion In combination with the predicted future distribution, the mechanism revealed by the historical response suggests that this species will not be able to fully occupy the future expanded areas of suitable climate or adapt to the unsuitable climate across the future contraction regions. As a result, we suggest assisted migration as an effective supplementary means of conserving this vulnerable species in the face of the unprecedentedly rapid climate change of the 21st century. As a study case, this work highlights the significance of introducing historical perspectives while researching species conservation, especially for currently vulnerable or endangered taxa that once had a wider distribution in geological time. PMID:29362700

Reconstruction of the High-Osmolarity Glycerol (HOG) Signaling Pathway from the Halophilic Fungus Wallemia ichthyophaga in Saccharomyces cerevisiae.

PubMed

Konte, Tilen; Terpitz, Ulrich; Plemenitaš, Ana

2016-01-01

The basidiomycetous fungus Wallemia ichthyophaga grows between 1.7 and 5.1 M NaCl and is the most halophilic eukaryote described to date. Like other fungi, W. ichthyophaga detects changes in environmental salinity mainly by the evolutionarily conserved high-osmolarity glycerol (HOG) signaling pathway. In Saccharomyces cerevisiae, the HOG pathway has been extensively studied in connection to osmotic regulation, with a valuable knock-out strain collection established. In the present study, we reconstructed the architecture of the HOG pathway of W. ichthyophaga in suitable S. cerevisiae knock-out strains, through heterologous expression of the W. ichthyophaga HOG pathway proteins. Compared to S. cerevisiae, where the Pbs2 (ScPbs2) kinase of the HOG pathway is activated via the SHO1 and SLN1 branches, the interactions between the W. ichthyophaga Pbs2 (WiPbs2) kinase and the W. ichthyophaga SHO1 branch orthologs are not conserved: as well as evidence of poor interactions between the WiSho1 Src-homology 3 (SH3) domain and the WiPbs2 proline-rich motif, the absence of a considerable part of the osmosensing apparatus in the genome of W. ichthyophaga suggests that the SHO1 branch components are not involved in HOG signaling in this halophilic fungus. In contrast, the conserved activation of WiPbs2 by the S. cerevisiae ScSsk2/ScSsk22 kinase and the sensitivity of W. ichthyophaga cells to fludioxonil, emphasize the significance of two-component (SLN1-like) signaling via Group III histidine kinase. Combined with protein modeling data, our study reveals conserved and non-conserved protein interactions in the HOG signaling pathway of W. ichthyophaga and therefore significantly improves the knowledge of hyperosmotic signal processing in this halophilic fungus.

Distributional dynamics of a vulnerable species in response to past and future climate change: a window for conservation prospects.

PubMed

Bai, Yunjun; Wei, Xueping; Li, Xiaoqiang

2018-01-01

The ongoing change in climate is predicted to exert unprecedented effects on Earth's biodiversity at all levels of organization. Biological conservation is important to prevent biodiversity loss, especially for species facing a high risk of extinction. Understanding the past responses of species to climate change is helpful for revealing response mechanisms, which will contribute to the development of effective conservation strategies in the future. In this study, we modelled the distributional dynamics of a 'Vulnerable' species, Pseudolarix amabilis , in response to late Quaternary glacial-interglacial cycles and future 2080 climate change using an ecological niche model (MaxEnt). We also performed migration vector analysis to reveal the potential migration of the population over time. Historical modelling indicates that the range dynamics of P. amabilis is highly sensitive to climate change and that its long-distance dispersal ability and potential for evolutionary adaption are limited. Compared to the current climatically suitable areas for this species, future modelling showed significant migration northward towards future potential climatically suitable areas. In combination with the predicted future distribution, the mechanism revealed by the historical response suggests that this species will not be able to fully occupy the future expanded areas of suitable climate or adapt to the unsuitable climate across the future contraction regions. As a result, we suggest assisted migration as an effective supplementary means of conserving this vulnerable species in the face of the unprecedentedly rapid climate change of the 21st century. As a study case, this work highlights the significance of introducing historical perspectives while researching species conservation, especially for currently vulnerable or endangered taxa that once had a wider distribution in geological time.

Individual perception of bees: Between perceived danger and willingness to protect

PubMed Central

Bogner, Franz Xaver

2017-01-01

The current loss of biodiversity has found its way into the media. Especially the loss of bees as pollinators has recently received much attention aiming to increase public awareness about the consequence of pollinator loss and strategies for protection. However, pollinating insects like bees often prompt considerable anxiety. Negative emotions such as fear and disgust often lead to lack of support for conservation and appropriate initiatives for protection. Our study monitored perceptions of bees in the contexts of conservation and danger bees possibly represent by applying a semantic differential using contrasting adjectives under the heading “I think bees are…”. Additionally, open questions were applied to examine individual perceptions of danger and conservation of bees. Respondents were students from primary school, secondary school and university. We compared these novices (n = 499) to experts (beekeepers, n = 153). An exploratory factor analysis of the semantic differential responses yielded three major oblique factors: Interest, Danger and Conservation & Usefulness. The inter-correlations of these factors were significant. Although all subgroups showed an overall high willingness to protect bees, the perception of danger scored medium. The individual experience of bee stings was the most prevalent reason for expressing fear. Educational programs focusing on pollinator conservation may reduce the perceived danger through removing misinformation, and supporting interest in the species. Based on the overall positive attitude toward bees, we suggest introducing bees (e.g., Apis mellifera) as a flagship species for pollinator conservation. PMID:28662124

Reductions in global biodiversity loss predicted from conservation spending.

PubMed

Waldron, Anthony; Miller, Daniel C; Redding, Dave; Mooers, Arne; Kuhn, Tyler S; Nibbelink, Nate; Roberts, J Timmons; Tobias, Joseph A; Gittleman, John L

2017-11-16

Halting global biodiversity loss is central to the Convention on Biological Diversity and United Nations Sustainable Development Goals, but success to date has been very limited. A critical determinant of success in achieving these goals is the financing that is committed to maintaining biodiversity; however, financing decisions are hindered by considerable uncertainty over the likely impact of any conservation investment. For greater effectiveness, we need an evidence-based model that shows how conservation spending quantitatively reduces the rate of biodiversity loss. Here we demonstrate such a model, and empirically quantify how conservation investment reduced biodiversity loss in 109 countries (signatories to the Convention on Biological Diversity and Sustainable Development Goals), by a median average of 29% per country between 1996 and 2008. We also show that biodiversity changes in signatory countries can be predicted with high accuracy, using a dual model that balances the effects of conservation investment against those of economic, agricultural and population growth (human development pressures). Decision-makers can use this model to forecast the improvement that any proposed biodiversity budget would achieve under various scenarios of human development pressure, and then compare these forecasts to any chosen policy target. We find that the impact of spending decreases as human development pressures grow, which implies that funding may need to increase over time. The model offers a flexible tool for balancing the Sustainable Development Goals of human development and maintaining biodiversity, by predicting the dynamic changes in conservation finance that will be needed as human development proceeds.

Reductions in global biodiversity loss predicted from conservation spending

NASA Astrophysics Data System (ADS)

Waldron, Anthony; Miller, Daniel C.; Redding, Dave; Mooers, Arne; Kuhn, Tyler S.; Nibbelink, Nate; Roberts, J. Timmons; Tobias, Joseph A.; Gittleman, John L.

2017-11-01

Halting global biodiversity loss is central to the Convention on Biological Diversity and United Nations Sustainable Development Goals, but success to date has been very limited. A critical determinant of success in achieving these goals is the financing that is committed to maintaining biodiversity; however, financing decisions are hindered by considerable uncertainty over the likely impact of any conservation investment. For greater effectiveness, we need an evidence-based model that shows how conservation spending quantitatively reduces the rate of biodiversity loss. Here we demonstrate such a model, and empirically quantify how conservation investment between 1996 and 2008 reduced biodiversity loss in 109 countries (signatories to the Convention on Biological Diversity and Sustainable Development Goals), by a median average of 29% per country. We also show that biodiversity changes in signatory countries can be predicted with high accuracy, using a dual model that balances the effects of conservation investment against those of economic, agricultural and population growth (human development pressures). Decision-makers can use this model to forecast the improvement that any proposed biodiversity budget would achieve under various scenarios of human development pressure, and then compare these forecasts to any chosen policy target. We find that the impact of spending decreases as human development pressures grow, which implies that funding may need to increase over time. The model offers a flexible tool for balancing the Sustainable Development Goals of human development and maintaining biodiversity, by predicting the dynamic changes in conservation finance that will be needed as human development proceeds.

75 FR 66119 - Proposed Information Collection; International Conservation Grant Programs

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-27

..., great apes, elephants, and many other highly cherished species. The Division of International Conservation administers 11 competitive grant programs funded under the: African Elephant Conservation Act (16 U.S.C. 4201-4245). Asian Elephant Conservation Act of 1997 (16 U.S.C. 4261). Great Apes Conservation...

Early Stage Blood Purification for Paraquat Poisoning: A Multicenter Retrospective Study.

PubMed

Li, An; Li, Wenxiong; Hao, Fengtong; Wang, Haishi

2016-01-01

To evaluate the efficacy of conservative treatment vs. hemoperfusion (HP) vs. HP + continuous veno-venous hemofiltration (CVVH) for acute Paraquat (PQ) poisoning. This was a multicenter retrospective study of patients with PQ poisoning between January 2013 and June 2014. Clinical data and PQ serum levels were collected at baseline and after 24, 48, and 72 h of treatment. Seventy-five, 65, and 43 underwent conservative treatment only (conservative treatment group), conservative treatment + HP (HP group), and conservative treatment + HP + CVVH (HP + CVVH group), respectively. PQ serum levels decreased in all groups after 72 h of treatment (p < 0.001); meanwhile, these values decreased faster in the HP and HP + CVVH groups compared with the conservative treatment group. More importantly, PQ blood levels were significantly lower in the HP + CVVH group compared with the HP group at 24 h (p < 0.05). Sequential organ failure assessment (ΔSOFA) values in the HP and HP + CVVH groups were significantly lower compared with that obtained for the conservative treatment group (p < 0.05). The 60-day survival rates were 21.3, 43.1 and 46.5%, respectively. Multivariate analysis indicated that age, PQ dose, admission PQ levels, and admission SOFA score were independently associated with mortality. HP and HP + CVVH were protective factors. Early HP or HP + CVVH after PQ poisoning could decrease PQ blood levels, alleviate organ damage, and increase survival. © 2016 S. Karger AG, Basel.

Using the NCBI Genome Databases to Compare the Genes for Human & Chimpanzee Beta Hemoglobin

ERIC Educational Resources Information Center

Offner, Susan

2010-01-01

The beta hemoglobin protein is identical in humans and chimpanzees. In this tutorial, students see that even though the proteins are identical, the genes that code for them are not. There are many more differences in the introns than in the exons, which indicates that coding regions of DNA are more highly conserved than non-coding regions.

Subirrigation for production of native plants in nurseries - concepts, current knowledge, and implementation

Treesearch

Justin L. Schmal; Kas Dumroese; Anthony S. Davis; Jeremy Pinto; Douglass F. Jacobs

2011-01-01

Subirrigation, a method whereby water is allowed to move upward into the growing medium by capillary action, has been the focus of recent research in forest and conservation nurseries growing a wide variety of native plants. Subirrigation reduces the amount of water needed for producing high-quality plants, discharged wastewater, and leaching of nutrients compared with...

Structural re-alignment in an immunologic surface region of ricin A chain

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

Zemla, A T; Zhou, C E

2007-07-24

We compared structure alignments generated by several protein structure comparison programs to determine whether existing methods would satisfactorily align residues at a highly conserved position within an immunogenic loop in ribosome inactivating proteins (RIPs). Using default settings, structure alignments generated by several programs (CE, DaliLite, FATCAT, LGA, MAMMOTH, MATRAS, SHEBA, SSM) failed to align the respective conserved residues, although LGA reported correct residue-residue (R-R) correspondences when the beta-carbon (Cb) position was used as the point of reference in the alignment calculations. Further tests using variable points of reference indicated that points distal from the beta carbon along a vector connectingmore » the alpha and beta carbons yielded rigid structural alignments in which residues known to be highly conserved in RIPs were reported as corresponding residues in structural comparisons between ricin A chain, abrin-A, and other RIPs. Results suggest that approaches to structure alignment employing alternate point representations corresponding to side chain position may yield structure alignments that are more consistent with observed conservation of functional surface residues than do standard alignment programs, which apply uniform criteria for alignment (i.e., alpha carbon (Ca) as point of reference) along the entirety of the peptide chain. We present the results of tests that suggest the utility of allowing user-specified points of reference in generating alternate structural alignments, and we present a web server for automatically generating such alignments.« less

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

PubMed

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

1999-12-01

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

Vaginismus and dyspareunia: relationship with general and sex-related moral standards.

PubMed

Borg, Charmaine; de Jong, Peter J; Weijmar Schultz, Willibrord

2011-01-01

Relatively strong adherence to conservative values and/or relatively strict sex-related moral standards logically restricts the sexual repertoire and will lower the threshold for experiencing negative emotions in a sexual context. In turn, this may generate withdrawal and avoidance behavior, which is at the nucleus of vaginismus. To examine whether indeed strong adherence to conservative morals and/or strict sexual standards may be involved in vaginismus. The Schwartz Value Survey (SVS) to investigate the individual's value pattern and the Sexual Disgust Questionnaire (SDQ) to index the willingness to perform certain sexual activities as an indirect measure of sex-related moral standards. The SVS and SDQ were completed by three groups: women diagnosed with vaginismus (N=24), a group of women diagnosed with dyspareunia (N=24), and a healthy control group of women without sexual complaints (N=32). Specifically, the vaginismus group showed relatively low scores on liberal values together with comparatively high scores on conservative values. Additionally, the vaginismus group was more restricted in their readiness to perform particular sex-related behaviors than the control group. The dyspareunia group, on both the SVS and the SDQ, placed between the vaginismus and the control group, but not significantly different than either of the groups. The findings are consistent with the view that low liberal and high conservative values, along with restricted sexual standards, are involved in the development/maintenance of vaginismus. © 2010 International Society for Sexual Medicine.

Discontinuous Spectral Difference Method for Conservation Laws on Unstructured Grids

NASA Technical Reports Server (NTRS)

Liu, Yen; Vinokur, Marcel; Wang, Z. J.

2004-01-01

A new, high-order, conservative, and efficient method for conservation laws on unstructured grids is developed. The concept of discontinuous and high-order local representations to achieve conservation and high accuracy is utilized in a manner similar to the Discontinuous Galerkin (DG) and the Spectral Volume (SV) methods, but while these methods are based on the integrated forms of the equations, the new method is based on the differential form to attain a simpler formulation and higher efficiency. A discussion on the Discontinuous Spectral Difference (SD) Method, locations of the unknowns and flux points and numerical results are also presented.

Personal circumstances and social characteristics as determinants of landholder participation in biodiversity conservation programs.

PubMed

Moon, Katie; Marshall, Nadine; Cocklin, Chris

2012-12-30

Adequate conservation of biodiversity on private land remains elusive due, in part, to a failure to understand the personal circumstances and social characteristics of private landholders. Our aim was to identify those personal and social dimensions of landholders that might contribute to improved conservation policy and program design and, thereby, participation in private land conservation. We tested whether personal circumstances of landholders (e.g., lifestyle and wellbeing, information and knowledge, financial security) and social characteristics (e.g., attitudes, norms, and trust) would be important predictors of landholders' capacity and willingness to participate in biodiversity conservation programs. Forty-five participants and twenty-nine non-participants of biodiversity conservation programs in north Queensland, Australia, were surveyed to: 1) examine differences between their personal circumstances and social characteristics that may influence participation; and 2) explore whether personal circumstances and social characteristics were influenced by participation. The results revealed that, compared to participants, non-participants in conservation programs had significantly different personal circumstances and social characteristics for four of eight measured variables. Compared to participants, non-participants demonstrated a reduced capacity and willingness to participate in conservation programs. Participation did not appear to have a strong influence on participants' personal circumstances or social characteristics, and when social norms supported conservation, programs did not demonstrate additionality. Conservation policies that maintain or improve landholders' personal circumstances and that promote pro-environmental norms may result in increased participation and thereby conservation outcomes. Copyright © 2012 Elsevier Ltd. All rights reserved.

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.

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.

Genetic diversity and structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China.

PubMed

Liu, Wei; Yin, Dongxue; Liu, Jianjun; Li, Na

2014-01-01

Sinopodophyllum hexandrum is an important medicinal plant whose genetic diversity must be conserved because it is endangered. The Qinling Mts. are a S. hexandrum distribution area that has unique environmental features that highly affect the evolution of the species. To provide the reference data for evolutionary and conservation studies, the genetic diversity and population structure of S. hexandrum in its overall natural distribution areas in the Qinling Mts. were investigated through inter-simple sequence repeats analysis of 32 natural populations. The 11 selected primers generated a total of 135 polymorphic bands. S. hexandrum genetic diversity was low within populations (average He = 0.0621), but higher at the species level (He = 0.1434). Clear structure and high genetic differentiation among populations were detected by using the unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. The clustering approaches supported a division of the 32 populations into three major groups, for which analysis of molecular variance confirmed significant variation (63.27%) among populations. The genetic differentiation may have been attributed to the limited gene flow (Nm = 0.3587) in the species. Isolation by distance among populations was determined by comparing genetic distance versus geographic distance by using the Mantel test. Result was insignificant (r = 0.212, P = 0.287) at 0.05, showing that their spatial pattern and geographic locations are not correlated. Given the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve S. hexandrum in Qinling Mts., and other populations must be sampled to retain as much genetic diversity of the species to achieve ex situ preservation as a supplement to in situ conservation.

Genetic Diversity and Structure of Sinopodophyllum hexandrum (Royle) Ying in the Qinling Mountains, China

PubMed Central

Liu, Wei; Yin, Dongxue; Liu, Jianjun; Li, Na

2014-01-01

Sinopodophyllum hexandrum is an important medicinal plant whose genetic diversity must be conserved because it is endangered. The Qinling Mts. are a S. hexandrum distribution area that has unique environmental features that highly affect the evolution of the species. To provide the reference data for evolutionary and conservation studies, the genetic diversity and population structure of S. hexandrum in its overall natural distribution areas in the Qinling Mts. were investigated through inter-simple sequence repeats analysis of 32 natural populations. The 11 selected primers generated a total of 135 polymorphic bands. S. hexandrum genetic diversity was low within populations (average He = 0.0621), but higher at the species level (He = 0.1434). Clear structure and high genetic differentiation among populations were detected by using the unweighted pair group method for arithmetic averages, principle coordinate analysis and Bayesian clustering. The clustering approaches supported a division of the 32 populations into three major groups, for which analysis of molecular variance confirmed significant variation (63.27%) among populations. The genetic differentiation may have been attributed to the limited gene flow (Nm = 0.3587) in the species. Isolation by distance among populations was determined by comparing genetic distance versus geographic distance by using the Mantel test. Result was insignificant (r = 0.212, P = 0.287) at 0.05, showing that their spatial pattern and geographic locations are not correlated. Given the low within-population genetic diversity, high differentiation among populations and the increasing anthropogenic pressure on the species, in situ conservation measures were recommended to preserve S. hexandrum in Qinling Mts., and other populations must be sampled to retain as much genetic diversity of the species to achieve ex situ preservation as a supplement to in situ conservation. PMID:25333788

Crystal Structure and Size-Dependent Neutralization Properties of HK20, a Human Monoclonal Antibody Binding to the Highly Conserved Heptad Repeat 1 of gp41

PubMed Central

Seaman, Mike S.; Lutje Hulsik, David; Hinz, Andreas; Vanzetta, Fabrizia; Agatic, Gloria; Silacci, Chiara; Mainetti, Lara; Scarlatti, Gabriella; Sallusto, Federica; Weiss, Robin; Lanzavecchia, Antonio; Weissenhorn, Winfried

2010-01-01

The human monoclonal antibody (mAb) HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1) of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2.3 Å resolution. HK20 employs its heavy chain CDR H2 and H3 loops to bind into a conserved hydrophobic HR1 pocket that is occupied by HR2 residues in the gp41 post fusion conformation. Compared to the previously described HR1-specific mAb D5, HK20 approaches its epitope with a different angle which might favor epitope access and thus contribute to its higher neutralization breadth and potency. Comparison of the neutralization activities of HK20 IgG, Fab and scFv employing both single cycle and multiple cycle neutralization assays revealed much higher potencies for the smaller Fab and scFv over IgG, implying that the target site is difficult to access for complete antibodies. Nevertheless, two thirds of sera from HIV-1 infected individuals contain significant titers of HK20-inhibiting antibodies. The breadth of neutralization of primary isolates across all clades, the higher potencies for C-clade viruses and the targeting of a distinct site as compared to the fusion inhibitor T-20 demonstrate the potential of HK20 scFv as a therapeutic tool. PMID:21124990

Crystal structure and size-dependent neutralization properties of HK20, a human monoclonal antibody binding to the highly conserved heptad repeat 1 of gp41.

PubMed

Sabin, Charles; Corti, Davide; Buzon, Victor; Seaman, Mike S; Lutje Hulsik, David; Hinz, Andreas; Vanzetta, Fabrizia; Agatic, Gloria; Silacci, Chiara; Mainetti, Lara; Scarlatti, Gabriella; Sallusto, Federica; Weiss, Robin; Lanzavecchia, Antonio; Weissenhorn, Winfried

2010-11-18

The human monoclonal antibody (mAb) HK20 neutralizes a broad spectrum of primary HIV-1 isolates by targeting the highly conserved heptad repeat 1 (HR1) of gp41, which is transiently exposed during HIV-1 entry. Here we present the crystal structure of the HK20 Fab in complex with a gp41 mimetic 5-Helix at 2.3 Å resolution. HK20 employs its heavy chain CDR H2 and H3 loops to bind into a conserved hydrophobic HR1 pocket that is occupied by HR2 residues in the gp41 post fusion conformation. Compared to the previously described HR1-specific mAb D5, HK20 approaches its epitope with a different angle which might favor epitope access and thus contribute to its higher neutralization breadth and potency. Comparison of the neutralization activities of HK20 IgG, Fab and scFv employing both single cycle and multiple cycle neutralization assays revealed much higher potencies for the smaller Fab and scFv over IgG, implying that the target site is difficult to access for complete antibodies. Nevertheless, two thirds of sera from HIV-1 infected individuals contain significant titers of HK20-inhibiting antibodies. The breadth of neutralization of primary isolates across all clades, the higher potencies for C-clade viruses and the targeting of a distinct site as compared to the fusion inhibitor T-20 demonstrate the potential of HK20 scFv as a therapeutic tool.

Trade-offs between pasture production and farmland bird conservation: exploration of options using a dynamic farm model.

PubMed

Sabatier, R; Teillard, F; Rossing, W A H; Doyen, L; Tichit, M

2015-05-01

In European grassland landscapes, grazing and mowing play a key role for the maintenance of high-quality habitats that host important bird populations. As grasslands are also key resources for cattle feeding, there is a need to develop management strategies that achieve the double objective of production and biodiversity conservation. The objective of this study was to use a modelling approach to generate recognisable patterns of bird dynamics in farms composed of different land use proportions, and to compare their production and ecological dimensions. We developed a dynamic model, which linked grassland management to bird population dynamics at the field and farm levels. The model was parameterised for two types of suckling farms corresponding to contrasting levels of grassland intensification and for two bird species of high conservation value. A viability algorithm was used to define and assess viable management strategies for production and ecological performance so as to draw the shape of the relationship between both types of performances for the two types of farms. Our results indicated that, at the farm level, there was a farming system effect with a negative and non-linear relationship linking performance. Improving bird population maintenance was less costly in extensive farms compared with intensive farms. At the field level, the model predicted the timing and intensity of land use, maximising either production or ecological performance. The results suggested that multi-objective grassland management would benefit from public policies that consider levels of organisation higher than the field level, such as the farm or the landscape.

Genetic Diversity in Endangered Guizhou Snub-Nosed Monkeys (Rhinopithecus brelichi): Contrasting Results from Microsatellite and Mitochondrial DNA Data

PubMed Central

Kolleck, Jakob; Yang, Mouyu; Zinner, Dietmar; Roos, Christian

2013-01-01

To evaluate the conservation status of a species or population it is necessary to gain insight into its ecological requirements, reproduction, genetic population structure, and overall genetic diversity. In our study we examined the genetic diversity of Rhinopithecus brelichi by analyzing microsatellite data and compared them with already existing data derived from mitochondrial DNA, which revealed that R. brelichi exhibits the lowest mitochondrial diversity of all so far studied Rhinopithecus species. In contrast, the genetic diversity of nuclear DNA is high and comparable to other Rhinopithecus species, i.e. the examined microsatellite loci are similarly highly polymorphic as in other species of the genus. An explanation for these differences in mitochondrial and nuclear genetic diversity could be a male biased dispersal. Females most likely stay within their natal band and males migrate between bands, thus mitochondrial DNA will not be exchanged between bands but nuclear DNA via males. A Bayesian Skyline Plot based on mitochondrial DNA sequences shows a strong decrease of the female effective population size (Nef) starting about 3,500 to 4,000 years ago, which concurs with the increasing human population in the area and respective expansion of agriculture. Given that we found no indication for a loss of nuclear DNA diversity in R. brelichi it seems that this factor does not represent the most prominent conservation threat for the long-term survival of the species. Conservation efforts should therefore focus more on immediate threats such as development of tourism and habitat destruction. PMID:24009761

[Physical therapy for idiopathic scoliosis].

PubMed

Steffan, K

2015-11-01

The objective is the description and summary of the current state of idiopathic scoliosis treatment with physical therapy based on new scientific knowledge and concluded from more than 15 years of experience as a leading physician in two well-known clinics specializing in the conservative treatment of scoliosis. Based on current scientific publications on physical therapy in scoliosis treatment and resulting from the considerable personal experience gained working with conservative treatment and consulting scoliosis patients (as inpatients and outpatients), the current methods of physical therapy have been compared and evaluated. Physical therapy according to Schroth and Vojta therapy are at present the most common and effective methods in the physical treatment of idiopathic scoliosis. These methods can be applied during inpatient or outpatient treatment or intensified in the practice of specialized therapists. As there are only a few scientific studies on this subject, the author's findings are based mainly on his own experiences of the conservative treatment of idiopathic scoliosis. Athough these experiences are the results of over 15 years of working in the field of therapy, and the Schroth method in combination with corrective bracing presents highly promising results, it would nevertheless be desirable to conduct detailed scientific studies to verify the effectiveness of conservative treatment.

Chemical-Induced Hearing Loss in Shipyard Workers.

PubMed

Schaal, Nicholas Cody; Slagley, Jeremy M; Richburg, Cynthia McCormick; Zreiqat, Majed M; Paschold, Helmut W

2018-01-01

The aim of this study was to determine the effect of lead, cadmium, arsenic, toluene, and xylene exposure on hearing compared with noise exposures alone. Personnel at a shipyard (n = 1266) were divided into four exposure groups on the basis of concentrations: low metals/low solvents/high noise (reference group), high metals/high solvents/low noise, high metals/low solvents/high noise, and high metals/high solvents/high noise. Hearing changes occurring from the years 2004 to 2015 were analyzed. Hearing changes were significantly worse at 1000 Hz (P = 0.007), averaged across 2000 to 4000 Hz (P = 0.014), and averaged across 500 to 6000 Hz (P = 0.014) for the high metals/high solvent/high noise group compared with the low metals/low solvents/high noise only reference group. Simultaneous exposures classified as high for metals/solvents/noise appear to damage hearing more than exposure to noise alone. Hearing conservation programs should take into consideration combined exposures to metals, solvents, and noise, not simply exposure to noise.

CORAL: aligning conserved core regions across domain families.

PubMed

Fong, Jessica H; Marchler-Bauer, Aron

2009-08-01

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

Conservative whole-organ scaling contrasts with highly labile suborgan scaling differences among compound eyes of closely related Formica ants.

PubMed

Perl, Craig D; Rossoni, Sergio; Niven, Jeremy E

2017-03-01

Static allometries determine how organ size scales in relation to body mass. The extent to which these allometric relationships are free to evolve, and how they differ among closely related species, has been debated extensively and remains unclear; changes in intercept appear common, but changes in slope are far rarer. Here, we compare the scaling relationships that govern the structure of compound eyes of four closely related ant species from the genus Formica . Comparison among these species revealed changes in intercept but not slope in the allometric scaling relationships governing eye area, facet number, and mean facet diameter. Moreover, the scaling between facet diameter and number was conserved across all four species. In contrast, facet diameters from distinct regions of the compound eye differed in both intercept and slope within a single species and when comparing homologous regions among species. Thus, even when species are conservative in the scaling of whole organs, they can differ substantially in regional scaling within organs. This, at least partly, explains how species can produce organs that adhere to genus wide scaling relationships while still being able to invest differentially in particular regions of organs to produce specific features that match their ecology.

[Amphioxus ortholog of ECSIT, an evolutionarily conserved adaptor in the Toll and BMP signaling pathways].

PubMed

Lin, Y H; Zhang, W; Li, J W; Zhang, H W; Chen, D Y

2017-01-01

In vertebrates, evolutionarily conserved signaling intermediate in the Toll pathway (ECSIT) interacts with the TNF-receptor associated factor 6 (TRAF6) to regulate the processing of MEKK1, activate NF-κB, and also control BMP target genes. However, the role of ECSIT in invertebrates remains largely unexplored. We performed comparative investigations of the expression, gene structure, and phylogeny of ECSIT, Toll-like receptor (TLR), and Smad4 in the cephalochordate Branchiostoma belcheri. Phylogenetic analysis indicated that, in amphioxus, ECSIT, TLR, and Smad4 form independent clusters at the base of Chordate   clusters. Interestingly, overall gene structures were comparable to those in vertebrate orthologs. Transcripts of AmphiECSIT were detectable at the mid-neural stage, and continued to be expressed in the epithelium of the pharyngeal region at later stages. In adult animals, strong expression was observed in the nerve cord, endostyle, epithelial cells of the gut and wheel organ, genital membrane of the testis, and coelom and lymphoid cavities, what is highly similar to AmphiTLR and AmphiSmad4 expression patterns during development and in adult organisms. Our data suggests that ECSIT is evolutionarily conserved. Its amphioxus ortholog functions during embryonic development and as part of the innate immune system and may be involved in TLR/BMP signaling.

Integrative analyses of conserved WNT clusters and their co-operative behaviour in human breast cancer

PubMed Central

Qurrat-ul-Ain; Seemab, Umair; Nawaz, Sulaman; Rashid, Sajid

2011-01-01

In human, WNT gene clusters are highly conserved at specie level and associated with carcinogenesis. Among them, WNT-10A and WNT-6 genes clustered in chromosome 2q35 are homologous to WNT-10B and WNT-1 located in chromosome 12q13, respectively. In an attempt to study co-regulation, the coordinated expression of these genes was monitored in human breast cancer tissues. As compared to normal tissue, both WNT-10A and WNT-10B genes exhibited lower expression while WNT-6 and WNT-1 showed increased expression in breast cancer tissues. The co-expression pattern was elaborated by detailed phylogenetic and syntenic analyses. Moreover, the intergenic and intragenic regions for these gene clusters were analyzed for studying the transcriptional regulation. In this context, adequate conserved binding sites for SOX and TCF family of transcriptional factors were observed. We propose that SOX9 and TCF4 may compete for binding at the promoters of WNT family genes thus regulating the disease phenotype. PMID:22355234

New Mass-Conserving Bedrock Topography for Pine Island Glacier Impacts Simulated Decadal Rates of Mass Loss

NASA Astrophysics Data System (ADS)

Nias, I. J.; Cornford, S. L.; Payne, A. J.

2018-04-01

High-resolution ice flow modeling requires bedrock elevation and ice thickness data, consistent with one another and with modeled physics. Previous studies have shown that gridded ice thickness products that rely on standard interpolation techniques (such as Bedmap2) can be inconsistent with the conservation of mass, given observed velocity, surface elevation change, and surface mass balance, for example, near the grounding line of Pine Island Glacier, West Antarctica. Using the BISICLES ice flow model, we compare results of simulations using both Bedmap2 bedrock and thickness data, and a new interpolation method that respects mass conservation. We find that simulations using the new geometry result in higher sea level contribution than Bedmap2 and reveal decadal-scale trends in the ice stream dynamics. We test the impact of several sliding laws and find that it is at least as important to accurately represent the bedrock and initial ice thickness as the choice of sliding law.

Conservation of sex chromosomes in lacertid lizards.

PubMed

Rovatsos, Michail; Vukić, Jasna; Altmanová, Marie; Johnson Pokorná, Martina; Moravec, Jiří; Kratochvíl, Lukáš

2016-07-01

Sex chromosomes are believed to be stable in endotherms, but young and evolutionary unstable in most ectothermic vertebrates. Within lacertids, the widely radiated lizard group, sex chromosomes have been reported to vary in morphology and heterochromatinization, which may suggest turnovers during the evolution of the group. We compared the partial gene content of the Z-specific part of sex chromosomes across major lineages of lacertids and discovered a strong evolutionary stability of sex chromosomes. We can conclude that the common ancestor of lacertids, living around 70 million years ago (Mya), already had the same highly differentiated sex chromosomes. Molecular data demonstrating an evolutionary conservation of sex chromosomes have also been documented for iguanas and caenophidian snakes. It seems that differences in the evolutionary conservation of sex chromosomes in vertebrates do not reflect the distinction between endotherms and ectotherms, but rather between amniotes and anamniotes, or generally, the differences in the life history of particular lineages. © 2016 John Wiley & Sons Ltd.

Development of a Conservative Model Validation Approach for Reliable Analysis

DTIC Science & Technology

2015-01-01

CIE 2015 August 2-5, 2015, Boston, Massachusetts, USA [DRAFT] DETC2015-46982 DEVELOPMENT OF A CONSERVATIVE MODEL VALIDATION APPROACH FOR RELIABLE...obtain a conservative simulation model for reliable design even with limited experimental data. Very little research has taken into account the...3, the proposed conservative model validation is briefly compared to the conventional model validation approach. Section 4 describes how to account

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…

Evolutionary and biophysical relationships among the papillomavirus E2 proteins.

PubMed

Blakaj, Dukagjin M; Fernandez-Fuentes, Narcis; Chen, Zigui; Hegde, Rashmi; Fiser, Andras; Burk, Robert D; Brenowitz, Michael

2009-01-01

Infection by human papillomavirus (HPV) may result in clinical conditions ranging from benign warts to invasive cancer. The HPV E2 protein represses oncoprotein transcription and is required for viral replication. HPV E2 binds to palindromic DNA sequences of highly conserved four base pair sequences flanking an identical length variable 'spacer'. E2 proteins directly contact the conserved but not the spacer DNA. Variation in naturally occurring spacer sequences results in differential protein affinity that is dependent on their sensitivity to the spacer DNA's unique conformational and/or dynamic properties. This article explores the biophysical character of this core viral protein with the goal of identifying characteristics that associated with risk of virally caused malignancy. The amino acid sequence, 3d structure and electrostatic features of the E2 protein DNA binding domain are highly conserved; specific interactions with DNA binding sites have also been conserved. In contrast, the E2 protein's transactivation domain does not have extensive surfaces of highly conserved residues. Rather, regions of high conservation are localized to small surface patches. Implications to cancer biology are discussed.

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.

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.

The city as a refuge for insect pollinators.

PubMed

Hall, Damon M; Camilo, Gerardo R; Tonietto, Rebecca K; Ollerton, Jeff; Ahrné, Karin; Arduser, Mike; Ascher, John S; Baldock, Katherine C R; Fowler, Robert; Frankie, Gordon; Goulson, Dave; Gunnarsson, Bengt; Hanley, Mick E; Jackson, Janet I; Langellotto, Gail; Lowenstein, David; Minor, Emily S; Philpott, Stacy M; Potts, Simon G; Sirohi, Muzafar H; Spevak, Edward M; Stone, Graham N; Threlfall, Caragh G

2017-02-01

Research on urban insect pollinators is changing views on the biological value and ecological importance of cities. The abundance and diversity of native bee species in urban landscapes that are absent in nearby rural lands evidence the biological value and ecological importance of cities and have implications for biodiversity conservation. Lagging behind this revised image of the city are urban conservation programs that historically have invested in education and outreach rather than programs designed to achieve high-priority species conservation results. We synthesized research on urban bee species diversity and abundance to determine how urban conservation could be repositioned to better align with new views on the ecological importance of urban landscapes. Due to insect pollinators' relatively small functional requirements-habitat range, life cycle, and nesting behavior-relative to larger mammals, we argue that pollinators put high-priority and high-impact urban conservation within reach. In a rapidly urbanizing world, transforming how environmental managers view the city can improve citizen engagement and contribute to the development of more sustainable urbanization. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Parallel, adaptive finite element methods for conservation laws

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Devine, Karen D.; Flaherty, Joseph E.

1994-01-01

We construct parallel finite element methods for the solution of hyperbolic conservation laws in one and two dimensions. Spatial discretization is performed by a discontinuous Galerkin finite element method using a basis of piecewise Legendre polynomials. Temporal discretization utilizes a Runge-Kutta method. Dissipative fluxes and projection limiting prevent oscillations near solution discontinuities. A posteriori estimates of spatial errors are obtained by a p-refinement technique using superconvergence at Radau points. The resulting method is of high order and may be parallelized efficiently on MIMD computers. We compare results using different limiting schemes and demonstrate parallel efficiency through computations on an NCUBE/2 hypercube. We also present results using adaptive h- and p-refinement to reduce the computational cost of the method.

Enhanced cadmium efflux and root-to-shoot translocation are conserved in the hyperaccumulator Sedum alfredii (Crassulaceae family).

PubMed

Zhang, Zhongchun; Yu, Qi; Du, Hanying; Ai, Wenli; Yao, Xuan; Mendoza-Cózatl, David G; Qiu, Baosheng

2016-06-01

Investigation on the molecular mechanisms of cadmium hyperaccumulation has been mostly focused on members of the Brassicaceae family. Here, we show using hyperaccumulating (HP) and nonhyperaccumulating (NHP) populations of Sedum alfredii (Crassulaceae), that Cd hypertolerance correlates with higher Cd efflux rates and less cadmium accumulation in suspension cells and roots. The heavy metal ATPase HMA2, but not HMA4, was highly expressed in suspension cultures and roots from HP plants compared to NHP cells and plants. Reciprocal grafting also showed that Cd translocation is more efficient in HP plants. These results suggest that cadmium efflux is a conserved mechanism among natural cadmium hyperaccumulator species. © 2016 Federation of European Biochemical Societies.

Targeted conservation to safeguard a biodiversity hotspot from climate and land-cover change.

PubMed

Struebig, Matthew J; Wilting, Andreas; Gaveau, David L A; Meijaard, Erik; Smith, Robert J; Fischer, Manuela; Metcalfe, Kristian; Kramer-Schadt, Stephanie

2015-02-02

Responses of biodiversity to changes in both land cover and climate are recognized [1] but still poorly understood [2]. This poses significant challenges for spatial planning as species could shift, contract, expand, or maintain their range inside or outside protected areas [2-4]. We examine this problem in Borneo, a global biodiversity hotspot [5], using spatial prioritization analyses that maximize species conservation under multiple environmental-change forecasts. Climate projections indicate that 11%-36% of Bornean mammal species will lose ≥ 30% of their habitat by 2080, and suitable ecological conditions will shift upslope for 23%-46%. Deforestation exacerbates this process, increasing the proportion of species facing comparable habitat loss to 30%-49%, a 2-fold increase on historical trends. Accommodating these distributional changes will require conserving land outside existing protected areas, but this may be less than anticipated from models incorporating deforestation alone because some species will colonize high-elevation reserves. Our results demonstrate the increasing importance of upland reserves and that relatively small additions (16,000-28,000 km(2)) to the current conservation estate could provide substantial benefits to biodiversity facing changes to land cover and climate. On Borneo, much of this land is under forestry jurisdiction, warranting targeted conservation partnerships to safeguard biodiversity in an era of global change. Copyright © 2015 Elsevier Ltd. All rights reserved.

Surgical versus conservative treatment following acute rupture of the Achilles tendon: is there a pedobarographic difference?

PubMed

Karaaslan, Fatih; Mermerkaya, Musa Uğur; Çıraklı, Alper; Karaoğlu, Sinan; Duygulu, Fuat

2016-01-01

Controversy remains regarding the optimal treatment method and postoperative rehabilitation of acute Achilles tendon ruptures. In this study, pedobarographic assessments of surgical and conservative treatments were compared. A prospective assessment was made of 16 patients (eight surgical, eight conservative) and eight healthy controls using a plantar pressure measurement system. Biomechanical gait parameters were obtained using the Footscan dynamic gait analysis system. Kruskal-Wallis and Mann-Whitney U-tests were used for the evaluation of data. Nineteen males and five females were assessed, with an average age of 42.0±11.9 years. Follow-up was completed in 16 patients. No statistically significant difference was determined between the two treatment groups with regard to the gait analysis, but a difference was observed with the control group (P<0.001). All patients were able to resume their prior activities after 6 months and regained normal ranges of motion, with a high rate of satisfaction. Most of the patients (75%) were able to return to their pre-injury level of activities. Satisfactory results were obtained through conservative treatment of acute ruptures of the Achilles tendon. No significant differences or complications were observed in the group managed conservatively versus the group treated surgically. Further studies including 3D gait analyses and tendon biomechanical research are required to further investigate this issue.

Knee arthroscopy versus conservative management in patients with degenerative knee disease: a systematic review.

PubMed

Brignardello-Petersen, Romina; Guyatt, Gordon H; Buchbinder, Rachelle; Poolman, Rudolf W; Schandelmaier, Stefan; Chang, Yaping; Sadeghirad, Behnam; Evaniew, Nathan; Vandvik, Per O

2017-05-11

To determine the effects and complications of arthroscopic surgery compared with conservative management strategies in patients with degenerative knee disease. Systematic review. Pain, function, adverse events. MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), Google Scholar and Open Grey up to August 2016. For effects, randomised clinical trials (RCTs) comparing arthroscopic surgery with a conservative management strategy (including sham surgery) in patients with degenerative knee disease. For complications, RCTs and observational studies. Two reviewers independently extracted data and assessed risk of bias for patient-important outcomes. A parallel guideline committee ( BMJ Rapid Recommendations) provided input on the design and interpretation of the systematic review, including selection of patient-important outcomes. We used the GRADE approach to rate the certainty (quality) of the evidence. We included 13 RCTs and 12 observational studies. With respect to pain, the review identified high-certainty evidence that knee arthroscopy results in a very small reduction in pain up to 3 months (mean difference =5.4 on a 100-point scale, 95% CI 2.0 to 8.8) and very small or no pain reduction up to 2 years (mean difference =3.1, 95% CI -0.2 to 6.4) when compared with conservative management. With respect to function, the review identified moderate-certainty evidence that knee arthroscopy results in a very small improvement in the short term (mean difference =4.9 on a 100-point scale, 95% CI 1.5 to 8.4) and very small or no improved function up to 2 years (mean difference =3.2, 95% CI -0.5 to 6.8). Alternative presentations of magnitude of effect, and associated sensitivity analyses, were consistent with the findings of the primary analysis. Low-quality evidence suggested a very low probability of serious complications after knee arthroscopy. Over the long term, patients who undergo knee arthroscopy versus those who receive conservative management strategies do not have important benefits in pain or function. PROSPERO CRD42016046242. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Knee arthroscopy versus conservative management in patients with degenerative knee disease: a systematic review

PubMed Central

Brignardello-Petersen, Romina; Guyatt, Gordon H; Buchbinder, Rachelle; Poolman, Rudolf W; Chang, Yaping; Sadeghirad, Behnam; Evaniew, Nathan; Vandvik, Per O

2017-01-01

Objective To determine the effects and complications of arthroscopic surgery compared with conservative management strategies in patients with degenerative knee disease. Design Systematic review. Main outcome measures Pain, function, adverse events. Data sources MEDLINE, EMBASE, the Cochrane Central Register of Controlled Trials (CENTRAL), Google Scholar and Open Grey up to August 2016. Eligibility criteria For effects, randomised clinical trials (RCTs) comparing arthroscopic surgery with a conservative management strategy (including sham surgery) in patients with degenerative knee disease. For complications, RCTs and observational studies. Review methods Two reviewers independently extracted data and assessed risk of bias for patient-important outcomes. A parallel guideline committee (BMJ Rapid Recommendations) provided input on the design and interpretation of the systematic review, including selection of patient-important outcomes. We used the GRADE approach to rate the certainty (quality) of the evidence. Results We included 13 RCTs and 12 observational studies. With respect to pain, the review identified high-certainty evidence that knee arthroscopy results in a very small reduction in pain up to 3 months (mean difference =5.4 on a 100-point scale, 95% CI 2.0 to 8.8) and very small or no pain reduction up to 2 years (mean difference =3.1, 95% CI −0.2 to 6.4) when compared with conservative management. With respect to function, the review identified moderate-certainty evidence that knee arthroscopy results in a very small improvement in the short term (mean difference =4.9 on a 100-point scale, 95% CI 1.5 to 8.4) and very small or no improved function up to 2 years (mean difference =3.2, 95% CI −0.5 to 6.8). Alternative presentations of magnitude of effect, and associated sensitivity analyses, were consistent with the findings of the primary analysis. Low-quality evidence suggested a very low probability of serious complications after knee arthroscopy. Conclusions Over the long term, patients who undergo knee arthroscopy versus those who receive conservative management strategies do not have important benefits in pain or function. Trial registration number PROSPERO CRD42016046242. PMID:28495819

Herbicide and cover crop residue integration in conservation tillage tomato

USDA-ARS?s Scientific Manuscript database

The increased adoption of conservation tillage in vegetable production requires more information on the role of various cover crops in weed control, tomato quality, and yield. Three conservation-tillage systems utilizing crimson clover, turnip, and cereal rye as winter cover crops were compared to a...

Cave Conservation Priority Index to Adopt a Rapid Protection Strategy: A Case Study in Brazilian Atlantic Rain Forest

NASA Astrophysics Data System (ADS)

Souza Silva, Marconi; Martins, Rogério Parentoni; Ferreira, Rodrigo Lopes

2015-02-01

Cave environments are characterized by possessing specialized fauna living in high environmental stability with limited food conditions. These fauna are highly vulnerable to impacts, because this condition can frequently be easily altered. Moreover, environmental determinants of the biodiversity patterns of caves remain poorly understood and protected. Therefore, the main goal of this work is to propose a cave conservation priority index (CCPi) for a rapid assessment for troglobiotic and troglophile protection. Furthermore, the troglobiotic diversity, distribution and threats have been mapped in the Brazilian Atlantic forest. To propose the CCPi, the human impacts and richness of troglobiotic and troglophile species of 100 caves were associated. Data related to troglomorphic/troglobiotic fauna from another 200 caves were used to map the troglobiotic diversity and distribution. The CCPi reveals extremely high conservation priority for 15 % of the caves, high for 36 % and average for 46 % of the caves. Fourteen caves with extremely high priorities should have urgent conservation and management actions. The geographical distribution of the 221 known troglobiotic/troglomorphic species allowed us to select 19 karst areas that need conservation actions. Seven areas were considered to have urgent priority for conservation actions. The two richest areas correspond to the "iron quadrangle" with iron ore caves (67 spp.) and the "Açungui limestone group" (56 spp.). Both areas have several caves and are important aquifers. The use of the CCPi can prevent future losses because it helps assessors to select caves with priorities for conservation which should receive emergency attention in relation to protection, management and conservation actions.

Rural aquaculture as a sustainable alternative for forest conservation in the Monarch Butterfly Biosphere Reserve, Mexico.

PubMed

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

2014-06-01

Forest conservation plays a significant role in environmental sustainability. In Mexico only 8.48 million ha of forest are used for conservation of biodiversity. Payment for Environmental Services in the Monarch Butterfly Biosphere Reserve, one of the most important national protected areas, contributes to the conservation of these forests. In the Reserve, production of rainbow trout has been important for the rural communities who need to conserve the forest cover in order to maintain the hibernation cycle of the butterfly. Aquaculture is a highly productive activity for these protected areas, since it harnesses the existing water resources. In this study, changes from 1999 to 2012 in vegetation and land-use cover in the El Lindero basin within the Reserve were evaluated in order to determine the conservation status and to consider the feasibility of aquaculture as a means of sustainable development at community level. Evaluation involved stereoscopic interpretation of digital aerial photographs from 1999 to 2012 at 1:10,000 scale, comparative analysis by orthocorrected mosaics and restitution on the mosaics. Between 1999 and 2012, forested land recovered by 28.57 ha (2.70%) at the expense of non-forested areas, although forest degradation was 3.59%. Forest density increased by 16.87%. In the 46 ha outside the Reserve, deforestation spread by 0.26%, and land use change was 0.11%. The trend towards change in forest cover is closely related to conservation programmes, particularly payment for not extracting timber, reforestation campaigns and surveillance, whose effects have been exploited for the development of rural aquaculture; this is a new way to improve the socio-economic status of the population, to avoid logging and to achieve environmental sustainability in the Reserve. Copyright © 2014 Elsevier Ltd. All rights reserved.

PPCPs in Jiulong River estuary (China): Spatiotemporal distributions, fate, and their use as chemical markers of wastewater.

PubMed

Sun, Qian; Li, Yan; Li, Mingyue; Ashfaq, Muhammad; Lv, Min; Wang, Hongjie; Hu, Anyi; Yu, Chang-Ping

2016-05-01

The occurrence and fate of 50 pharmaceuticals and personal care products (PPCPs) were investigated in the surface water of Jiulong River estuary in the southeast of China in spring, wet season, summer, autumn and winter. Results demonstrated a wide distribution of PPCPs in Jiulong River estuary, where 34 PPCPs were detected at least once and 5 PPCPs were detected in all the samples, including caffeine, diclofenac, metoprolol, methyl paraben, and propyl paraben. Spatial and seasonal variations were observed. Special emphasis was placed on the PPCP fate in the estuary. Most PPCPs showed a non-conservative behavior in the estuary, while the non-steroidal anti-inflammatory drugs and bisphenol A showed a pseudo-conservative behavior. The non-conservative and pseudo-conservative behavior was attributed to the combination of the seawater dilution, the introduction of PPCPs via the sewage water, and the physical, chemical, or biological removal processes. Furthermore, PPCP concentrations showed drastic variations in the turbidity maximum zones. To our best knowledge, this is the first work to indicate the pseudo-conservative behavior of PPCPs in the estuary, and to show the drastic variations of PPCPs in the turbidity maximum zone. In addition, the ratio of labile to conservative PPCPs was calculated to track the source of untreated sewage contamination. Results showed a significantly higher ratio compared to the average value in WWTP effluents, indicating the ubiquitous discharge of untreated domestic wastewater in Jiulong River estuary. In addition, the high ratio of bisphenol A to conservative PPCPs implied the potential input of untreated industrial wastewater in Jiulong River estuary. Copyright © 2016 Elsevier Ltd. All rights reserved.

A preliminary assessment of the effectiveness of the Mesoamerican Biological Corridor for protecting potential Baird's tapir (Tapirus bairdii) habitat in Southern Mexico.

PubMed

Mendoza, Eduardo; Fuller, Trevon L; Thomassen, Henri A; Buermann, Wolfgang; Ramírez-Mejía, Diana; Smith, Thomas B

2013-03-01

Baird's tapir (Tapirus bairdii) is one of the most emblematic mammals of Mesoamerica, but like other large-bodied animals, it is facing an increasing risk of extinction due primarily to habitat loss. Mexico's 'ortion of the Mesoamerican Biological Corridor (MBC-M) is located in one of the main strongholds for Bairds tapir. To assess the MBC-M's effectiveness for tapir conservation, we estimated the distribution of the species' potential habitat by applying 2 modelling approaches (random forest and Maxent) to a set of uncorrelated environmental variables and a 157-point presence dataset. We calculated the extent of tapir habitat in within the MBC-M and modelled new corridors and conservation areas, which we compared to the MBC-M. Moreover, we assessed deforestation patterns in the region. Twenty-seven percent of highly suitable tapir habitat occurred in protected areas, 15% in corridors and 58.3% was outside the MBC-M and associated reserves. The spatial configuration of the MBC-M was partially concordant with the modelled set of conservation areas and corridors. The main dissimilarity was that the modelled corridors traversed forests in Belize and Guatemala to connect conservation areas. Analyses of deforestation since 1993 and human population density in the vicinity of the MBC-M indicated that future conservation efforts should give particular attention to the Montes Azules-El Triunfo Corridor due to greater habitat threat. The MBC-M has a great potential to play a prominent role in the conservation of tapir habitat but there is an urgent need to implement management plans that reinforce and complement this conservation initiative. © 2012 Wiley Publishing Asia Pty Ltd, ISZS and IOZ/CAS.

Overlooked mountain rock pools in deserts are critical local hotspots of biodiversity.

PubMed

Vale, Cândida Gomes; Pimm, Stuart L; Brito, José Carlos

2015-01-01

The world is undergoing exceptional biodiversity loss. Most conservation efforts target biodiversity hotspots at large scales. Such approach overlooks small-sized local hotspots, which may be rich in endemic and highly threatened species. We explore the importance of mountain rock pools (gueltas) as local biodiversity hotspots in the Sahara-Sahel. Specifically, we considered how many vertebrates (total and endemics) use gueltas, what factors predict species richness, and which gueltas are of most priority for conservation. We expected to provide management recommendations, improve local biodiversity conservation, and simultaneously contribute with a framework for future enhancement of local communities' economy. The identification of local hotspots of biodiversity is important for revaluating global conservation priorities. We quantified the number of vertebrate species from each taxonomic group and endemics present in 69 gueltas in Mauritania, then compared these with species present in a surrounding area and recorded in the country. We evaluated the predictors of species number's present in each guelta through a multiple regression model. We ranked gueltas by their priority for conservation taking into account the percentage of endemics and threats to each guelta. Within a mere aggregate extent of 43 ha, gueltas hold about 32% and 78% of the total taxa analysed and endemics of Mauritania, respectively. The number of species present in each guelta increased with the primary productivity and area of gueltas and occurrence of permanent water. Droughts and human activities threaten gueltas, while 64% of them are currently unprotected. Gueltas are crucial for local biodiversity conservation and human activities. They require urgent management plans in Mauritania's mountains. They could provide refugia under climate change being important for long-term conservation of Sahara-Sahel biodiversity. Given their disproportional importance in relation to their size, they are local hotspots of biodiversity deserving global attention.

Clinical Outcomes of Conservative Treatment and Arthroscopic Repair of Rotator Cuff Tears: A Retrospective Observational Study.

PubMed

Lee, Woo Hyung; Do, Hyun Kyung; Lee, Joong Hoon; Kim, Bo Ram; Noh, Jee Hyun; Choi, Soo Hyun; Chung, Sun Gun; Lee, Shi-Uk; Choi, Ji Eun; Kim, Seihee; Kim, Min Jee; Lim, Jae-Young

2016-04-01

To compare the clinical outcomes following conservative treatment and arthroscopic repair in patients with a rotator cuff tear. In this retrospective study, patients aged >50 years with a symptomatic rotator cuff tear were reviewed. The rotator cuff tendons were evaluated using ultrasonography, shoulder magnetic resonance imaging or MR arthrography, and the patients with either a high-grade partial-thickness or small-to-medium-sized (≤3 cm) full-thickness tear were included in this study. The primary outcome measures were a pain assessment score and range of motion (ROM) at 1-year follow-up. The secondary outcomes were the rate of tear progression or retear along with the rate of symptom aggravation after the treatments. A total of 357 patients were enrolled, including 183 patients that received conservative treatment and 174 patients who received an arthroscopic repair. The pain assessment score (p<0.001) and the ROM in forward flexion (p<0.001) were significantly improved in both groups. The ROM in internal rotation did not significantly change after conservative treatment and arthroscopic repair. The pain assessment score and ROM were not significantly different between the two groups. Retear was observed in 9.6% of patients who had an arthroscopic repair and tear progression was found in 6.7% of those who underwent conservative treatment. The proportion of aggravation for pain and ROM did not significantly differ between the two groups. The effectiveness of conservative treatment is not inferior to arthroscopic repair for patients >50 years old with a less than medium-sized rotator cuff tear in a 1-year follow-up period. Further study is warranted to find the optimal combination of conservative treatment for a symptomatic rotator cuff tear.

Porcine MYF6 gene: sequence, homology analysis, and variation in the promoter region.

PubMed

Wyszyńska-Koko, J; Kurył, J

2004-01-01

MYF6 gene codes for the bHLH transcription factor belonging to MyoD family. Its expression accompanies the processes of differentiation and maturation of myotubes during embriogenesis and continues on a relatively high level after birth, affecting the muscle phenotype. The porcine MYF6 gene was amplified and sequenced and compared with MYF6 gene sequences of other species. The amino acid sequence was deduced and an interspecies homology analysis was performed. Myf-6 protein shows a high conservation among species of 99 and 97% identity when comparing pig with cow and human, respectively, and of 93% when comparing pig with mouse and rat. The single nucleotide polymorphism (SNP) was revealed within the promoter region, which appeared to be T --> C transition recognized by a MspI restriction enzyme.

Comparative genome analysis reveals a conserved family of actin-like proteins in apicomplexan parasites

PubMed Central

Gordon, Jennifer L; Sibley, L David

2005-01-01

Background The phylum Apicomplexa is an early-branching eukaryotic lineage that contains a number of important human and animal pathogens. Their complex life cycles and unique cytoskeletal features distinguish them from other model eukaryotes. Apicomplexans rely on actin-based motility for cell invasion, yet the regulation of this system remains largely unknown. Consequently, we focused our efforts on identifying actin-related proteins in the recently completed genomes of Toxoplasma gondii, Plasmodium spp., Cryptosporidium spp., and Theileria spp. Results Comparative genomic and phylogenetic studies of apicomplexan genomes reveals that most contain only a single conventional actin and yet they each have 8–10 additional actin-related proteins. Among these are a highly conserved Arp1 protein (likely part of a conserved dynactin complex), and Arp4 and Arp6 homologues (subunits of the chromatin-remodeling machinery). In contrast, apicomplexans lack canonical Arp2 or Arp3 proteins, suggesting they lost the Arp2/3 actin polymerization complex on their evolutionary path towards intracellular parasitism. Seven of these actin-like proteins (ALPs) are novel to apicomplexans. They show no phylogenetic associations to the known Arp groups and likely serve functions specific to this important group of intracellular parasites. Conclusion The large diversity of actin-like proteins in apicomplexans suggests that the actin protein family has diverged to fulfill various roles in the unique biology of intracellular parasites. Conserved Arps likely participate in vesicular transport and gene expression, while apicomplexan-specific ALPs may control unique biological traits such as actin-based gliding motility. PMID:16343347

Microarray-based comparative genomic profiling of reference strains and selected Canadian field isolates of Actinobacillus pleuropneumoniae

PubMed Central

Gouré, Julien; Findlay, Wendy A; Deslandes, Vincent; Bouevitch, Anne; Foote, Simon J; MacInnes, Janet I; Coulton, James W; Nash, John HE; Jacques, Mario

2009-01-01

Background Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, is a highly contagious respiratory pathogen that causes severe losses to the swine industry worldwide. Current commercially-available vaccines are of limited value because they do not induce cross-serovar immunity and do not prevent development of the carrier state. Microarray-based comparative genomic hybridizations (M-CGH) were used to estimate whole genomic diversity of representative Actinobacillus pleuropneumoniae strains. Our goal was to identify conserved genes, especially those predicted to encode outer membrane proteins and lipoproteins because of their potential for the development of more effective vaccines. Results Using hierarchical clustering, our M-CGH results showed that the majority of the genes in the genome of the serovar 5 A. pleuropneumoniae L20 strain were conserved in the reference strains of all 15 serovars and in representative field isolates. Fifty-eight conserved genes predicted to encode for outer membrane proteins or lipoproteins were identified. As well, there were several clusters of diverged or absent genes including those associated with capsule biosynthesis, toxin production as well as genes typically associated with mobile elements. Conclusion Although A. pleuropneumoniae strains are essentially clonal, M-CGH analysis of the reference strains of the fifteen serovars and representative field isolates revealed several classes of genes that were divergent or absent. Not surprisingly, these included genes associated with capsule biosynthesis as the capsule is associated with sero-specificity. Several of the conserved genes were identified as candidates for vaccine development, and we conclude that M-CGH is a valuable tool for reverse vaccinology. PMID:19239696

Effects of logging on roadless space in intact forest landscapes of the Congo Basin.

PubMed

Kleinschroth, Fritz; Healey, John R; Gourlet-Fleury, Sylvie; Mortier, Frédéric; Stoica, Radu S

2017-04-01

Forest degradation in the tropics is often associated with roads built for selective logging. The protection of intact forest landscapes (IFL) that are not accessible by roads is high on the biodiversity conservation agenda and a challenge for logging concessions certified by the Forest Stewardship Council (FSC). A frequently advocated conservation objective is to maximize the retention of roadless space, a concept that is based on distance to the nearest road from any point. We developed a novel use of the empty-space function - a general statistical tool based on stochastic geometry and random sets theory - to calculate roadless space in a part of the Congo Basin where road networks have been expanding rapidly. We compared the temporal development of roadless space in certified and uncertified logging concessions inside and outside areas declared IFL in 2000. Inside IFLs, road-network expansion led to a decrease in roadless space by more than half from 1999 to 2007. After 2007, loss leveled out in most areas to close to 0 due to an equilibrium between newly built roads and abandoned roads that became revegetated. However, concessions in IFL certified by FSC since around 2007 continuously lost roadless space and reached a level comparable to all other concessions. Only national parks remained mostly roadless. We recommend that forest-management policies make the preservation of large connected forest areas a top priority by effectively monitoring - and limiting - the occupation of space by roads that are permanently accessible. © 2016 The Authors. Conservation Biology published by Wiley Periodicals, Inc. on behalf of Society for Conservation Biology.

Use of gastrografin in the management of worm-induced small bowel obstruction in children.

PubMed

Hamid, Raashid; Bhat, Nisar; Baba, Aejaz; Mufti, Gowhar; Khursheed, Sheikh; Wani, Sajad A; Ali, Imran; Hassan, Faheem

2015-12-01

Ascaris-induced small bowel obstruction (SBO) is a common sequel of Ascaris lumbricoides (AL) infestation. Most cases respond to conservative treatment practiced in different centers worldwide. We conceived a prospective randomized trial to compare the conservative treatment with gastrografin administered in addition to the conservative treatment. This prospective randomized study was conducted between January 2011 and June 2014 at Department of Paediatric and Neonatal Surgery, a tertiary-care hospital. Patients were divided into two groups, one group received conservative treatment and the other received gastrografin in addition to conservative treatment. Forty patients having uncomplicated AL-induced SBO were included in each group. Gastrografin was administered through nasogastric tube and serial clinical and radiological monitoring was performed. The duration of hospital stay, time between admission and first oral feed, passage of worms/flatus were compared in the two groups. Student's t test was used for comparing these variables. Average time for passage of flatus or worms and resolution of abdominal signs and was shorter in gastrografin group as compared to the conservative group. This difference was found to be statistically significant. The average duration of hospital stay in gastrografin group was 25.20 ± 8.01 h whereas it was 61.12 ± 14.64 h in the conservative group (P < 0.001). The difference in the operation rate was statistically insignificant (2 in gastrografin group and 3 in the conservative group).No serious adverse reaction was noted after gastrografin administration. Use of gastrografin resulted in faster relief of signs and symptoms of AL-induced SBO, early passage of worms/flatus and return to oral feeds. However, the role of gastrografin role in reducing the likelihood of laparotomy remains inconclusive. Adverse effects of gastrografin can be prevented if it is used in well-hydrated patients.

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...

Effects of Community-Based Natural Resource Management on Household Welfare in Namibia

PubMed Central

Riehl, Brianne; Zerriffi, Hisham; Naidoo, Robin

2015-01-01

Biodiversity conservation, as an environmental goal, is increasingly recognized to be connected to the socioeconomic well-being of local communities. The development of a widespread community-based natural resource management (CBNRM) program in Namibia makes it an ideal location to analyze the connection between conservation and socioeconomic well-being of local communities. Namibia’s CBNRM program involves the formation of communal conservancies within rural communities and previous studies have found it to be successful on both ecological and economic fronts. In order to broaden the understanding of the program’s impact to include social factors, we have conducted a comparative analysis to determine the effects of this program on household welfare outcomes. Data from two rounds of the Namibia Demographic and Health Surveys (2000 and 2006/07) and quasi-experimental statistical methods were used to evaluate changes in various health, education and wealth outcomes of those living in conservancies, relative to non-conservancy comparison groups. Regression results indicate mixed effects of the conservancy program at the household level. The program had positive effects on some health outcome variables, including bednet ownership, which was twice as likely to increase over time in conservancy compared to non-conservancy households. Program impacts were negative for education outcomes, with the proportion of school attendance of conservancy children being 45% less likely to increase over time than non-conservancy children. Wealth outcome results were inconclusive. Our findings highlight the importance of analyzing community conservation programs at a variety of scales when evaluating overall impact, as community-level benefits may not necessarily extend down to the household level (and vice versa). PMID:25965379

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...

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...

Factors Influencing Schoolchildren's Responses to a Questionnaire in Wildlife Conservation Education

ERIC Educational Resources Information Center

Ballouard, Jean-Marie; Mullin, Stephen J.; Ajtic, Rastko; Brito, José Carlos; ElMouden, El Hassan; Erdogan, Mehmet; Feriche, Monica; Pleguezuelos, Juan M.; Prokop, Pavol; Sánchez, Aida; Santos, Xavier; Slimani, Tahar; Sterijovski, Bogoljub; Tomovic, Ljiljana; Usak, Muhammet; Zuffi, Marco; Bonnet, Xavier

2015-01-01

Questionnaires are important tools for assessing attitudes regarding conservation issues. However, they are not easily comparable and their reliability has been insufficiently assessed. We examined factors influencing responses to open- and closed-ended questions about animal conservation to more than 600 schoolchildren (9 years old on average).…

In silico simulations of STAT1 and STAT3 inhibitors predict SH2 domain cross-binding specificity.

PubMed

Szelag, Malgorzata; Sikorski, Krzysztof; Czerwoniec, Anna; Szatkowska, Katarzyna; Wesoly, Joanna; Bluyssen, Hans A R

2013-11-15

Signal transducers and activators of transcription (STATs) comprise a family of transcription factors that are structurally related and which participate in signaling pathways activated by cytokines, growth factors and pathogens. Activation of STAT proteins is mediated by the highly conserved Src homology 2 (SH2) domain, which interacts with phosphotyrosine motifs for specific contacts between STATs and receptors and for STAT dimerization. By generating new models for human (h)STAT1, hSTAT2 and hSTAT3 we applied comparative in silico docking to determine SH2-binding specificity of the STAT3 inhibitor stattic, and of fludarabine (STAT1 inhibitor). Thus, we provide evidence that by primarily targeting the highly conserved phosphotyrosine (pY+0) SH2 binding pocket stattic is not a specific hSTAT3 inhibitor, but is equally effective towards hSTAT1 and hSTAT2. This was confirmed in Human Micro-vascular Endothelial Cells (HMECs) in vitro, in which stattic inhibited interferon-α-induced phosphorylation of all three STATs. Likewise, fludarabine inhibits both hSTAT1 and hSTAT3 phosphorylation, but not hSTAT2, by competing with the highly conserved pY+0 and pY-X binding sites, which are less well-preserved in hSTAT2. Moreover we observed that in HMECs in vitro fludarabine inhibits cytokine and lipopolysaccharide-induced phosphorylation of hSTAT1 and hSTAT3 but does not affect hSTAT2. Finally, multiple sequence alignment of STAT-SH2 domain sequences confirmed high conservation between hSTAT1 and hSTAT3, but not hSTAT2, with respect to stattic and fludarabine binding sites. Together our data offer a molecular basis that explains STAT cross-binding specificity of stattic and fludarabine, thereby questioning the present selection strategies of SH2 domain-based competitive small inhibitors. © 2013 Elsevier B.V. All rights reserved.

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...

Human Population Density and Extinction Risk in the World's Carnivores

PubMed Central

Purvis, Andy; Sechrest, Wes; Gittleman, John L; Bielby, Jon; Mace, Georgina M

2004-01-01

Understanding why some species are at high risk of extinction, while others remain relatively safe, is central to the development of a predictive conservation science. Recent studies have shown that a species' extinction risk may be determined by two types of factors: intrinsic biological traits and exposure to external anthropogenic threats. However, little is known about the relative and interacting effects of intrinsic and external variables on extinction risk. Using phylogenetic comparative methods, we show that extinction risk in the mammal order Carnivora is predicted more strongly by biology than exposure to high-density human populations. However, biology interacts with human population density to determine extinction risk: biological traits explain 80% of variation in risk for carnivore species with high levels of exposure to human populations, compared to 45% for carnivores generally. The results suggest that biology will become a more critical determinant of risk as human populations expand. We demonstrate how a model predicting extinction risk from biology can be combined with projected human population density to identify species likely to move most rapidly towards extinction by the year 2030. African viverrid species are particularly likely to become threatened, even though most are currently considered relatively safe. We suggest that a preemptive approach to species conservation is needed to identify and protect species that may not be threatened at present but may become so in the near future. PMID:15252445

Conservative Protestantism and attitudes toward corporal punishment, 1986-2014.

PubMed

Hoffmann, John P; Ellison, Christopher G; Bartkowski, John P

2017-03-01

Research indicates that conservative Protestants are highly supportive of corporal punishment. Yet, Americans' support for this practice has waned during the past several decades. This study aggregates repeated cross-sectional data from the General Social Surveys (GSS) to consider three models that address whether attitudes toward spanking among conservative Protestants shifted relative to those of other Americans from 1986 to 2014. Although initial results reveal a growing gap between conservative Protestants and the broader American public, we find that average levels of support have remained most robust among less educated conservative Protestants, with some erosion among more highly educated conservative Protestants. Moreover, trends in variability suggest that conservative Protestants exhibit more cohesive support for this practice than do others. These results provide a window into the cultural contours of religious change and the social factors that facilitate such change. Copyright © 2016 Elsevier Inc. All rights reserved.

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

PubMed

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

2000-12-15

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

Incorporating land-use requirements and environmental constraints in low-carbon electricity planning for California.

PubMed

Wu, Grace C; Torn, Margaret S; Williams, James H

2015-02-17

The land-use implications of deep decarbonization of the electricity sector (e.g., 80% below 1990 emissions) have not been well-characterized quantitatively or spatially. We assessed the operational-phase land-use requirements of different low-carbon scenarios for California in 2050 and found that most scenarios have comparable direct land footprints. While the per MWh footprint of renewable energy (RE) generation is initially higher, that of fossil and nuclear generation increases over time with continued fuel use. We built a spatially explicit model to understand the interactions between resource quality and environmental constraints in a high RE scenario (>70% of total generation). We found that there is sufficient land within California to meet the solar and geothermal targets, but areas with the highest quality wind and solar resources also tend to be those with high conservation value. Development of some land with lower conservation value results in lower average capacity factors, but also provides opportunity for colocation of different generation technologies, which could significantly improve land-use efficiency and reduce permitting, leasing, and transmission infrastructure costs. Basing siting decisions on environmentally-constrained long-term RE build-out requirements produces significantly different results, including better conservation outcomes, than implied by the current piecemeal approach to planning.

cisprimertool: software to implement a comparative genomics strategy for the development of conserved intron scanning (CIS) markers.

PubMed

Jayashree, B; Jagadeesh, V T; Hoisington, D

2008-05-01

The availability of complete, annotated genomic sequence information in model organisms is a rich resource that can be extended to understudied orphan crops through comparative genomic approaches. We report here a software tool (cisprimertool) for the identification of conserved intron scanning regions using expressed sequence tag alignments to a completely sequenced model crop genome. The method used is based on earlier studies reporting the assessment of conserved intron scanning primers (called CISP) within relatively conserved exons located near exon-intron boundaries from onion, banana, sorghum and pearl millet alignments with rice. The tool is freely available to academic users at http://www.icrisat.org/gt-bt/CISPTool.htm. © 2007 ICRISAT.

Management of Spinal Deformities and Evidence of Treatment Effectiveness

PubMed Central

Bettany-Saltikov, Josette; Turnbull, Deborah; Ng, Shu Yan; Webb, Richard

2017-01-01

Introduction: The review evaluates the up-to-date evidence for the treatment of spinal deformities, including scoliosis and hyperkyphosis in adolescents and adults. Material and Methods: The PubMed database was searched for review articles, prospective controlled trials and randomized controlled trials related to the treatment of spinal deformities. Articles on syndromic scoliosis were excluded and so were the articles on hyperkyphosis of the spine with causes other than Scheuermann’s disease and osteoporosis. Articles on conservative and surgical treatments of idiopathic scoliosis, adult scoliosis and hyperkyphosis were also included. For retrospective papers, only studies with a follow up period exceeding 10 years were included. Results: The review showed that early-onset idiopathic scoliosis has a worse outcome than late-onset idiopathic scoliosis, which is rather benign. Patients with AIS function well as adults; they have no more health problems when compared to patients without scoliosis, other than a slight increase in back pain and aesthetic concern. Conservative treatment of adolescent idiopathic scoliosis (AIS) using physiotherapeutic scoliosis-specific exercises (PSSE), specifically PSSR and rigid bracing was supported by level I evidence. Yet to date, there is no high quality evidence (RCT`s) demonstrating that surgical treatment is superior to conservative treatment for the management of AIS. For adult scoliosis, there are only a few studies on the effectiveness of PSSEs and a conclusion cannot as yet be drawn. For hyperkyphosis, there is no high-quality evidence for physiotherapy, bracing or surgery for the treatment of adolescents and adults. However, bracing has been found to reduce thoracic hyperkyphosis, ranging from 55 to 80° in adolescents. In patients over the age of 60, bracing improves the balance score, and reduces spinal deformity and pain. Surgery is indicated in adolescents and adults in the presence of progression of kyphosis, refractory pain and loss of balance. Discussion: The available evidence reviewed has suggested that different approaches are needed towards the management of different spinal deformities. Specific exercises should be prescribed in children and adolescents with a Cobb angle in excess of 15°. In progressive curves, they should be used in conjunction with bracing. Clarity regarding differences and similarities is given as to what makes PSSE and PSSR specific exercises. As AIS is relatively benign in nature, conservative treatment should be tried when the curve is at a surgical threshold, before surgery is considered. Similarly, bracing and exercises should be prescribed for patients with hyperkyphosis, particularly when the lumbar spine is afflicted. Surgery should be considered only when the symptoms cannot be managed conservatively. Conclusion: There is at present high quality evidence in support of the conservative treatment of AIS. The current evidence supports the use of PSSE, especially those using PSSR, together with bracing in the treatment of AIS. In view of the lack of medical consequences in adults with AIS, conservative treatment should be considered for curves exceeding the formerly assumed range of conservative indications. There is, however a lack of evidence in support of any treatment of choice for hyperkyphosis in adolescents and spinal deformities in adults. Yet, conservative treatment should be considered first. Yet to date, there is no high quality evidence (RCT`s) demonstrating that surgical treatment is superior to conservative treatment for the management of AIS and hyperkyphosis. Additionally, surgery needs to be considered with caution, as it is associated with a number of long-term complications. PMID:29399227

Conserving migratory mule deer through the umbrella of sage-grouse

USGS Publications Warehouse

Copeland, H. E.; Sawyer, H.; Monteith, K. L.; Naugle, D.E.; Pocewicz, Amy; Graf, N.; Kauffman, Matthew J.

2014-01-01

Conserving migratory ungulates in increasingly human-dominated landscapes presents a difficult challenge to land managers and conservation practitioners. Nevertheless, ungulates may receive ancillary benefits from conservation actions designed to protect species of greater conservation priority where their ranges are sympatric. Greater Sage-Grouse (Centrocerus urophasianus), for example, have been proposed as an umbrella species for other sagebrush (Artemesia spp.)-dependent fauna. We examined a landscape where conservation efforts for sage-grouse overlap spatially with mule deer (Odocoileus hemionus) to determine whether sage-grouse conservation measures also might protect important mule deer migration routes and seasonal ranges. We conducted a spatial analysis to determine what proportion of migration routes, stopover areas, and winter ranges used by mule deer were located in areas managed for sage-grouse conservation. Conservation measures overlapped with 66–70% of migration corridors, 74–75% of stopovers, and 52–91% of wintering areas for two mule deer populations in the upper Green River Basin of Wyoming. Of those proportions, conservation actions targeted towards sage-grouse accounted for approximately half of the overlap in corridors and stopover areas, and nearly all overlap on winter ranges, indicating that sage-grouse conservation efforts represent an important step in conserving migratory mule deer. Conservation of migratory species presents unique challenges because although overlap with conserved lands may be high, connectivity of the entire route must be maintained as barriers to movement anywhere within the migration corridor could render it unviable. Where mule deer habitats overlap with sage-grouse core areas, our results indicate that increased protection is afforded to winter ranges and migration routes within the umbrella of sage-grouse conservation, but this protection is contingent on concentrated developments within core areas not intersecting with high-priority stopovers or corridors, and that the policy in turn does not encourage development on deer ranges outside of core areas. With the goal of protecting entire migration routes, our analysis highlights areas of potential conservation focus for mule deer, which are characterized by high exposure to residential development and use by a large proportion of migrating deer.

Conservation biogeography of the Cerrado's wild edible plants under climate change: Linking biotic stability with agricultural expansion.

PubMed

de Oliveira, Guilherme; Lima-Ribeiro, Matheus Souza; Terribile, Levi Carina; Dobrovolski, Ricardo; Telles, Mariana Pires de Campos; Diniz-Filho, José Alexandre Felizola

2015-06-01

REMISE OF THE STUDY: Wild edible plants (WEPs) have an important cultural and economic role in human population worldwide. Human impacts are quickly converting natural habitats in agricultural, cattle ranch, and urbanized lands, putting native species on peril of risk of extinction, including some WEPs. Moreover, global climate changes also can pose another threat to species persistency. Here, we established conservation priorities for the Cerrado, a neotropical region in South America with high levels of plant endemism and vulnerability, aiming to assure long-term persistency of 16 most important WEPs. We evaluated these conservation priorities using a conservation biogeography framework using ecological patterns and process at a biogeographical scale to deal with species conservation features. We built ecological niche models for 16 WEPs from Cerrado in the neotropics using climate models for preindustrial, past (Last Glacial Maximum) and future (year 2080) time periods to establish climatically stable areas through time, finding refugias for these WEPs. We used a spatial prioritization algorithm based on the spatial pattern of irreplaceability across the neotropics, aiming to ensure the persistence of at least 25% of range size in climatically stable areas for each WEP, using agricultural models as constraints. The Southeast Cerrado was the most biotically stable and irreplaceable region for the WEPs compared with other areas across the neotropics. Our findings strongly suggest that the Southeast Cerrado should be considered a conservation priority, with new protected areas to be sustainably managed and restored, to guarantee the supply of cultural and ecosystem services provided from the Cerrado's WEPs. © 2015 Botanical Society of America, Inc.

Phylogenetic distribution of plant snoRNA families.

PubMed

Patra Bhattacharya, Deblina; Canzler, Sebastian; Kehr, Stephanie; Hertel, Jana; Grosse, Ivo; Stadler, Peter F

2016-11-24

Small nucleolar RNAs (snoRNAs) are one of the most ancient families amongst non-protein-coding RNAs. They are ubiquitous in Archaea and Eukarya but absent in bacteria. Their main function is to target chemical modifications of ribosomal RNAs. They fall into two classes, box C/D snoRNAs and box H/ACA snoRNAs, which are clearly distinguished by conserved sequence motifs and the type of chemical modification that they govern. Similarly to microRNAs, snoRNAs appear in distinct families of homologs that affect homologous targets. In animals, snoRNAs and their evolution have been studied in much detail. In plants, however, their evolution has attracted comparably little attention. In order to chart the phylogenetic distribution of individual snoRNA families in plants, we applied a sophisticated approach for identifying homologs of known plant snoRNAs across the plant kingdom. In response to the relatively fast evolution of snoRNAs, information on conserved sequence boxes, target sequences, and secondary structure is combined to identify additional snoRNAs. We identified 296 families of snoRNAs in 24 species and traced their evolution throughout the plant kingdom. Many of the plant snoRNA families comprise paralogs. We also found that targets are well-conserved for most snoRNA families. The sequence conservation of snoRNAs is sufficient to establish homologies between phyla. The degree of this conservation tapers off, however, between land plants and algae. Plant snoRNAs are frequently organized in highly conserved spatial clusters. As a resource for further investigations we provide carefully curated and annotated alignments for each snoRNA family under investigation.

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

PubMed

Chakravorty, S; Sarkar, S; Gachhui, R

2015-01-01

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

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...

Ex situ conservation of Holstein-Friesian cattle: Comparing the Dutch, French and USA germplasm collections

USDA-ARS?s Scientific Manuscript database

Holstein-Friesian (HF) gene bank collections were established in France, the Netherlands and USA in order to conserve genetic diversity for this breed. Genetic diversity of HF collections within and between countries was assessed and compared with active HF bulls in each country by using pedigree da...

Highly designable phenotypes and mutational buffers emerge from a systematic mapping between network topology and dynamic output.

PubMed

Nochomovitz, Yigal D; Li, Hao

2006-03-14

Deciphering the design principles for regulatory networks is fundamental to an understanding of biological systems. We have explored the mapping from the space of network topologies to the space of dynamical phenotypes for small networks. Using exhaustive enumeration of a simple model of three- and four-node networks, we demonstrate that certain dynamical phenotypes can be generated by an atypically broad spectrum of network topologies. Such dynamical outputs are highly designable, much like certain protein structures can be designed by an unusually broad spectrum of sequences. The network topologies that encode a highly designable dynamical phenotype possess two classes of connections: a fully conserved core of dedicated connections that encodes the stable dynamical phenotype and a partially conserved set of variable connections that controls the transient dynamical flow. By comparing the topologies and dynamics of the three- and four-node network ensembles, we observe a large number of instances of the phenomenon of "mutational buffering," whereby addition of a fourth node suppresses phenotypic variation amongst a set of three-node networks.

Quantifying high resolution transitional breaks in plant and mammal distributions at regional extent and their association with climate, topography and geology.

PubMed

Di Virgilio, Giovanni; Laffan, Shawn W; Ebach, Malte C

2013-01-01

We quantify spatial turnover in communities of 1939 plant and 59 mammal species at 2.5 km resolution across a topographically heterogeneous region in south-eastern Australia to identify distributional breaks and low turnover zones where multiple species distributions overlap. Environmental turnover is measured to determine how climate, topography and geology influence biotic turnover differently across a variety of biogeographic breaks and overlaps. We identify the genera driving turnover and confirm the versatility of this approach across spatial scales and locations. Directional moving window analyses, rotated through 360°, were used to measure spatial turnover variation in different directions between gridded cells containing georeferenced plant and mammal occurrences and environmental variables. Generalised linear models were used to compare taxic turnover results with equivalent analyses for geology, regolith weathering, elevation, slope, solar radiation, annual precipitation and annual mean temperature, both uniformly across the entire study area and by stratifying it into zones of high and low turnover. Identified breaks and transitions were compared to a conservation bioregionalisation framework widely used in Australia. Detailed delineations of plant and mammal turnover zones with gradational boundaries denoted subtle variation in species assemblages. Turnover patterns often diverged from bioregion boundaries, though plant turnover adhered most closely. A prominent break zone contained either comparable or greater numbers of unique genera than adjacent overlaps, but these were concentrated in a small subsection relatively under-protected by conservation reserves. The environmental correlates of biotic turnover varied for different turnover zones in different subsections of the study area. Topography and temperature showed much stronger relationships with plant turnover in a topographically complex overlap, relative to a lowland overlap where weathering was most predictive. This method can quantify transitional turnover patterns from small to broad extents, at different resolutions for any location, and complements broad-scale bioregionalisation schemes in conservation planning.

External beam boost versus interstitial high-dose-rate brachytherapy boost in the adjuvant radiotherapy following breast-conserving therapy in early-stage breast cancer: a dosimetric comparison

PubMed Central

Melchert, Corinna; Kovács, György

2016-01-01

Purpose This study aims to compare the dosimetric data of local tumor's bed dose escalation (boost) with photon beams (external beam radiation therapy – EBRT) versus high-dose-rate interstitial brachytherapy (HDR-BT) after breast-conserving treatment in women with early-stage breast cancer. Material and methods We analyzed the treatment planning data of 136 irradiated patients, treated between 2006 and 2013, who underwent breast-conserving surgery and adjuvant whole breast irradiation (WBI; 50.4 Gy) and boost (HDR-BT: 10 Gy in one fraction [n = 36]; EBRT: 10 Gy in five fractions [n = 100]). Organs at risk (OAR; heart, ipsilateral lung, skin, most exposed rib segment) were delineated. Dosimetric parameters were calculated with the aid of dose-volume histograms (DVH). A non-parametric test was performed to compare the two different boost forms. Results There was no difference for left-sided cancers regarding the maximum dose to the heart (HDR-BT 29.8% vs. EBRT 29.95%, p = 0.34). The maximum doses to the other OAR were significantly lower for HDR-BT (Dmax lung 47.12% vs. 87.7%, p < 0.01; rib 61.17% vs. 98.5%, p < 0.01; skin 57.1% vs. 94.75%, p < 0.01; in the case of right-sided breast irradiation, dose of the heart 6.00% vs. 16.75%, p < 0.01). Conclusions Compared to EBRT, local dose escalation with HDR-BT presented a significant dose reduction to the investigated OAR. Only left-sided irradiation showed no difference regarding the maximum dose to the heart. Reducing irradiation exposure to OAR could result in a reduction of long-term side effects. Therefore, from a dosimetric point of view, an interstitial boost complementary to WBI via EBRT seems to be more advantageous in the adjuvant radiotherapy of breast cancer. PMID:27648082

The Effectiveness of Conservative Management for Acute Whiplash Associated Disorder (WAD) II: A Systematic Review and Meta-Analysis of Randomised Controlled Trials

PubMed Central

Wiangkham, Taweewat; Duda, Joan; Haque, Sayeed; Madi, Mohammad; Rushton, Alison

2015-01-01

Objective To evaluate the effectiveness of conservative management (except drug therapy) for acute Whiplash Associated Disorder (WAD) II. Design Systematic review and meta-analysis of Randomised Controlled Trials (RCTs) using a pre-defined protocol. Two independent reviewers searched information sources, decided eligibility of studies, and assessed risk of bias (RoB) of included trials. Data were extracted by one reviewer and checked by the other. A third reviewer mediated any disagreements throughout. Qualitative trial and RoB data were summarised descriptively. Quantitative syntheses were conducted across trials for comparable interventions, outcome measures and assessment points. Meta-analyses compared effect sizes with random effects, using STATA version 12. Data Sources PEDro, Medline, Embase, AMED, CINAHL, PsycINFO, and Cochrane Library with manual searching in key journals, reference lists, British National Bibliography for Report Literature, Center for International Rehabilitation Research Information & Exchange, and National Technical Information Service were searched from inception to 15th April 2015. Active researchers in the field were contacted to determine relevant studies. Eligibility Criteria for Selecting Studies RCTs evaluating acute (<4 weeks) WADII, any conservative intervention, with outcome measures important to the International Classification of Function, Disability and Health. Results Fifteen RCTs all assessed as high RoB (n=1676 participants) across 9 countries were included. Meta-analyses enabled 4 intervention comparisons: conservative versus standard/control, active versus passive, behavioural versus standard/control, and early versus late. Conservative intervention was more effective for pain reduction at 6 months (95%CI: -20.14 to -3.38) and 1-3 years (-25.44 to -3.19), and improvement in cervical mobility in the horizontal plane at <3 months (0.43 to 5.60) compared with standard/control intervention. Active intervention was effective for pain alleviation at 6 months (-17.19 to -3.23) and 1-3 years (-26.39 to -10.08) compared with passive intervention. Behavioural intervention was more effective than standard/control intervention for pain reduction at 6 months (-15.37 to -1.55), and improvement in cervical movement in the coronal (0.93 to 4.38) and horizontal planes at 3-6 months (0.43 to 5.46). For early (<4 days) versus late (>10 days) interventions, there were no statistically significant differences in all outcome measures between interventions at any time. Conclusions Conservative and active interventions may be useful for pain reduction in patients with acute WADII. Additionally, cervical horizontal mobility could be improved by conservative intervention. The employment of a behavioural intervention (e.g. act-as-usual, education and self-care including regularly exercise) could have benefits for pain reduction and improvement in cervical movement in the coronal and horizontal planes. The evidence was evaluated as low/very low level according to the Grading of Recommendations Assessment, Development and Evaluation system. PMID:26196127

Percutaneous Vertebroplasty Versus Conservative Treatment and Rehabilitation in Women with Vertebral Fractures due to Osteoporosis: A Prospective Comparative Study.

PubMed

Macías-Hernández, Salvador Israel; Chávez-Arias, Daniel David; Miranda-Duarte, Antonio; Coronado-Zarco, Roberto; Diez-García, María Pilar

2015-01-01

Percutaneous vertebroplasty is commonly used in the management of osteoporosis-related vertebral fractures, although there is controversy on its superiority over conservative treatment. Here we compare pain and function in women with vertebral osteoporotic fractures who underwent percutaneous vertebroplasty versus conservative treatment with a protocolized rehabilitation program. A longitudinal and comparative prospective study was conducted. Women ≥ 60 years of age with a diagnosis of osteoporosis who had at least one vertebral thoracic or lumbar compression fracture were included and divided into two groups, conservative treatment or vertebroplasty. The Visual Analogue Scale (VAS) and Oswestry Disability Index (ODI) were used to assess pain and function, respectively, as the outcome measures. We included 31 patients, 13 (42%) treated with percutaneous vertebroplasty and 18 (58%) with conservative treatment. Baseline clinical characteristics, bone densitometry and fracture data were similar in both groups. At baseline, VAS was 73.1 ± 28.36 in the vertebroplasty group and 68.6 ± 36.1 mm in the conservative treatment group (p = 0.632); at three months it was 33.11 ± 10.1 vs. 42 ± 22.21 mm (p = 0.111); and at 12 months, 32.3 ± 11.21 vs. 36.1 ± 12.36 mm (p = 0.821). The ODI at baseline was 83% in the vertebroplasty group vs. 85% for conservative management (p = 0.34); at three months, 36 vs. 39% (p = 0.36); and at 12 months, 29.38 vs. 28.33% (p = 0.66). Treatment with percutaneous vertebroplasty had no advantages over conservative treatment for pain and function in this group of women ≥ 60 years of age with osteoporosis.

7 CFR 12.22 - Highly erodible field determination criteria.

Code of Federal Regulations, 2010 CFR

2010-01-01

... of changing field boundaries. When field boundaries are changed to include areas of land that were... Section 12.22 Agriculture Office of the Secretary of Agriculture HIGHLY ERODIBLE LAND AND WETLAND CONSERVATION Highly Erodible Land Conservation § 12.22 Highly erodible field determination criteria. (a...

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…

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.

Anthropogenic disturbance in tropical forests can double biodiversity loss from deforestation.

PubMed

Barlow, Jos; Lennox, Gareth D; Ferreira, Joice; Berenguer, Erika; Lees, Alexander C; Mac Nally, Ralph; Thomson, James R; Ferraz, Silvio Frosini de Barros; Louzada, Julio; Oliveira, Victor Hugo Fonseca; Parry, Luke; Solar, Ricardo Ribeiro de Castro; Vieira, Ima C G; Aragão, Luiz E O C; Begotti, Rodrigo Anzolin; Braga, Rodrigo F; Cardoso, Thiago Moreira; de Oliveira, Raimundo Cosme; Souza, Carlos M; Moura, Nárgila G; Nunes, Sâmia Serra; Siqueira, João Victor; Pardini, Renata; Silveira, Juliana M; Vaz-de-Mello, Fernando Z; Veiga, Ruan Carlo Stulpen; Venturieri, Adriano; Gardner, Toby A

2016-07-07

Concerted political attention has focused on reducing deforestation, and this remains the cornerstone of most biodiversity conservation strategies. However, maintaining forest cover may not reduce anthropogenic forest disturbances, which are rarely considered in conservation programmes. These disturbances occur both within forests, including selective logging and wildfires, and at the landscape level, through edge, area and isolation effects. Until now, the combined effect of anthropogenic disturbance on the conservation value of remnant primary forests has remained unknown, making it impossible to assess the relative importance of forest disturbance and forest loss. Here we address these knowledge gaps using a large data set of plants, birds and dung beetles (1,538, 460 and 156 species, respectively) sampled in 36 catchments in the Brazilian state of Pará. Catchments retaining more than 69–80% forest cover lost more conservation value from disturbance than from forest loss. For example, a 20% loss of primary forest, the maximum level of deforestation allowed on Amazonian properties under Brazil’s Forest Code, resulted in a 39–54% loss of conservation value: 96–171% more than expected without considering disturbance effects. We extrapolated the disturbance-mediated loss of conservation value throughout Pará, which covers 25% of the Brazilian Amazon. Although disturbed forests retained considerable conservation value compared with deforested areas, the toll of disturbance outside Pará’s strictly protected areas is equivalent to the loss of 92,000–139,000 km2 of primary forest. Even this lowest estimate is greater than the area deforested across the entire Brazilian Amazon between 2006 and 2015 (ref. 10). Species distribution models showed that both landscape and within-forest disturbances contributed to biodiversity loss, with the greatest negative effects on species of high conservation and functional value. These results demonstrate an urgent need for policy interventions that go beyond the maintenance of forest cover to safeguard the hyper-diversity of tropical forest ecosystems.

An efficient algorithm for pairwise local alignment of protein interaction networks

DOE PAGES

Chen, Wenbin; Schmidt, Matthew; Tian, Wenhong; ...

2015-04-01

Recently, researchers seeking to understand, modify, and create beneficial traits in organisms have looked for evolutionarily conserved patterns of protein interactions. Their conservation likely means that the proteins of these conserved functional modules are important to the trait's expression. In this paper, we formulate the problem of identifying these conserved patterns as a graph optimization problem, and develop a fast heuristic algorithm for this problem. We compare the performance of our network alignment algorithm to that of the MaWISh algorithm [Koyuturk M, Kim Y, Topkara U, Subramaniam S, Szpankowski W, Grama A, Pairwise alignment of protein interaction networks, J Computmore » Biol 13(2): 182-199, 2006.], which bases its search algorithm on a related decision problem formulation. We find that our algorithm discovers conserved modules with a larger number of proteins in an order of magnitude less time. In conclusion, the protein sets found by our algorithm correspond to known conserved functional modules at comparable precision and recall rates as those produced by the MaWISh algorithm.« less

Design of COSMIC: a randomized, multi-centre controlled trial comparing conservative or early surgical management of incomplete cervical cord syndrome without spinal instability.

PubMed

Bartels, Ronald H M A; Hosman, Allard J F; van de Meent, Henk; Hofmeijer, Jeannette; Vos, Pieter E; Slooff, Willem Bart; Öner, F Cumhur; Coppes, Maarten H; Peul, Wilco C; Verbeek, André L M

2013-01-31

Incomplete cervical cord syndrome without spinal instability is a very devastating event for the patient and the family. It is estimated that up to 25% of all traumatic spinal cord lesions belong to this category. The treatment for this type of spinal cord lesion is still subject of discussion. From a biological point of view early surgery could prevent secondary damage due to ongoing compression of the already damaged spinal cord. Historically, however, conservative treatment was propagated with good clinical results. Proponents for early surgery as well those favoring conservative treatment are still in debate. The proposed trial will contribute to the discussion and hopefully also to a decrease in the variability of clinical practice. A randomized controlled trial is designed to compare the clinical outcome of early surgical strategy versus a conservative approach. The primary outcome is clinical outcome according to mJOA. This also measured by ASIA score, DASH score and SCIM III score. Other endpoints are duration of the stay at a high care department (medium care, intensive care), duration of the stay at the hospital, complication rate, mortality rate, sort of rehabilitation, and quality of life. A sample size of 36 patients per group was calculated to reach a power of 95%. The data will be analyzed as intention-to-treat at regular intervals, but the end evaluation will take place at two years post-injury. At the end of the study, clinical outcomes between treatments attitudes can be compared. Efficacy, but also efficiency can be determined. A goal of the study is to determine which treatment will result in the best quality of life for the patients. This study will certainly contribute to more uniformity of treatment offered to patients with a special sort of spinal cord injury. Gov: NCT01367405.

Comparative genomics and prediction of conditionally dispensable sequences in legume-infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors.

PubMed

Williams, Angela H; Sharma, Mamta; Thatcher, Louise F; Azam, Sarwar; Hane, James K; Sperschneider, Jana; Kidd, Brendan N; Anderson, Jonathan P; Ghosh, Raju; Garg, Gagan; Lichtenzveig, Judith; Kistler, H Corby; Shea, Terrance; Young, Sarah; Buck, Sally-Anne G; Kamphuis, Lars G; Saxena, Rachit; Pande, Suresh; Ma, Li-Jun; Varshney, Rajeev K; Singh, Karam B

2016-03-05

Soil-borne fungi of the Fusarium oxysporum species complex cause devastating wilt disease on many crops including legumes that supply human dietary protein needs across many parts of the globe. We present and compare draft genome assemblies for three legume-infecting formae speciales (ff. spp.): F. oxysporum f. sp. ciceris (Foc-38-1) and f. sp. pisi (Fop-37622), significant pathogens of chickpea and pea respectively, the world's second and third most important grain legumes, and lastly f. sp. medicaginis (Fom-5190a) for which we developed a model legume pathosystem utilising Medicago truncatula. Focusing on the identification of pathogenicity gene content, we leveraged the reference genomes of Fusarium pathogens F. oxysporum f. sp. lycopersici (tomato-infecting) and F. solani (pea-infecting) and their well-characterised core and dispensable chromosomes to predict genomic organisation in the newly sequenced legume-infecting isolates. Dispensable chromosomes are not essential for growth and in Fusarium species are known to be enriched in host-specificity and pathogenicity-associated genes. Comparative genomics of the publicly available Fusarium species revealed differential patterns of sequence conservation across F. oxysporum formae speciales, with legume-pathogenic formae speciales not exhibiting greater sequence conservation between them relative to non-legume-infecting formae speciales, possibly indicating the lack of a common ancestral source for legume pathogenicity. Combining predicted dispensable gene content with in planta expression in the model legume-infecting isolate, we identified small conserved regions and candidate effectors, four of which shared greatest similarity to proteins from another legume-infecting ff. spp. We demonstrate that distinction of core and potential dispensable genomic regions of novel F. oxysporum genomes is an effective tool to facilitate effector discovery and the identification of gene content possibly linked to host specificity. While the legume-infecting isolates didn't share large genomic regions of pathogenicity-related content, smaller regions and candidate effector proteins were highly conserved, suggesting that they may play specific roles in inducing disease on legume hosts.

Use of population viability analysis to evaluate CITES trade-management options for threatened marine fishes.

PubMed

Curtis, Janelle M R; Vincent, Amanda C J

2008-10-01

Achieving multiple conservation objectives can be challenging, particularly under high uncertainty. Having agreed to limit seahorse (Hippocampus) exports to sustainable levels, signatories to the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) were offered the option of a single 10-cm minimum size limit (MSL) as an interim management measure for all Hippocampus species (> or =34). Although diverse stakeholders supported the recommended MSL, its biological and socioeconomic implications were not assessed quantitatively. We combined population viability analysis, model sensitivity analysis, and economic information to evaluate the trade-off between conservation threat to and long-term cumulative income from these exploited marine fishes of high conservation concern. We used the European long-snouted seahorse (Hippocampus guttulatus) as a representative species to compare the performance of MSLs set at alternative biological reference points. Our sensitivity analyses showed that in most of our scenarios, setting the MSL just above size at maturity (9.7 cm in H. guttulatus) would not prevent exploited populations from becoming listed as vulnerable. By contrast, the relative risk of decline and extinction were almost halved--at a cost of only a 5.6% reduction in long-term catches--by increasing the MSL to the size reached after at least one full reproductive season. On the basis of our analysis, a precautionary increase in the MSL could be compatible with sustaining fishers' livelihoods and international trade. Such management tactics that aid species conservation and have minimal effects on long term catch trends may help bolster the case for CITES trade management of other valuable marine fishes.

Resource selection and space use by sea ducks during the non-breeding season: Implications for habitat conservation planning in urbanized estuaries

USGS Publications Warehouse

De La Cruz, Susan E. W.; Eadie, John M.; Miles, A. Keith; Yee, Julie; Spragens, Kyle A.; Palm, Eric C.; Takekawa, John Y.

2014-01-01

Wide-ranging marine birds rely on multiple habitats for wintering, breeding, and migrating, and their conservation may be dependent on protecting networks of key areas. Urbanized estuaries are critical wintering and stopover areas for many declining sea ducks in North America; however, conservation measures within estuaries are difficult to establish given lack of knowledge about habitat use by these species and the variety of competing human interests. We applied hierarchical modeling to evaluate resource selection of sea ducks (surf scoters, Melanitta perspicillata) wintering in San Francisco Bay, California, USA, a large and highly urbanized estuary. We also examined their distribution, home range, and movements with respect to key habitat features and regions within the estuary. Herring roe was the strongest predictor of bird locations; however, eelgrass, water depth and salinity were also highly-ranked, with sea ducks using deeper areas of higher salinity associated with herring roe and eelgrass presence during mid-winter. Sea ducks were also strongly associated with ferry routes, suggesting these areas may contain resources that are too important to avoid and emphasizing the need to better understand water traffic effects. Movements and home range size differed between males and females in early winter but became more similar in late winter. Birds traveled farther and used several sub-bays in early winter compared to mid-winter when herring roe availability peaked in the Central Bay. Our findings identified key environmental variables, highlighted core use areas, and documented critical periods for consideration when developing conservation plans for sea ducks in urbanized estuaries.

Identification and Expression of Acetylcholinesterase in Octopus vulgaris Arm Development and Regeneration: a Conserved Role for ACHE?

PubMed

Fossati, Sara Maria; Candiani, Simona; Nödl, Marie-Therese; Maragliano, Luca; Pennuto, Maria; Domingues, Pedro; Benfenati, Fabio; Pestarino, Mario; Zullo, Letizia

2015-08-01

Acetylcholinesterase (ACHE) is a glycoprotein with a key role in terminating synaptic transmission in cholinergic neurons of both vertebrates and invertebrates. ACHE is also involved in the regulation of cell growth and morphogenesis during embryogenesis and regeneration acting through its non-cholinergic sites. The mollusk Octopus vulgaris provides a powerful model for investigating the mechanisms underlying tissue morphogenesis due to its high regenerative power. Here, we performed a comparative investigation of arm morphogenesis during adult arm regeneration and embryonic arm development which may provide insights on the conserved ACHE pathways. In this study, we cloned and characterized O. vulgaris ACHE, finding a single highly conserved ACHE hydrophobic variant, characterized by prototypical catalytic sites and a putative consensus region for a glycosylphosphatidylinositol (GPI)-anchor attachment at the COOH-terminus. We then show that its expression level is correlated to the stage of morphogenesis in both adult and embryonic arm. In particular, ACHE is localized in typical neuronal sites when adult-like arm morphology is established and in differentiating cell locations during the early stages of arm morphogenesis. This possibility is also supported by the presence in the ACHE sequence and model structure of both cholinergic and non-cholinergic sites. This study provides insights into ACHE conserved roles during processes of arm morphogenesis. In addition, our modeling study offers a solid basis for predicting the interaction of the ACHE domains with pharmacological blockers for in vivo investigations. We therefore suggest ACHE as a target for the regulation of tissue morphogenesis.

Extensive Conserved Synteny of Genes between the Karyotypes of Manduca sexta and Bombyx mori Revealed by BAC-FISH Mapping

PubMed Central

Tanaka-Okuyama, Makiko; Shibata, Fukashi; Yoshido, Atsuo; Marec, František; Wu, Chengcang; Zhang, Hongbin; Goldsmith, Marian R.

2009-01-01

Background Genome sequencing projects have been completed for several species representing four highly diverged holometabolous insect orders, Diptera, Hymenoptera, Coleoptera, and Lepidoptera. The striking evolutionary diversity of insects argues a need for efficient methods to apply genome information from such models to genetically uncharacterized species. Constructing conserved synteny maps plays a crucial role in this task. Here, we demonstrate the use of fluorescence in situ hybridization with bacterial artificial chromosome probes as a powerful tool for physical mapping of genes and comparative genome analysis in Lepidoptera, which have numerous and morphologically uniform holokinetic chromosomes. Methodology/Principal Findings We isolated 214 clones containing 159 orthologs of well conserved single-copy genes of a sequenced lepidopteran model, the silkworm, Bombyx mori, from a BAC library of a sphingid with an unexplored genome, the tobacco hornworm, Manduca sexta. We then constructed a BAC-FISH karyotype identifying all 28 chromosomes of M. sexta by mapping 124 loci using the corresponding BAC clones. BAC probes from three M. sexta chromosomes also generated clear signals on the corresponding chromosomes of the convolvulus hawk moth, Agrius convolvuli, which belongs to the same subfamily, Sphinginae, as M. sexta. Conclusions/Significance Comparison of the M. sexta BAC physical map with the linkage map and genome sequence of B. mori pointed to extensive conserved synteny including conserved gene order in most chromosomes. Only a few rearrangements, including three inversions, three translocations, and two fission/fusion events were estimated to have occurred after the divergence of Bombycidae and Sphingidae. These results add to accumulating evidence for the stability of lepidopteran genomes. Generating signals on A. convolvuli chromosomes using heterologous M. sexta probes demonstrated that BAC-FISH with orthologous sequences can be used for karyotyping a wide range of related and genetically uncharacterized species, significantly extending the ability to develop synteny maps for comparative and functional genomics. PMID:19829706

Convergent occurrence of the developmental hourglass in plant and animal embryogenesis?

PubMed

Cridge, Andrew G; Dearden, Peter K; Brownfield, Lynette R

2016-04-01

The remarkable similarity of animal embryos at particular stages of development led to the proposal of a developmental hourglass. In this model, early events in development are less conserved across species but lead to a highly conserved 'phylotypic period'. Beyond this stage, the model suggests that development once again becomes less conserved, leading to the diversity of forms. Recent comparative studies of gene expression in animal groups have provided strong support for the hourglass model. How and why might such an hourglass pattern be generated? More importantly, how might early acting events in development evolve while still maintaining a later conserved stage? The discovery that an hourglass pattern may also exist in the embryogenesis of plants provides comparative data that may help us explain this phenomenon. Whether the developmental hourglass occurs in plants, and what this means for our understanding of embryogenesis in plants and animals is discussed. Models by which conserved early-acting genes might change their functional role in the evolution of gene networks, how networks buffer these changes, and how that might constrain, or confer diversity, of the body plan are also discused. Evidence of a morphological and molecular hourglass in plant and animal embryogenesis suggests convergent evolution. This convergence is likely due to developmental constraints imposed upon embryogenesis by the need to produce a viable embryo with an established body plan, controlled by the architecture of the underlying gene regulatory networks. As the body plan is largely laid down during the middle phases of embryo development in plants and animals, then it is perhaps not surprising this stage represents the narrow waist of the hourglass where the gene regulatory networks are the oldest and most robust and integrated, limiting species diversity and constraining morphological space. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company.

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...

Strong minor groove base conservation in sequence logos implies DNA distortion or base flipping during replication and transcription initiation.

PubMed

Schneider, T D

2001-12-01

The sequence logo for DNA binding sites of the bacteriophage P1 replication protein RepA shows unusually high sequence conservation ( approximately 2 bits) at a minor groove that faces RepA. However, B-form DNA can support only 1 bit of sequence conservation via contacts into the minor groove. The high conservation in RepA sites therefore implies a distorted DNA helix with direct or indirect contacts to the protein. Here I show that a high minor groove conservation signature also appears in sequence logos of sites for other replication origin binding proteins (Rts1, DnaA, P4 alpha, EBNA1, ORC) and promoter binding proteins (sigma(70), sigma(D) factors). This finding implies that DNA binding proteins generally use non-B-form DNA distortion such as base flipping to initiate replication and transcription.

Generating spatially optimized habitat in a trade-off between social optimality and budget efficiency.

PubMed

Drechsler, Martin

2017-02-01

Auctions have been proposed as alternatives to payments for environmental services when spatial interactions and costs are better known to landowners than to the conservation agency (asymmetric information). Recently, an auction scheme was proposed that delivers optimal conservation in the sense that social welfare is maximized. I examined the social welfare and the budget efficiency delivered by this scheme, where social welfare represents the difference between the monetized ecological benefit and the conservation cost incurred to the landowners and budget efficiency is defined as maximizing the ecological benefit for a given conservation budget. For the analysis, I considered a stylized landscape with land patches that can be used for agriculture or conservation. The ecological benefit was measured by an objective function that increases with increasing number and spatial aggregation of conserved land patches. I compared the social welfare and the budget efficiency of the auction scheme with an agglomeration payment, a policy scheme that considers spatial interactions and that was proposed recently. The auction delivered a higher level of social welfare than the agglomeration payment. However, the agglomeration payment was more efficient budgetarily than the auction, so the comparative performances of the 2 schemes depended on the chosen policy criterion-social welfare or budget efficiency. Both policy criteria are relevant for conservation. Which one should be chosen depends on the problem at hand, for example, whether social preferences should be taken into account in the decision of how much money to invest in conservation or whether the available conservation budget is strictly limited. © 2016 Society for Conservation Biology.

Endoscopic Ultrasound in Barrett's Oesophagitis with Dysplasia

PubMed Central

Wray, Andrew; Rice, Paul; Love, Mark

2012-01-01

Purpose With the advent of conservative therapies including photodynamic therapy and endoscopic mucosal resection for Barrett's and high grade dysplasia, accurate staging has become increasingly important. We report our experience with endoscopic ultrasound (EUS) in these patients. Materials and Methods Retrospective review of 25 consecutive patients referred for EUS for assessment of Barrett's with high grade dysplasia and /or stricture or polyp. The findings were compared with subsequent surgical pathology, or endoscopy and biopsy follow up. Results Nine patients were found to have invasive tumour on EUS and this was confirmed in all 9 either by oesophagectomy, OGD and oncology follow up, or by endoscopic mucosal resection. Eight patients underwent oesophagectomy, 5 for invasive tumour and 3 for dysplasia only, with pathological agreement with EUS findings in 7 out of 8 cases. The one discrepancy was a EUS case of mucosal thickening only with no invasion, but pathology showed a T1 lesion. Thirteen patients with no evidence of invasion were managed conservatively, with 11 patients being followed up for 6-12 months with serial OGD and biopsy, and no cases of more invasive disease occurring. Therefore, in our experience the sensitivity, specificity and positive predictive value of EUS in complex Barrett's is 90%, 100% and 100% respectively. Conclusion EUS is valuable in the assessment of high grade dysplasia in cases where conservative therapy is being considered, defining those with more deeply invasive tumour for whom radical treatment is the only option. PMID:23526576

Improving environmental and social targeting through adaptive management in Mexico's payments for hydrological services program.

PubMed

Sims, Katharine R E; Alix-Garcia, Jennifer M; Shapiro-Garza, Elizabeth; Fine, Leah R; Radeloff, Volker C; Aronson, Glen; Castillo, Selene; Ramirez-Reyes, Carlos; Yañez-Pagans, Patricia

2014-10-01

Natural resource managers are often expected to achieve both environmental protection and economic development even when there are fundamental trade-offs between these goals. Adaptive management provides a theoretical structure for program administrators to balance social priorities in the presence of trade-offs and to improve conservation targeting. We used the case of Mexico's federal Payments for Hydrological Services program (PSAH) to illustrate the importance of adaptive management for improving program targeting. We documented adaptive elements of PSAH and corresponding changes in program eligibility and selection criteria. To evaluate whether these changes resulted in enrollment of lands of high environmental and social priority, we compared the environmental and social characteristics of the areas enrolled in the program with the characteristics of all forested areas in Mexico, all areas eligible for the program, and all areas submitted for application to the program. The program successfully enrolled areas of both high ecological and social priority, and over time, adaptive changes in the program's criteria for eligibility and selection led to increased enrollment of land scoring high on both dimensions. Three factors facilitated adaptive management in Mexico and are likely to be generally important for conservation managers: a supportive political environment, including financial backing and encouragement to experiment from the federal government; availability of relatively good social and environmental data; and active participation in the review process by stakeholders and outside evaluators. © 2014 Society for Conservation Biology.

Isolated Ficus trees deliver dual conservation and development benefits in a rural landscape.

PubMed

Cottee-Jones, H Eden W; Bajpai, Omesh; Chaudhary, Lal B; Whittaker, Robert J

2015-11-01

Many of the world's rural populations are dependent on the local provision of economically and medicinally important plant resources. However, increasing land-use intensity is depleting these resources, reducing human welfare, and thereby constraining development. Here we investigate a low cost strategy to manage the availability of valuable plant resources, facilitated by the use of isolated Ficus trees as restoration nuclei. We surveyed the plants growing under 207 isolated trees in Assam, India, and categorized them according to their local human-uses. We found that Ficus trees were associated with double the density of important high-grade timber, firewood, human food, livestock fodder, and medicinal plants compared to non-Ficus trees. Management practices were also important in determining the density of valuable plants, with grazing pressure and land-use intensity significantly affecting densities in most categories. Community management practices that conserve isolated Ficus trees, and restrict livestock grazing and high-intensity land-use in their vicinity, can promote plant growth and the provision of important local resources.

Comparative qualitative phosphoproteomics analysis identifies shared phosphorylation motifs and associated biological processes in evolutionary divergent plants.

PubMed

Al-Momani, Shireen; Qi, Da; Ren, Zhe; Jones, Andrew R

2018-06-15

Phosphorylation is one of the most prevalent post-translational modifications and plays a key role in regulating cellular processes. We carried out a bioinformatics analysis of pre-existing phosphoproteomics data, to profile two model species representing the largest subclasses in flowering plants the dicot Arabidopsis thaliana and the monocot Oryza sativa, to understand the extent to which phosphorylation signaling and function is conserved across evolutionary divergent plants. We identified 6537 phosphopeptides from 3189 phosphoproteins in Arabidopsis and 2307 phosphopeptides from 1613 phosphoproteins in rice. We identified phosphorylation motifs, finding nineteen pS motifs and two pT motifs shared in rice and Arabidopsis. The majority of shared motif-containing proteins were mapped to the same biological processes with similar patterns of fold enrichment, indicating high functional conservation. We also identified shared patterns of crosstalk between phosphoserines with enrichment for motifs pSXpS, pSXXpS and pSXXXpS, where X is any amino acid. Lastly, our results identified several pairs of motifs that are significantly enriched to co-occur in Arabidopsis proteins, indicating cross-talk between different sites, but this was not observed in rice. Our results demonstrate that there are evolutionary conserved mechanisms of phosphorylation-mediated signaling in plants, via analysis of high-throughput phosphorylation proteomics data from key monocot and dicot species: rice and Arabidposis thaliana. The results also suggest that there is increased crosstalk between phosphorylation sites in A. thaliana compared with rice. The results are important for our general understanding of cell signaling in plants, and the ability to use A. thaliana as a general model for plant biology. Copyright © 2018 The Authors. Published by Elsevier B.V. All rights reserved.

Ciona as a Simple Chordate Model for Heart Development and Regeneration

PubMed Central

Evans Anderson, Heather; Christiaen, Lionel

2016-01-01

Cardiac cell specification and the genetic determinants that govern this process are highly conserved among Chordates. Recent studies have established the importance of evolutionarily-conserved mechanisms in the study of congenital heart defects and disease, as well as cardiac regeneration. As a basal Chordate, the Ciona model system presents a simple scaffold that recapitulates the basic blueprint of cardiac development in Chordates. Here we will focus on the development and cellular structure of the heart of the ascidian Ciona as compared to other Chordates, principally vertebrates. Comparison of the Ciona model system to heart development in other Chordates presents great potential for dissecting the genetic mechanisms that underlie congenital heart defects and disease at the cellular level and might provide additional insight into potential pathways for therapeutic cardiac regeneration. PMID:27642586

SH3 interactome conserves general function over specific form

PubMed Central

Xin, Xiaofeng; Gfeller, David; Cheng, Jackie; Tonikian, Raffi; Sun, Lin; Guo, Ailan; Lopez, Lianet; Pavlenco, Alevtina; Akintobi, Adenrele; Zhang, Yingnan; Rual, Jean-François; Currell, Bridget; Seshagiri, Somasekar; Hao, Tong; Yang, Xinping; Shen, Yun A; Salehi-Ashtiani, Kourosh; Li, Jingjing; Cheng, Aaron T; Bouamalay, Dryden; Lugari, Adrien; Hill, David E; Grimes, Mark L; Drubin, David G; Grant, Barth D; Vidal, Marc; Boone, Charles; Sidhu, Sachdev S; Bader, Gary D

2013-01-01

Src homology 3 (SH3) domains bind peptides to mediate protein–protein interactions that assemble and regulate dynamic biological processes. We surveyed the repertoire of SH3 binding specificity using peptide phage display in a metazoan, the worm Caenorhabditis elegans, and discovered that it structurally mirrors that of the budding yeast Saccharomyces cerevisiae. We then mapped the worm SH3 interactome using stringent yeast two-hybrid and compared it with the equivalent map for yeast. We found that the worm SH3 interactome resembles the analogous yeast network because it is significantly enriched for proteins with roles in endocytosis. Nevertheless, orthologous SH3 domain-mediated interactions are highly rewired. Our results suggest a model of network evolution where general function of the SH3 domain network is conserved over its specific form. PMID:23549480

Upwind methods for the Baer–Nunziato equations and higher-order reconstruction using artificial viscosity

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

Fraysse, F., E-mail: francois.fraysse@rs2n.eu; E. T. S. de Ingeniería Aeronáutica y del Espacio, Universidad Politécnica de Madrid, Madrid; Redondo, C.

This article is devoted to the numerical discretisation of the hyperbolic two-phase flow model of Baer and Nunziato. A special attention is paid on the discretisation of intercell flux functions in the framework of Finite Volume and Discontinuous Galerkin approaches, where care has to be taken to efficiently approximate the non-conservative products inherent to the model equations. Various upwind approximate Riemann solvers have been tested on a bench of discontinuous test cases. New discretisation schemes are proposed in a Discontinuous Galerkin framework following the criterion of Abgrall and the path-conservative formalism. A stabilisation technique based on artificial viscosity is appliedmore » to the high-order Discontinuous Galerkin method and compared against classical TVD-MUSCL Finite Volume flux reconstruction.« less

A Coulomb collision algorithm for weighted particle simulations

NASA Technical Reports Server (NTRS)

Miller, Ronald H.; Combi, Michael R.

1994-01-01

A binary Coulomb collision algorithm is developed for weighted particle simulations employing Monte Carlo techniques. Charged particles within a given spatial grid cell are pair-wise scattered, explicitly conserving momentum and implicitly conserving energy. A similar algorithm developed by Takizuka and Abe (1977) conserves momentum and energy provided the particles are unweighted (each particle representing equal fractions of the total particle density). If applied as is to simulations incorporating weighted particles, the plasma temperatures equilibrate to an incorrect temperature, as compared to theory. Using the appropriate pairing statistics, a Coulomb collision algorithm is developed for weighted particles. The algorithm conserves energy and momentum and produces the appropriate relaxation time scales as compared to theoretical predictions. Such an algorithm is necessary for future work studying self-consistent multi-species kinetic transport.

Comparative transcriptome analysis reveals vertebrate phylotypic period during organogenesis

PubMed Central

Irie, Naoki; Kuratani, Shigeru

2011-01-01

One of the central issues in evolutionary developmental biology is how we can formulate the relationships between evolutionary and developmental processes. Two major models have been proposed: the 'funnel-like' model, in which the earliest embryo shows the most conserved morphological pattern, followed by diversifying later stages, and the 'hourglass' model, in which constraints are imposed to conserve organogenesis stages, which is called the phylotypic period. Here we perform a quantitative comparative transcriptome analysis of several model vertebrate embryos and show that the pharyngula stage is most conserved, whereas earlier and later stages are rather divergent. These results allow us to predict approximate developmental timetables between different species, and indicate that pharyngula embryos have the most conserved gene expression profiles, which may be the source of the basic body plan of vertebrates. PMID:21427719

Comparative Genome Sequence Analysis of the Bpa/Str Region in Mouse and Man

PubMed Central

Mallon, A.-M.; Platzer, M.; Bate, R.; Gloeckner, G.; Botcherby, M.R.M.; Nordsiek, G.; Strivens, M.A.; Kioschis, P.; Dangel, A.; Cunningham, D.; Straw, R.N.A.; Weston, P.; Gilbert, M.; Fernando, S.; Goodall, K.; Hunter, G.; Greystrong, J.S.; Clarke, D.; Kimberley, C.; Goerdes, M.; Blechschmidt, K.; Rump, A.; Hinzmann, B.; Mundy, C.R.; Miller, W.; Poustka, A.; Herman, G.E.; Rhodes, M.; Denny, P.; Rosenthal, A.; Brown, S.D.M.

2000-01-01

The progress of human and mouse genome sequencing programs presages the possibility of systematic cross-species comparison of the two genomes as a powerful tool for gene and regulatory element identification. As the opportunities to perform comparative sequence analysis emerge, it is important to develop parameters for such analyses and to examine the outcomes of cross-species comparison. Our analysis used gene prediction and a database search of 430 kb of genomic sequence covering the Bpa/Str region of the mouse X chromosome, and 745 kb of genomic sequence from the homologous human X chromosome region. We identified 11 genes in mouse and 13 genes and two pseudogenes in human. In addition, we compared the mouse and human sequences using pairwise alignment and searches for evolutionary conserved regions (ECRs) exceeding a defined threshold of sequence identity. This approach aided the identification of at least four further putative conserved genes in the region. Comparative sequencing revealed that this region is a mosaic in evolutionary terms, with considerably more rearrangement between the two species than realized previously from comparative mapping studies. Surprisingly, this region showed an extremely high LINE and low SINE content, low G+C content, and yet a relatively high gene density, in contrast to the low gene density usually associated with such regions. [The sequence data described in this paper have been submitted to EMBL under the following accession nos.: Mouse Genomic Sequence: Mouse contig A (AL021127), Mouse contig B (AL049866), BAC41M10 (AL136328), PAC303O11(AL136329). Human Genomic Sequence: Human contig 1 (U82671, U82670), Human contig 2 (U82695).] PMID:10854409

Role of DNA barcoding in marine biodiversity assessment and conservation: An update

PubMed Central

Trivedi, Subrata; Aloufi, Abdulhadi A.; Ansari, Abid A.; Ghosh, Sankar K.

2015-01-01

More than two third area of our planet is covered by oceans and assessment of marine biodiversity is a challenging task. With the increasing global population, there is a tendency to exploit marine resources for food, energy and other requirements. This puts pressure on the fragile marine environment and necessitates sustainable conservation efforts. Marine species identification using traditional taxonomical methods is often burdened with taxonomic controversies. Here we discuss the comparatively new concept of DNA barcoding and its significance in marine perspective. This molecular technique can be useful in the assessment of cryptic species which is widespread in marine environment and linking the different life cycle stages to the adult which is difficult to accomplish in the marine ecosystem. Other advantages of DNA barcoding include authentication and safety assessment of seafood, wildlife forensics, conservation genetics and detection of invasive alien species (IAS). Global DNA barcoding efforts in the marine habitat include MarBOL, CeDAMar, CMarZ, SHARK-BOL, etc. An overview on DNA barcoding of different marine groups ranging from the microbes to mammals is revealed. In conjugation with newer and faster techniques like high-throughput sequencing, DNA barcoding can serve as an effective modern tool in marine biodiversity assessment and conservation. PMID:26980996

Global status of and prospects for protection of terrestrial geophysical diversity.

PubMed

Sanderson, Eric W; Segan, Daniel B; Watson, James E M

2015-06-01

Conservation of representative facets of geophysical diversity may help conserve biological diversity as the climate changes. We conducted a global classification of terrestrial geophysical diversity and analyzed how land protection varies across geophysical diversity types. Geophysical diversity was classified in terms of soil type, elevation, and biogeographic realm and then compared to the global distribution of protected areas in 2012. We found that 300 (45%) of 672 broad geophysical diversity types currently meet the Convention on Biological Diversity's Aichi Target 11 of 17% terrestrial areal protection, which suggested that efforts to implement geophysical diversity conservation have a substantive basis on which to build. However, current protected areas were heavily biased toward high elevation and low fertility soils. We assessed 3 scenarios of protected area expansion and found that protection focused on threatened species, if fully implemented, would also protect an additional 29% of geophysical diversity types, ecoregional-focused protection would protect an additional 24%, and a combined scenario would protect an additional 42%. Future efforts need to specifically target low-elevation sites with productive soils for protection and manage for connectivity among geophysical diversity types. These efforts may be hampered by the sheer number of geophysical diversity facets that the world contains, which makes clear target setting and prioritization an important next step. © 2015 Society for Conservation Biology.

[Two- and three-dimensional power Doppler ultrasound in the follow-up of placenta accreta treated conservatively].

PubMed

Roulot, A; Barranger, E; Morel, O; Soyer, P; Héquet, D

2015-02-01

To determinate the potential of 2D and 3D-ultrasound in the follow-up of patients with placenta accreta treated conservatively. Seven patients with placenta accreta treated conservatively during June 2007 and September 2009 were included. The follow-up consisted in clinical examination and 2D/3D-ultrasound once a month. Criteria studied included clinical outcome, echogenicity at 2D-ultrasound, vascularisation at colour Doppler, Mean Grey at 3D-ultrasound and vascularisation, flow and perfusion index. Seven women with invasive placenta (3 placentas accreta and 2 percreta) were studied. The mean follow-up was 228 days [75-369]. Mean delay for complete elimination of residual placenta was 280 days [120-365]. The two main results were: presence of an increased anechogenicpart in residual placenta before complete resorption for all patients; a systematic and concomitant stop of genital haemorrhage and vascularisation at colour Doppler. High degrees of variability in parameters measured at 3D-ultrasound were observed between patients so that correlations with clinical outcome were found. Long and regular follow-up is essential after conservative management but the role of 3D-ultrasound compared to 2D-ultrasound was not demonstrated in this study. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Nitrous Oxide and Methane Fluxes in Responses to Conservation Management across Cropping Systems in Asia from a Data-Model Integration Perspective

NASA Astrophysics Data System (ADS)

Ren, W.; Huang, Y.; Tao, B.; Zhu, X.; Tian, H.

2017-12-01

The agriculture sector is estimated to be responsible for 12% of the total greenhouse gas emissions, particularly for 52% of CH4 and 84% of N2O. It has been predicted that the world population would reach 9.7 billion by 2050 and require a 60 percent increase in total agricultural production above the level of 2005-07, which would potentially further boost greenhouse gas emissions from agroecosystems. The growing concerns over food security and rapid rate of global warming necessitates the development of conservation management (or climate-smart soil management) that can ensure high crop yield and meanwhile markedly enhance soil sequestration and reduce GHG emissions. In this study, we synthesize multi-source datasets and apply an improved agroecosystem model to quantitatively investigate the dynamics of CH4 and N2O fluxes as influenced by conservation management practices in cropping systems of Asia (such as wheat, corn, and rice) for exploring the potential of those practices to mitigate and adapt to climate change. Our preliminary results suggest that the conservation tillage (e.g., reduced and no tillage) can largely suppress CH4 emissions from Asia's rice paddies, although they, to some extent, may stimulate NO2 emissions, comparing with the conventional tillage.

Evaluating the conservation potential of tributaries for native fishes in the Upper Colorado River Basin

USGS Publications Warehouse

Laub, Brian G.; Thiede, Gary P.; Macfarlane, William W.; Budy, Phaedra

2018-01-01

We explored the conservation potential of tributaries in the upper Colorado River basin by modeling native fish species richness as a function of river discharge, temperature, barrier‐free length, and distance to nearest free‐flowing main‐stem section. We investigated a historic period prior to large‐scale water development and a contemporary period. In the historic period, species richness was log‐linearly correlated to variables capturing flow magnitude, particularly mean annual discharge. In the contemporary period, the log‐linear relationship between discharge and species richness was still evident but weaker. Tributaries with lower average temperature and separated from free‐flowing main‐stem sections often had fewer native species compared to tributaries with similar discharge but with warmer temperature and directly connected to free‐flowing main stems. Thus, tributaries containing only a small proportion of main‐stem discharge, especially those at lower elevations with warmer temperatures and connected to free‐flowing main stems, can support a relatively high species richness. Tributaries can help maintain viable populations by providing ecological processes disrupted on large regulated rivers, such as natural flow and temperature regimes, and may present unique conservation opportunities. Efforts to improve fish passage, secure environmental flows, and restore habitat in these tributaries could greatly contribute to conservation of native fish richness throughout the watershed.

Habitat fragmentation effects on annual survival of the federally protected eastern indigo snake

USGS Publications Warehouse

Breininger, D.R.; Mazerolle, M.J.; Bolt, M.R.; Legare, M.L.; Drese, J.H.; Hines, J.E.

2012-01-01

The eastern indigo snake (Drymarchon couperi) is a federally listed species, most recently threatened by habitat loss and habitat degradation. In an effort to estimate snake survival, a total of 103 individuals (59 males, 44 females) were followed using radio-tracking from January 1998 to March 2004 in three landscape types that had increasing levels of habitat fragmentation: (1) conservation cores; (2) conservation areas along highways; (3) suburbs. Because of a large number of radio-tracking locations underground for which the state of snakes (i.e. alive or dead) could not be assessed, we employed a multistate approach to model snake apparent survival and encounter probability of live and dead snakes. We predicted that male snakes in suburbs would have the lowest annual survival. We found a transmitter implantation effect on snake encounter probability, as snakes implanted on a given occasion had a lower encounter probability on the next visit compared with snakes not implanted on the previous occasion. Our results indicated that adult eastern indigo snakes have relatively high survival in conservation core areas, but greatly reduced survival in conservation areas along highways and in suburbs. These findings indicate that habitat fragmentation is likely to be the critical factor for species' persistence.

Comparative genomics of 9 novel Paenibacillus larvae bacteriophages

PubMed Central

Stamereilers, Casey; LeBlanc, Lucy; Yost, Diane; Amy, Penny S.; Tsourkas, Philippos K.

2016-01-01

ABSTRACT American Foulbrood Disease, caused by the bacterium Paenibacillus larvae, is one of the most destructive diseases of the honeybee, Apis mellifera. Our group recently published the sequences of 9 new phages with the ability to infect and lyse P. larvae. Here, we characterize the genomes of these P. larvae phages, compare them to each other and to other sequenced P. larvae phages, and putatively identify protein function. The phage genomes are 38–45 kb in size and contain 68–86 genes, most of which appear to be unique to P. larvae phages. We classify P. larvae phages into 2 main clusters and one singleton based on nucleotide sequence identity. Three of the new phages show sequence similarity to other sequenced P. larvae phages, while the remaining 6 do not. We identified functions for roughly half of the P. larvae phage proteins, including structural, assembly, host lysis, DNA replication/metabolism, regulatory, and host-related functions. Structural and assembly proteins are highly conserved among our phages and are located at the start of the genome. DNA replication/metabolism, regulatory, and host-related proteins are located in the middle and end of the genome, and are not conserved, with many of these genes found in some of our phages but not others. All nine phages code for a conserved N-acetylmuramoyl-L-alanine amidase. Comparative analysis showed the phages use the “cohesive ends with 3′ overhang” DNA packaging strategy. This work is the first in-depth study of P. larvae phage genomics, and serves as a marker for future work in this area. PMID:27738559

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements.

PubMed

De Witte, Dieter; Van de Velde, Jan; Decap, Dries; Van Bel, Michiel; Audenaert, Pieter; Demeester, Piet; Dhoedt, Bart; Vandepoele, Klaas; Fostier, Jan

2015-12-01

The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species. Existing methods for comparative motif discovery usually rely on pregenerated multiple sequence alignments, which are difficult to obtain for more diverged species such as plants. As a consequence, misaligned regulatory elements often remain undetected. We present a novel algorithm that supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and screened for conservation using the branch length score. Additionally, a confidence score is established in a genome-wide fashion. In order to take advantage of a cloud computing infrastructure, the MapReduce programming model is adopted. The method is applied to four monocotyledon plant species and it is shown that high-scoring motifs are significantly enriched for open chromatin regions in Oryza sativa and for transcription factor binding sites inferred through protein-binding microarrays in O.sativa and Zea mays. Furthermore, the method is shown to recover experimentally profiled ga2ox1-like KN1 binding sites in Z.mays. BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be. Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press.

BLSSpeller: exhaustive comparative discovery of conserved cis-regulatory elements

PubMed Central

De Witte, Dieter; Van de Velde, Jan; Decap, Dries; Van Bel, Michiel; Audenaert, Pieter; Demeester, Piet; Dhoedt, Bart; Vandepoele, Klaas; Fostier, Jan

2015-01-01

Motivation: The accurate discovery and annotation of regulatory elements remains a challenging problem. The growing number of sequenced genomes creates new opportunities for comparative approaches to motif discovery. Putative binding sites are then considered to be functional if they are conserved in orthologous promoter sequences of multiple related species. Existing methods for comparative motif discovery usually rely on pregenerated multiple sequence alignments, which are difficult to obtain for more diverged species such as plants. As a consequence, misaligned regulatory elements often remain undetected. Results: We present a novel algorithm that supports both alignment-free and alignment-based motif discovery in the promoter sequences of related species. Putative motifs are exhaustively enumerated as words over the IUPAC alphabet and screened for conservation using the branch length score. Additionally, a confidence score is established in a genome-wide fashion. In order to take advantage of a cloud computing infrastructure, the MapReduce programming model is adopted. The method is applied to four monocotyledon plant species and it is shown that high-scoring motifs are significantly enriched for open chromatin regions in Oryza sativa and for transcription factor binding sites inferred through protein-binding microarrays in O.sativa and Zea mays. Furthermore, the method is shown to recover experimentally profiled ga2ox1-like KN1 binding sites in Z.mays. Availability and implementation: BLSSpeller was written in Java. Source code and manual are available at http://bioinformatics.intec.ugent.be/blsspeller Contact: Klaas.Vandepoele@psb.vib-ugent.be or jan.fostier@intec.ugent.be Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26254488

Sporulation in Bacteria: Beyond the Standard Model.

PubMed

Hutchison, Elizabeth A; Miller, David A; Angert, Esther R

2014-10-01

Endospore formation follows a complex, highly regulated developmental pathway that occurs in a broad range of Firmicutes. Although Bacillus subtilis has served as a powerful model system to study the morphological, biochemical, and genetic determinants of sporulation, fundamental aspects of the program remain mysterious for other genera. For example, it is entirely unknown how most lineages within the Firmicutes regulate entry into sporulation. Additionally, little is known about how the sporulation pathway has evolved novel spore forms and reproductive schemes. Here, we describe endospore and internal offspring development in diverse Firmicutes and outline progress in characterizing these programs. Moreover, comparative genomics studies are identifying highly conserved sporulation genes, and predictions of sporulation potential in new isolates and uncultured bacteria can be made from these data. One surprising outcome of these comparative studies is that core regulatory and some structural aspects of the program appear to be universally conserved. This suggests that a robust and sophisticated developmental framework was already in place in the last common ancestor of all extant Firmicutes that produce internal offspring or endospores. The study of sporulation in model systems beyond B. subtilis will continue to provide key information on the flexibility of the program and provide insights into how changes in this developmental course may confer advantages to cells in diverse environments.

Perspectives provided by leopard and other cat genomes: how diet determined the evolutionary history of carnivores, omnivores, and herbivores

PubMed Central

Kim, Soonok; Cho, Yun Sung; Bhak, Jong; O’Brian, Stephen J.; Yeo, Joo-Hong

2017-01-01

Recent advances in genome sequencing technologies have enabled humans to generate and investigate the genomes of wild species. This includes the big cat family, such as tigers, lions, and leopards. Adding the first high quality leopard genome, we have performed an in-depth comparative analysis to identify the genomic signatures in the evolution of felid to become the top predators on land. Our study focused on how the carnivore genomes, as compared to the omnivore or herbivore genomes, shared evolutionary adaptations in genes associated with nutrient metabolism, muscle strength, agility, and other traits responsible for hunting and meat digestion. We found genetic evidence that genomes represent what animals eat through modifying genes. Highly conserved genetically relevant regions were discovered in genomes at the family level. Also, the Felidae family genomes exhibited low levels of genetic diversity associated with decreased population sizes, presumably because of their strict diet, suggesting their vulnerability and critical conservation status. Our findings can be used for human health enhancement, since we share the same genes as cats with some variation. This is an example how wildlife genomes can be a critical resource for human evolution, providing key genetic marker information for disease treatment. PMID:28042784

Comparative analyses reveal high levels of conserved colinearity between the finger millet and rice genomes.

PubMed

Srinivasachary; Dida, Mathews M; Gale, Mike D; Devos, Katrien M

2007-08-01

Finger millet is an allotetraploid (2n = 4x = 36) grass that belongs to the Chloridoideae subfamily. A comparative analysis has been carried out to determine the relationship of the finger millet genome with that of rice. Six of the nine finger millet homoeologous groups corresponded to a single rice chromosome each. Each of the remaining three finger millet groups were orthologous to two rice chromosomes, and in all the three cases one rice chromosome was inserted into the centromeric region of a second rice chromosome to give the finger millet chromosomal configuration. All observed rearrangements were, among the grasses, unique to finger millet and, possibly, the Chloridoideae subfamily. Gene orders between rice and finger millet were highly conserved, with rearrangements being limited largely to single marker transpositions and small putative inversions encompassing at most three markers. Only some 10% of markers mapped to non-syntenic positions in rice and finger millet and the majority of these were located in the distal 14% of chromosome arms, supporting a possible correlation between recombination and sequence evolution as has previously been observed in wheat. A comparison of the organization of finger millet, Panicoideae and Pooideae genomes relative to rice allowed us to infer putative ancestral chromosome configurations in the grasses.

Increased diversification rates follow shifts to bisexuality in liverworts.

PubMed

Laenen, Benjamin; Machac, Antonin; Gradstein, S Robbert; Shaw, Blanka; Patiño, Jairo; Désamoré, Aurélie; Goffinet, Bernard; Cox, Cymon J; Shaw, A Jonathan; Vanderpoorten, Alain

2016-05-01

Shifts in sexual systems are one of the key drivers of species diversification. In contrast to angiosperms, unisexuality prevails in bryophytes. Here, we test the hypotheses that bisexuality evolved from an ancestral unisexual condition and is a key innovation in liverworts. We investigate whether shifts in sexual systems influence diversification using hidden state speciation and extinction analysis (HiSSE). This new method compares the effects of the variable of interest to the best-fitting latent variable, yielding robust and conservative tests. We find that the transitions in sexual systems are significantly biased toward unisexuality, even though bisexuality is coupled with increased diversification. Sexual systems are strongly conserved deep within the liverwort tree but become much more labile toward the present. Bisexuality appears to be a key innovation in liverworts. Its effects on diversification are presumably mediated by the interplay of high fertilization rates, massive spore production and long-distance dispersal, which may separately or together have facilitated liverwort speciation, suppressed their extinction, or both. Importantly, shifts in liverwort sexual systems have the opposite effect when compared to angiosperms, leading to contrasting diversification patterns between the two groups. The high prevalence of unisexuality among liverworts suggests, however, a strong selection for sexual dimorphism. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

Complete Genome Sequence and Comparative Analysis of the Fish Pathogen Lactococcus garvieae

PubMed Central

Oshima, Kenshiro; Yoshizaki, Mariko; Kawanishi, Michiko; Nakaya, Kohei; Suzuki, Takehito; Miyauchi, Eiji; Ishii, Yasuo; Tanabe, Soichi; Murakami, Masaru; Hattori, Masahira

2011-01-01

Lactococcus garvieae causes fatal haemorrhagic septicaemia in fish such as yellowtail. The comparative analysis of genomes of a virulent strain Lg2 and a non-virulent strain ATCC 49156 of L. garvieae revealed that the two strains shared a high degree of sequence identity, but Lg2 had a 16.5-kb capsule gene cluster that is absent in ATCC 49156. The capsule gene cluster was composed of 15 genes, of which eight genes are highly conserved with those in exopolysaccharide biosynthesis gene cluster often found in Lactococcus lactis strains. Sequence analysis of the capsule gene cluster in the less virulent strain L. garvieae Lg2-S, Lg2-derived strain, showed that two conserved genes were disrupted by a single base pair deletion, respectively. These results strongly suggest that the capsule is crucial for virulence of Lg2. The capsule gene cluster of Lg2 may be a genomic island from several features such as the presence of insertion sequences flanked on both ends, different GC content from the chromosomal average, integration into the locus syntenic to other lactococcal genome sequences, and distribution in human gut microbiomes. The analysis also predicted other potential virulence factors such as haemolysin. The present study provides new insights into understanding of the virulence mechanisms of L. garvieae in fish. PMID:21829716

Neuronal patterning of the tubular collar cord is highly conserved among enteropneusts but dissimilar to the chordate neural tube.

PubMed

Kaul-Strehlow, Sabrina; Urata, Makoto; Praher, Daniela; Wanninger, Andreas

2017-08-01

A tubular nervous system is present in the deuterostome groups Chordata (cephalochordates, tunicates, vertebrates) and in the non-chordate Enteropneusta. However, the worm-shaped enteropneusts possess a less complex nervous system featuring only a short hollow neural tube, whereby homology to its chordate counterpart remains elusive. Since the majority of data on enteropneusts stem from the harrimaniid Saccoglossus kowalevskii, putative interspecific variations remain undetected resulting in an unreliable ground pattern that impedes homology assessments. In order to complement the missing data from another enteropneust family, we investigated expression of key neuronal patterning genes in the ptychoderid Balanoglossus misakiensis. The collar cord of B. misakiensis shows anterior Six3/6 and posterior Otx + Engrailed expression, in a region corresponding to the chordate brain. Neuronal Nk2.1/Nk2.2 expression is absent. Interestingly, we found median Dlx and lateral Pax6 expression domains, i.e., a condition that is reversed compared to chordates. Comparative analyses reveal that adult nervous system patterning is highly conserved among the enteropneust families Harrimaniidae, Spengelidae and Ptychoderidae. BmiDlx and BmiPax6 have no corresponding expression domains in the chordate brain, which may be indicative of independent acquisition of a tubular nervous system in Enteropneusta and Chordata.

Rapid assessment of risks to a mobile marine mammal in an ecosystem-scale marine protected area.

PubMed

Grech, A; Marsh, H

2008-06-01

Ecosystem-scale networks of marine protected areas (MPAs) are important conservation tools, but their effectiveness is difficult to quantify in a time frame appropriate to species conservation because of uncertainties in the data available. The dugong (Dugong dugon) is a mobile marine species that occurs in shallow inshore waters of an ecosystem-scale network of MPAs (the Great Barrier Reef World Heritage Area [GBRWHA]). We developed a rapid approach to assess risk to dugongs in the region and evaluate options to ameliorate that risk. We used expert opinion and a Delphi technique to identify and rank 5 human factors with the potential to adversely affect dugongs and their sea grass habitats: netting, indigenous hunting, trawling, vessel traffic, and poor-quality terrestrial runoff. We then quantified and compared the distribution of these factors with a spatially explicit model of dugong distribution. We estimated that approximately 96% of habitat of high conservation value for dugongs in the GBRWHA is at low risk from human activities. Using a sensitivity analysis, we found that to decrease risk, commercial netting or indigenous hunting had to be reduced in remote areas and the effects of vessel traffic, terrestrial runoff, and commercial netting had to be reduced in urban areas. This approach enabled us to compare and rank risks so as to identify the most severe risks and locate specific sites that require further management attention.

Rapid comparison of protein binding site surfaces with Property Encoded Shape Distributions (PESD)

PubMed Central

Das, Sourav; Kokardekar, Arshad

2009-01-01

Patterns in shape and property distributions on the surface of binding sites are often conserved across functional proteins without significant conservation of the underlying amino-acid residues. To explore similarities of these sites from the viewpoint of a ligand, a sequence and fold-independent method was created to rapidly and accurately compare binding sites of proteins represented by property-mapped triangulated Gauss-Connolly surfaces. Within this paradigm, signatures for each binding site surface are produced by calculating their property-encoded shape distributions (PESD), a measure of the probability that a particular property will be at a specific distance to another on the molecular surface. Similarity between the signatures can then be treated as a measure of similarity between binding sites. As postulated, the PESD method rapidly detected high levels of similarity in binding site surface characteristics even in cases where there was very low similarity at the sequence level. In a screening experiment involving each member of the PDBBind 2005 dataset as a query against the rest of the set, PESD was able to retrieve a binding site with identical E.C. (Enzyme Commission) numbers as the top match in 79.5% of cases. The ability of the method in detecting similarity in binding sites with low sequence conservations were compared with state-of-the-art binding site comparison methods. PMID:19919089

Comparative genomic analysis of isoproturon-mineralizing sphingomonads reveals the isoproturon catabolic mechanism.

PubMed

Yan, Xin; Gu, Tao; Yi, Zhongquan; Huang, Junwei; Liu, Xiaowei; Zhang, Ji; Xu, Xihui; Xin, Zhihong; Hong, Qing; He, Jian; Spain, Jim C; Li, Shunpeng; Jiang, Jiandong

2016-12-01

The worldwide use of the phenylurea herbicide, isoproturon (IPU), has resulted in considerable concern about its environmental fate. Although many microbial metabolites of IPU are known and IPU-mineralizing bacteria have been isolated, the molecular mechanism of IPU catabolism has not been elucidated yet. In this study, complete genes that encode the conserved IPU catabolic pathway were revealed, based on comparative analysis of the genomes of three IPU-mineralizing sphingomonads and subsequent experimental validation. The complete genes included a novel hydrolase gene ddhA, which is responsible for the cleavage of the urea side chain of the IPU demethylated products; a distinct aniline dioxygenase gene cluster adoQTA1A2BR, which has a broad substrate range; and an inducible catechol meta-cleavage pathway gene cluster adoXEGKLIJC. Furthermore, the initial mono-N-demethylation genes pdmAB were further confirmed to be involved in the successive N-demethylation of the IPU mono-N-demethylated product. These IPU-catabolic genes were organized into four transcription units and distributed on three plasmids. They were flanked by multiple mobile genetic elements and highly conserved among IPU-mineralizing sphingomonads. The elucidation of the molecular mechanism of IPU catabolism will enhance our understanding of the microbial mineralization of IPU and provide insights into the evolutionary scenario of the conserved IPU-catabolic pathway. © 2016 The Authors. Environmental Microbiology published by Society for Applied Microbiology and John Wiley & Sons Ltd.

Comparative Analysis of Wolbachia Genomes Reveals Streamlining and Divergence of Minimalist Two-Component Systems

PubMed Central

Christensen, Steen; Serbus, Laura Renee

2015-01-01

Two-component regulatory systems are commonly used by bacteria to coordinate intracellular responses with environmental cues. These systems are composed of functional protein pairs consisting of a sensor histidine kinase and cognate response regulator. In contrast to the well-studied Caulobacter crescentus system, which carries dozens of these pairs, the streamlined bacterial endosymbiont Wolbachia pipientis encodes only two pairs: CckA/CtrA and PleC/PleD. Here, we used bioinformatic tools to compare characterized two-component system relays from C. crescentus, the related Anaplasmataceae species Anaplasma phagocytophilum and Ehrlichia chaffeensis, and 12 sequenced Wolbachia strains. We found the core protein pairs and a subset of interacting partners to be highly conserved within Wolbachia and these other Anaplasmataceae. Genes involved in two-component signaling were positioned differently within the various Wolbachia genomes, whereas the local context of each gene was conserved. Unlike Anaplasma and Ehrlichia, Wolbachia two-component genes were more consistently found clustered with metabolic genes. The domain architecture and key functional residues standard for two-component system proteins were well-conserved in Wolbachia, although residues that specify cognate pairing diverged substantially from other Anaplasmataceae. These findings indicate that Wolbachia two-component signaling pairs share considerable functional overlap with other α-proteobacterial systems, whereas their divergence suggests the potential for regulatory differences and cross-talk. PMID:25809075

Comparative Bioinformatic Analysis of Active Site Structures in Evolutionarily Remote Homologues of α,β-Hydrolase Superfamily Enzymes.

PubMed

Suplatov, D A; Arzhanik, V K; Svedas, V K

2011-01-01

Comparative bioinformatic analysis is the cornerstone of the study of enzymes' structure-function relationship. However, numerous enzymes that derive from a common ancestor and have undergone substantial functional alterations during natural selection appear not to have a sequence similarity acceptable for a statistically reliable comparative analysis. At the same time, their active site structures, in general, can be conserved, while other parts may largely differ. Therefore, it sounds both plausible and appealing to implement a comparative analysis of the most functionally important structural elements - the active site structures; that is, the amino acid residues involved in substrate binding and the catalytic mechanism. A computer algorithm has been developed to create a library of enzyme active site structures based on the use of the PDB database, together with programs of structural analysis and identification of functionally important amino acid residues and cavities in the enzyme structure. The proposed methodology has been used to compare some α,β-hydrolase superfamily enzymes. The insight has revealed a high structural similarity of catalytic site areas, including the conservative organization of a catalytic triad and oxyanion hole residues, despite the wide functional diversity among the remote homologues compared. The methodology can be used to compare the structural organization of the catalytic and substrate binding sites of various classes of enzymes, as well as study enzymes' evolution and to create of a databank of enzyme active site structures.

Developing High Quality Decision-Making Discussions about Biological Conservation in a Normal Classroom Setting

ERIC Educational Resources Information Center

Grace, Marcus

2009-01-01

The conservation of biodiversity is an important socio-scientific issue that is often regarded as a precondition to sustainable development. The foundation for citizens' understanding of conservation issues can be laid down in formal school education. This research focuses on decision-making discussions about biological conservation issues among…

Evaluating the importance of human-modified lands for neotropical bird conservation

USGS Publications Warehouse

Petit, L.J.; Petit, D.R.

2003-01-01

Development of effective conservation plans for terrestrial animals will require some assessment of which human-modified and natural habitats can support populations of priority species. We examined bird communities associated with 11 natural and human-modified habitats in Panama and assessed the importance of those habitats for species of different vulnerability to disturbance. We calculated habitat importance scores using both relative habitat preferences and vulnerability scores for all species present. Species of moderate and high vulnerability were primarily those categorized as forest specialists or forest generalists. As expected, even species-rich nonforest habitats provided little conservation value for the most vulnerable species. However, shaded coffee plantations and gallery forest corridors were modified habitats with relatively high conservation value. Sugar cane fields and Caribbean pine plantations offered virtually no conservation value for birds. Our method of assessing the conservation importance of different habitats is useful because it considers the types of species present and the potential role of the habitat in the conservation of those species (i.e., habitat preference). This method of habitat evaluation could be tailored to other conservation contexts with any measure of species vulnerability desired.

High-order central ENO finite-volume scheme for hyperbolic conservation laws on three-dimensional cubed-sphere grids

NASA Astrophysics Data System (ADS)

Ivan, L.; De Sterck, H.; Susanto, A.; Groth, C. P. T.

2015-02-01

A fourth-order accurate finite-volume scheme for hyperbolic conservation laws on three-dimensional (3D) cubed-sphere grids is described. The approach is based on a central essentially non-oscillatory (CENO) finite-volume method that was recently introduced for two-dimensional compressible flows and is extended to 3D geometries with structured hexahedral grids. Cubed-sphere grids feature hexahedral cells with nonplanar cell surfaces, which are handled with high-order accuracy using trilinear geometry representations in the proposed approach. Varying stencil sizes and slope discontinuities in grid lines occur at the boundaries and corners of the six sectors of the cubed-sphere grid where the grid topology is unstructured, and these difficulties are handled naturally with high-order accuracy by the multidimensional least-squares based 3D CENO reconstruction with overdetermined stencils. A rotation-based mechanism is introduced to automatically select appropriate smaller stencils at degenerate block boundaries, where fewer ghost cells are available and the grid topology changes, requiring stencils to be modified. Combining these building blocks results in a finite-volume discretization for conservation laws on 3D cubed-sphere grids that is uniformly high-order accurate in all three grid directions. While solution-adaptivity is natural in the multi-block setting of our code, high-order accurate adaptive refinement on cubed-sphere grids is not pursued in this paper. The 3D CENO scheme is an accurate and robust solution method for hyperbolic conservation laws on general hexahedral grids that is attractive because it is inherently multidimensional by employing a K-exact overdetermined reconstruction scheme, and it avoids the complexity of considering multiple non-central stencil configurations that characterizes traditional ENO schemes. Extensive numerical tests demonstrate fourth-order convergence for stationary and time-dependent Euler and magnetohydrodynamic flows on cubed-sphere grids, and robustness against spurious oscillations at 3D shocks. Performance tests illustrate efficiency gains that can be potentially achieved using fourth-order schemes as compared to second-order methods for the same error level. Applications on extended cubed-sphere grids incorporating a seventh root block that discretizes the interior of the inner sphere demonstrate the versatility of the spatial discretization method.

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

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.

Conservation of transcription factor binding events predicts gene expression across species

PubMed Central

Hemberg, Martin; Kreiman, Gabriel

2011-01-01

Recent technological advances have made it possible to determine the genome-wide binding sites of transcription factors (TFs). Comparisons across species have suggested a relatively low degree of evolutionary conservation of experimentally defined TF binding events (TFBEs). Using binding data for six different TFs in hepatocytes and embryonic stem cells from human and mouse, we demonstrate that evolutionary conservation of TFBEs within orthologous proximal promoters is closely linked to function, defined as expression of the target genes. We show that (i) there is a significantly higher degree of conservation of TFBEs when the target gene is expressed in both species; (ii) there is increased conservation of binding events for groups of TFs compared to individual TFs; and (iii) conserved TFBEs have a greater impact on the expression of their target genes than non-conserved ones. These results link conservation of structural elements (TFBEs) to conservation of function (gene expression) and suggest a higher degree of functional conservation than implied by previous studies. PMID:21622661

Accounting for results: how conservation organizations report performance information.

PubMed

Rissman, Adena R; Smail, Robert

2015-04-01

Environmental program performance information is in high demand, but little research suggests why conservation organizations differ in reporting performance information. We compared performance measurement and reporting by four private-land conservation organizations: Partners for Fish and Wildlife in the US Fish and Wildlife Service (national government), Forest Stewardship Council-US (national nonprofit organization), Land and Water Conservation Departments (local government), and land trusts (local nonprofit organization). We asked: (1) How did the pattern of performance reporting relationships vary across organizations? (2) Was political conflict among organizations' principals associated with greater performance information? and (3) Did performance information provide evidence of program effectiveness? Based on our typology of performance information, we found that most organizations reported output measures such as land area or number of contracts, some reported outcome indicators such as adherence to performance standards, but few modeled or measured environmental effects. Local government Land and Water Conservation Departments reported the most types of performance information, while local land trusts reported the fewest. The case studies suggest that governance networks influence the pattern and type of performance reporting, that goal conflict among principles is associated with greater performance information, and that performance information provides unreliable causal evidence of program effectiveness. Challenging simple prescriptions to generate more data as evidence, this analysis suggests (1) complex institutional and political contexts for environmental program performance and (2) the need to supplement performance measures with in-depth evaluations that can provide causal inferences about program effectiveness.

The South African Experience of Conservation and Social Forestry Outreach Nurseries

NASA Astrophysics Data System (ADS)

Botha, Jenny; Witkowski, Ed T. F.; Cock, Jacklyn

2006-11-01

Outreach nurseries are favored conservation and social forestry tools globally, but, as with many integrated conservation and development programs (ICDPs), they do not always produce anticipated results. A synopsis of the experience of South African practitioners is provided in this study of 65 outreach nurseries. South African outreach nurseries frequently include financial objectives, creating additional challenges in simultaneously attaining conservation and socioeconomic goals. Progress was hindered by biophysical problems (e.g., lack of water, poor soils, etc.) as well as the harsh socioeconomic conditions facing most communities in which nurseries had been established. Attaining financial viability was challenging. Business management skills were often restricted, and few viability studies included adequate market research. Costs to community participants were usually high, and benefits were limited. Conservation objectives were frequently lost in the struggle to attain financial viability. The management of social processes also proved challenging. Although small scale and relatively straightforward compared with many ICDPs, nurseries usually require substantial institutional support, including a range of technical, business, and development services. Project time frames need to be reconsidered, as practitioners estimate that it takes 5-10 years for nurseries to start meeting objectives, and donors and implementing agencies often operate on 2-3-year project cycles. Detailed viability studies are essential, incorporating a social probe and an assessment of potential impacts of projects on community participants. Progress needs to be continuously evaluated to enable institutions and community participants to adapt to changing conditions as well as ensure that the spectrum of objectives are being achieved.

The South African experience of conservation and social forestry outreach nurseries.

PubMed

Botha, Jenny; Witkowski, Ed T F; Cock, Jacklyn

2006-11-01

Outreach nurseries are favored conservation and social forestry tools globally, but, as with many integrated conservation and development programs (ICDPs), they do not always produce anticipated results. A synopsis of the experience of South African practitioners is provided in this study of 65 outreach nurseries. South African outreach nurseries frequently include financial objectives, creating additional challenges in simultaneously attaining conservation and socioeconomic goals. Progress was hindered by biophysical problems (e.g., lack of water, poor soils, etc.) as well as the harsh socioeconomic conditions facing most communities in which nurseries had been established. Attaining financial viability was challenging. Business management skills were often restricted, and few viability studies included adequate market research. Costs to community participants were usually high, and benefits were limited. Conservation objectives were frequently lost in the struggle to attain financial viability. The management of social processes also proved challenging. Although small scale and relatively straightforward compared with many ICDPs, nurseries usually require substantial institutional support, including a range of technical, business, and development services. Project time frames need to be reconsidered, as practitioners estimate that it takes 5-10 years for nurseries to start meeting objectives, and donors and implementing agencies often operate on 2-3-year project cycles. Detailed viability studies are essential, incorporating a social probe and an assessment of potential impacts of projects on community participants. Progress needs to be continuously evaluated to enable institutions and community participants to adapt to changing conditions as well as ensure that the spectrum of objectives are being achieved.

Accounting for Results: How Conservation Organizations Report Performance Information

NASA Astrophysics Data System (ADS)

Rissman, Adena R.; Smail, Robert

2015-04-01

Environmental program performance information is in high demand, but little research suggests why conservation organizations differ in reporting performance information. We compared performance measurement and reporting by four private-land conservation organizations: Partners for Fish and Wildlife in the US Fish and Wildlife Service (national government), Forest Stewardship Council—US (national nonprofit organization), Land and Water Conservation Departments (local government), and land trusts (local nonprofit organization). We asked: (1) How did the pattern of performance reporting relationships vary across organizations? (2) Was political conflict among organizations' principals associated with greater performance information? and (3) Did performance information provide evidence of program effectiveness? Based on our typology of performance information, we found that most organizations reported output measures such as land area or number of contracts, some reported outcome indicators such as adherence to performance standards, but few modeled or measured environmental effects. Local government Land and Water Conservation Departments reported the most types of performance information, while local land trusts reported the fewest. The case studies suggest that governance networks influence the pattern and type of performance reporting, that goal conflict among principles is associated with greater performance information, and that performance information provides unreliable causal evidence of program effectiveness. Challenging simple prescriptions to generate more data as evidence, this analysis suggests (1) complex institutional and political contexts for environmental program performance and (2) the need to supplement performance measures with in-depth evaluations that can provide causal inferences about program effectiveness.

Efficiency of incentives to jointly increase carbon sequestration and species conservation on a landscape

Treesearch

Erik Nelson; Stephen Polasky; David J. Lewis; Andrew J. Plantinga; Eric Lonsdorf; Denis White; David Bael; Joshua Lawler

2008-01-01

We develop an integrated model to predict private land-use decisions in response to policy incentives designed to increase the provision of carbon sequestration and species conservation across heterogeneous landscapes. Using data from the Willamette Basin, Oregon, we compare the provision of carbon sequestration and species conservation under five simple policies that...

A comparative study of the nonuniqueness problem of the potential equation

NASA Technical Reports Server (NTRS)

Salas, M. D.; Jameson, A.; Melnik, R. E.

1985-01-01

The nonuniqueness problem occurring at transonic speeds with the conservative potential equation is investigated numerically. The study indicates that the problem is not an inviscid phenomenon, but results from approximate treatment of shock waves inherent in the conservative potential model. A new bound on the limit of validity of the conservative potential model is proposed.

Energy conservation and air transportation

NASA Technical Reports Server (NTRS)

1973-01-01

Air transportation demand and passenger energy demand are discussed, in relation to energy conservation. Alternatives to air travel are reviewed, along with airline advertising and ticket pricing. Cargo energy demand and airline systems efficiency are also examined, as well as fuel conservation techniques. Maximum efficiency of passenger aircraft, from B-747 to V/STOL to British Concorde, is compared.

Extension of landscape-based population viability models to ecoregional scales for conservation planning

Treesearch

Thomas W. Bonnot; Frank R. III Thompson; Joshua Millspaugh

2011-01-01

Landscape-based population models are potentially valuable tools in facilitating conservation planning and actions at large scales. However, such models have rarely been applied at ecoregional scales. We extended landscape-based population models to ecoregional scales for three species of concern in the Central Hardwoods Bird Conservation Region and compared model...

A Historical Analysis of Special Education Services in Conservative Christian Schools Since 1950

ERIC Educational Resources Information Center

Craig, Kristi-Lynn

2010-01-01

This study examines the historical progression of the availability of special education in Conservative Christian Schools in the United States since 1950. Due to the limited nature of research in this field, a historical analysis was used to better understand how the development of special education in Conservative Christian Schools compares to…

Comparison of statistical and theoretical habitat models for conservation planning: the benefit of ensemble prediction

Treesearch

D. Todd Jones-Farrand; Todd M. Fearer; Wayne E. Thogmartin; Frank R. Thompson; Mark D. Nelson; John M. Tirpak

2011-01-01

Selection of a modeling approach is an important step in the conservation planning process, but little guidance is available. We compared two statistical and three theoretical habitat modeling approaches representing those currently being used for avian conservation planning at landscape and regional scales: hierarchical spatial count (HSC), classification and...

Ground-water flow and ground- and surface-water interaction at McBaine Bottoms, Columbia, Missouri--2000-02

USGS Publications Warehouse

Smith, Brenda J.

2003-01-01

McBaine Bottoms southwest of Columbia, Missouri, is the site of 4,269 acres of the Eagle Bluffs Conservation Area operated by the Missouri Department of Conservation, about 130 acres of the city of Columbia wastewater-treat-ment wetlands, and the city of Columbia munici-pal-supply well field. The city of Columbia wastewater-treatment wetlands supply treated effluent to the Eagle Bluffs Conservation Area. The presence of a sustained ground-water high underlying the Eagle Bluffs Conservation Area has indicated that ground-water flow is toward the municipal well field that supplies drinking water to the city of Columbia. The U.S. Geological Survey, in cooperation with the Missouri Department of Conservation and the city of Columbia, measured the ground-water levels in about 88 monitoring wells and the surface-water elevation at 4 sites monthly during a 27-month period to determine the ground-water flow and the ground- and surface-water interaction at McBaine Bottoms. Lateral ground-water flow was dominated by the presence of a ground-water high that was beneath the Eagle Bluffs Conservation Area and the presence of a cone of depression in the northern part of the study area. The ground-water high was present during all months of the study. Ground-water flow was radially away from the apex of the ground-water high; west and south of the high, flow was toward the Missouri River, east of the high, flow was toward Perche Creek, and north of the high, flow was toward the north toward the city of Columbia well field. The cone of depression was centered around the city of Columbia well field. Another permanent feature on the water-level maps was a ground-water high beneath treatment wetland unit 1. Although the ground-water high beneath the Eagle Bluffs Conservation Area was present throughout the study period, the configuration of the high changed depending on hydrologic conditions. Generally in the spring, the height of the ground-water high began to decrease and hydraulic gradients around the high became more shallow than in the winter months. In early summer, the high was the least pronounced. During mid-sum-mer, the high became more pronounced, and it continued to become higher, increasing until it reached its maximum height in late fall or early winter. Fluctuations in the ground-water high were partially produced by the cycle of flooding of the Eagle Bluffs Conservation Area wetland pools in the fall and subsequent drainage so crops could be planted in many of the wetland pools. The cone of depression in the northern part of the study area generally extended from the base of the ground-water high in the northern part of the Eagle Bluffs Conservation Area throughout the rest of the study area. The depth of the cone primarily was affected by the altitude of the Missouri River and the quantity of water being pumped from the alluvial aquifer by the city of Columbia well field. Ground-water flow in the alluvial aquifer in McBaine Bottoms in the late 1960?s before the development of the city of Columbia well field and the Eagle Bluffs Conservation Area was from northwest to southeast approximately parallel to the Missouri River. The ground-water high beneath the Eagle Bluffs Conservation Area and the cone of depression around the city of Columbia well field were not present in water-level maps for 1968 and 1978. The Missouri River can be a source of recharge to the alluvial aquifer. Generally the altitude of the river in the northern part of the study area was higher than the water table in the aquifer. Ground-water flow in this area was from the river into the alluvial aquifer. In the southern part of the study area adjacent to the Eagle Bluffs Conservation Area, the Missouri River was lower than the water table in the alluvial aquifer, indicating that the river was receiving water from the alluvial aquifer beneath the Eagle Bluffs Conservation Area.

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.

Comparative genomic analysis of the false killer whale (Pseudorca crassidens) LMBR1 locus.

PubMed

Kim, Dae-Won; Choi, Sang-Haeng; Kim, Ryong Nam; Kim, Sun-Hong; Paik, Sang-Gi; Nam, Seong-Hyeuk; Kim, Dong-Wook; Kim, Aeri; Kang, Aram; Park, Hong-Seog

2010-09-01

The sequencing and comparative genomic analysis of LMBR1 loci in mammals or other species, including human, would be very important in understanding evolutionary genetic changes underlying the evolution of limb development. In this regard, comparative genomic annotation of the false killer whale LMBR1 locus could shed new light on the evolution of limb development. We sequenced two false killer whale BAC clones, corresponding to 156 kb and 144 kb, respectively, harboring the tightly linked RNF32, LMBR1, and NOM1 genes. Our annotation of the false killer whale LMBR1 gene showed that it consists of 17 exons (1473 bp), in contrast to 18 exons (1596 bp) in human, and it displays 93.1% and 95.6% nucleotide and amino acid sequence similarity, respectively, compared with the human gene. In particular, we discovered that exon 10, deleted in the false killer whale LMBR1 gene, is present only in primates, and this fact strongly implies that exon 10 might be crucial in determining primate-specific limb development. ZRS and TFBS sequences have been well conserved across 11 species, suggesting that these regions could be involved in an important function of limb development and limb patterning. The neighboring gene RNF32 showed several lineage-conserved exons, such as exons 2 through 9 conserved in eutherian mammals, exons 3 through 9 conserved in mammals, and exons 5 through 9 conserved in vertebrates. The other neighboring gene, NOM1, had undergone a substitution (ATG→GTA) at the start codon, giving rise to a 36 bp shorter N-terminal sequence compared with the human sequence. Our comparative analysis of the false killer whale LMBR1 genomic locus provides important clues regarding the genetic regions that may play crucial roles in limb development and patterning.

High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species

PubMed Central

2013-01-01

Background Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient “off-the-shelf” markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. Results We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. Conclusions When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense of microsatellite isolation for a wide range of genetic studies, including avian parentage and population analyses, but will also now enable comparisons of genetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available. PMID:23497230

Life history, larval dispersal, and connectivity in coral reef fish among the Scattered Islands of the Mozambique Channel

NASA Astrophysics Data System (ADS)

O'Donnell, James L.; Beldade, Ricardo; Mills, Suzanne C.; Williams, Hannah E.; Bernardi, Giacomo

2017-03-01

The Western Indian Ocean harbors one of the world's most diverse marine biota yet is threatened by exploitation with few conservation measures in place. Primary candidates for conservation in the region are the Scattered Islands (Îles Éparses), a group of relatively pristine and uninhabited islands in the Mozambique Channel. However, while optimal conservation strategies depend on the degree of population connectivity among spatially isolated habitats, very few studies have been conducted in the area. Here, we use highly variable microsatellite markers from two damselfishes ( Amphiprion akallopisos and Dascyllus trimaculatus) with differing life history traits [pelagic larval duration (PLD), adult habitat] to compare genetic structure and connectivity among these islands using classic population structure indices as well as Bayesian clustering methods. All classical fixation indexes F ST, R ST, G'ST, and Jost's D show stronger genetic differentiation among islands for A. akallopisos compared to D. trimaculatus, consistent with the former species' shorter PLD and stronger adult site attachment, which may restrict larval dispersal potential. In agreement with these results, the Bayesian analysis revealed clear genetic differentiation among the islands in A. akallopisos, separating the southern group (Bassas da India and Europa) from the center (Juan de Nova) and northern (Îles Glorieuses) islands, but not for D. trimaculatus. Local oceanographic patterns such as eddies that occur along the Mozambique Channel appear to parallel the results reported for A. akallopisos, but such features seem to have little effect on the genetic differentiation of D. trimaculatus. The contrasting patterns of genetic differentiation between species within the same family highlight the importance of accounting for diverse life history traits when assessing community-wide connectivity, an increasingly common consideration in conservation planning.

Conserved extended haplotypes discriminate HLA-DR3-homozygous Basque patients with type 1 diabetes mellitus and celiac disease.

PubMed

Bilbao, J R; Calvo, B; Aransay, A M; Martin-Pagola, A; Perez de Nanclares, G; Aly, T A; Rica, I; Vitoria, J C; Gaztambide, S; Noble, J; Fain, P R; Awdeh, Z L; Alper, C A; Castaño, L

2006-10-01

The major susceptibility locus for type 1 diabetes mellitus (T1D) maps to the human lymphocyte antigen (HLA) class II region in the major histocompatibility complex on chromosome 6p21. In southern European populations, like the Basques, the greatest risk to T1D is associated with DR3 homo- and heterozygosity and is comparable to that of DR3/DR4, the highest risk genotype in northern European populations. Celiac disease (CD) is another DR3-associated autoimmune disorder showing certain overlap with T1D that has been explained by the involvement of common genetic determinants, a situation more frequent in DR3-rich populations, like the Basques. As both T1D- and CD-associated HLA alleles are part of conserved extended haplotypes (CEH), we compared DR3-homozygous T1D and CD patients to determine whether CEHs were equally distributed between both disorders or there was a differential contribution of different haplotypes. We observed a very pronounced distribution bias (P<10(-5)) of the two major DR3 CEHs, with DR3-B18 predominating in T1D and DR3-B8 in CD. Additionally, high-density single nucleotide polymorphism (SNP) analysis of the complete CEH [A*30-B*18-MICA*4-F1C30-DRB1*0301-DQB1*0201-DPB1*0202] revealed extraordinary conservation throughout the 4.9 Mbp analyzed supporting the existence of additional diabetogenic variants (other than HLA-DRB1*0301-DQB1*0201), conserved within the DR3-B18 CEH (but not in other DR3 haplotypes) that could explain its enhanced diabetogenicity.

Outcome after conservative management or intervention for unruptured brain arteriovenous malformations.

PubMed

Al-Shahi Salman, Rustam; White, Philip M; Counsell, Carl E; du Plessis, Johann; van Beijnum, Janneke; Josephson, Colin B; Wilkinson, Tim; Wedderburn, Catherine J; Chandy, Zoe; St George, E Jerome; Sellar, Robin J; Warlow, Charles P

Whether conservative management is superior to interventional treatment for unruptured brain arteriovenous malformations (bAVMs) is uncertain because of the shortage of long-term comparative data. To compare the long-term outcomes of conservative management vs intervention for unruptured bAVM. Population-based inception cohort study of 204 residents of Scotland aged 16 years or older who were first diagnosed as having an unruptured bAVM during 1999-2003 or 2006-2010 and followed up prospectively for 12 years. Conservative management (no intervention) vs intervention (any endovascular embolization, neurosurgical excision, or stereotactic radiosurgery alone or in combination). Cox regression analyses, with multivariable adjustment for prognostic factors and baseline imbalances if hazards were proportional, to compare rates of the primary outcome (death or sustained morbidity of any cause by Oxford Handicap Scale [OHS] score ≥2 for ≥2 successive years [0 = no symptoms and 6 = death]) and the secondary outcome (nonfatal symptomatic stroke or death due to bAVM, associated arterial aneurysm, or intervention). Of 204 patients, 103 underwent intervention. Those who underwent intervention were younger, more likely to have presented with seizure, and less likely to have large bAVMs than patients managed conservatively. During a median follow-up of 6.9 years (94% completeness), the rate of progression to the primary outcome was lower with conservative management during the first 4 years of follow-up (36 vs 39 events; 9.5 vs 9.8 per 100 person-years; adjusted hazard ratio, 0.59; 95% CI, 0.35-0.99), but rates were similar thereafter. The rate of the secondary outcome was lower with conservative management during 12 years of follow-up (14 vs 38 events; 1.6 vs 3.3 per 100 person-years; adjusted hazard ratio, 0.37; 95% CI, 0.19-0.72). Among patients aged 16 years or older diagnosed as having unruptured bAVM, use of conservative management compared with intervention was associated with better clinical outcomes for up to 12 years. Longer follow-up is required to understand whether this association persists.

High- Versus Low-Gradient Severe Aortic Stenosis: Demographics, Clinical Outcomes, and Effects of the Initial Aortic Valve Replacement Strategy on Long-Term Prognosis.

PubMed

Taniguchi, Tomohiko; Morimoto, Takeshi; Shiomi, Hiroki; Ando, Kenji; Kanamori, Norio; Murata, Koichiro; Kitai, Takeshi; Kawase, Yuichi; Izumi, Chisato; Miyake, Makoto; Mitsuoka, Hirokazu; Kato, Masashi; Hirano, Yutaka; Matsuda, Shintaro; Inada, Tsukasa; Nagao, Kazuya; Murakami, Tomoyuki; Takeuchi, Yasuyo; Yamane, Keiichiro; Toyofuku, Mamoru; Ishii, Mitsuru; Minamino-Muta, Eri; Kato, Takao; Inoko, Moriaki; Ikeda, Tomoyuki; Komasa, Akihiro; Ishii, Katsuhisa; Hotta, Kozo; Higashitani, Nobuya; Kato, Yoshihiro; Inuzuka, Yasutaka; Maeda, Chiyo; Jinnai, Toshikazu; Morikami, Yuko; Saito, Naritatsu; Minatoya, Kenji; Kimura, Takeshi

2017-05-01

There is considerable debate on the management of patients with low-gradient severe aortic stenosis (LG-AS), defined as aortic valve area <1 cm 2 with peak aortic jet velocity ≤4.0 m/s, and mean aortic pressure gradient ≤40 mm Hg. In the CURRENT AS registry (Contemporary Outcomes After Surgery and Medical Treatment in Patients With Severe Aortic Stenosis), there were 2097 patients (initial aortic valve replacement [AVR] strategy: n=977, and conservative strategy: n=1120) with high-gradient severe aortic stenosis (HG-AS) and 1712 patients (initial AVR strategy: n=219, and conservative strategy: n=1493) with LG-AS. AVR was more frequently performed in HG-AS patients than in LG-AS patients (60% versus 28%) during the entire follow-up. In the comparison between the initial AVR and conservative groups, the propensity score-matched cohorts were developed in both HG-AS (n=887 for each group) and LG-AS (n=218 for each group) strata. The initial AVR strategy when compared with the conservative strategy was associated with markedly lower risk for a composite of aortic valve-related death or heart failure hospitalization in both HG-AS and LG-AS strata (hazard ratio, 0.30; 95% confidence interval, 0.25-0.37; P <0.001 and hazard ratio, 0.46; 95% confidence interval, 0.32-0.67; P <0.001, respectively). Among 1358 patients with LG-AS with preserved left ventricular ejection fraction, the initial AVR strategy was associated with a better outcome than the conservative strategy (adjusted hazard ratio, 0.37; 95% confidence interval, 0.23-0.59; P <0.001). The initial AVR strategy was associated with better outcomes than the conservative strategy in both HG-AS and LG-AS patients, although AVR was less frequently performed in LG-AS patients than in HG-AS patients. The favorable effect of initial AVR strategy was also seen in patients with LG-AS with preserved left ventricular ejection fraction. URL: http://www.umin.ac.jp/ctr/index.htm. Unique identifier: UMIN000012140. © 2017 American Heart Association, Inc.

Structure and function of ameloblastin as an extracellular matrix protein: adhesion, calcium binding, and CD63 interaction in human and mouse.

PubMed

Zhang, Xu; Diekwisch, Thomas G H; Luan, Xianghong

2011-12-01

The functional significance of extracellular matrix proteins in the life of vertebrates is underscored by a high level of sequence variability in tandem with a substantial degree of conservation in terms of cell-cell and cell-matrix adhesion interactions. Many extracellular matrix proteins feature multiple adhesion domains for successful attachment to substrates, such as integrin, CD63, and heparin. Here we have used homology and ab initio modeling algorithms to compare mouse ameloblastin (mAMBN) and human ameloblastin (hABMN) isoforms and to analyze their potential for cell adhesion and interaction with other matrix molecules as well as calcium binding. Sequence comparison between mAMBN and hAMBN revealed a 26-amino-acid deletion in mAMBN, corresponding to a helix-loop-helix frameshift. The human AMBN domain (174Q-201G), homologous to the mAMBN 157E-178I helix-loop-helix region, formed a helix-loop motif with an extended loop, suggesting a higher degree of flexibility of hAMBN compared with mAMBN, as confirmed by molecular dynamics simulation. Heparin-binding domains, CD63-interaction domains, and calcium-binding sites in both hAMBN and mAMBN support the concept of AMBN as an extracellular matrix protein. The high level of conservation between AMBN functional domains related to adhesion and differentiation was remarkable when compared with only 61% amino acid sequence homology. © 2011 Eur J Oral Sci.

An integrated sampling and analysis approach for improved biodiversity monitoring

USGS Publications Warehouse

DeWan, Amielle A.; Zipkin, Elise

2010-01-01

Successful biodiversity conservation requires high quality monitoring data and analyses to ensure scientifically defensible policy, legislation, and management. Although monitoring is a critical component in assessing population status and trends, many governmental and non-governmental organizations struggle to develop and implement effective sampling protocols and statistical analyses because of the magnitude and diversity of species in conservation concern. In this article we describe a practical and sophisticated data collection and analysis framework for developing a comprehensive wildlife monitoring program that includes multi-species inventory techniques and community-level hierarchical modeling. Compared to monitoring many species individually, the multi-species approach allows for improved estimates of individual species occurrences, including rare species, and an increased understanding of the aggregated response of a community to landscape and habitat heterogeneity. We demonstrate the benefits and practicality of this approach to address challenges associated with monitoring in the context of US state agencies that are legislatively required to monitor and protect species in greatest conservation need. We believe this approach will be useful to regional, national, and international organizations interested in assessing the status of both common and rare species.

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.

The Yeast Saccharomyces cerevisiae as a Model for Understanding RAS Proteins and Their Role in Human Tumorigenesis

PubMed Central

Cazzanelli, Giulia; Francisco, Rita; Azevedo, Luísa; Carvalho, Patrícia Dias; Almeida, Ana; Côrte-Real, Manuela; Oliveira, Maria José; Lucas, Cândida; Sousa, Maria João

2018-01-01

The exploitation of the yeast Saccharomyces cerevisiae as a biological model for the investigation of complex molecular processes conserved in multicellular organisms, such as humans, has allowed fundamental biological discoveries. When comparing yeast and human proteins, it is clear that both amino acid sequences and protein functions are often very well conserved. One example of the high degree of conservation between human and yeast proteins is highlighted by the members of the RAS family. Indeed, the study of the signaling pathways regulated by RAS in yeast cells led to the discovery of properties that were often found interchangeable with RAS proto-oncogenes in human pathways, and vice versa. In this work, we performed an updated critical literature review on human and yeast RAS pathways, specifically highlighting the similarities and differences between them. Moreover, we emphasized the contribution of studying yeast RAS pathways for the understanding of human RAS and how this model organism can contribute to unveil the roles of RAS oncoproteins in the regulation of mechanisms important in the tumorigenic process, like autophagy. PMID:29463063

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 update historical information. PMID:25061858

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 update historical information.

Incorporating threat in hotspots and coldspots of biodiversity and ecosystem services.

PubMed

Schröter, Matthias; Kraemer, Roland; Ceauşu, Silvia; Rusch, Graciela M

2017-11-01

Spatial prioritization could help target conservation actions directed to maintain both biodiversity and ecosystem services. We delineate hotspots and coldspots of two biodiversity conservation features and five regulating and cultural services by incorporating an indicator of 'threat', i.e. timber harvest profitability for forest areas in Telemark (Norway). We found hotspots, where high values of biodiversity, ecosystem services and threat coincide, ranging from 0.1 to 7.1% of the area, depending on varying threshold levels. Targeting of these areas for conservation follows reactive conservation approaches. In coldspots, high biodiversity and ecosystem service values coincide with low levels of threat, and cover 0.1-3.4% of the forest area. These areas might serve proactive conservation approaches at lower opportunity cost (foregone timber harvest profits). We conclude that a combination of indicators of biodiversity, ecosystem services and potential threat is an appropriate approach for spatial prioritization of proactive and reactive conservation strategies.

Potential relocation of climatic environments suggests high rates of climate displacement within the North American protection network.

PubMed

Batllori, Enric; Parisien, Marc-André; Parks, Sean A; Moritz, Max A; Miller, Carol

2017-08-01

Ongoing climate change may undermine the effectiveness of protected area networks in preserving the set of biotic components and ecological processes they harbor, thereby jeopardizing their conservation capacity into the future. Metrics of climate change, particularly rates and spatial patterns of climatic alteration, can help assess potential threats. Here, we perform a continent-wide climate change vulnerability assessment whereby we compare the baseline climate of the protected area network in North America (Canada, United States, México-NAM) to the projected end-of-century climate (2071-2100). We estimated the projected pace at which climatic conditions may redistribute across NAM (i.e., climate velocity), and identified future nearest climate analogs to quantify patterns of climate relocation within, among, and outside protected areas. Also, we interpret climatic relocation patterns in terms of associated land-cover types. Our analysis suggests that the conservation capacity of the NAM protection network is likely to be severely compromised by a changing climate. The majority of protected areas (~80%) might be exposed to high rates of climate displacement that could promote important shifts in species abundance or distribution. A small fraction of protected areas (<10%) could be critical for future conservation plans, as they will host climates that represent analogs of conditions currently characterizing almost a fifth of the protected areas across NAM. However, the majority of nearest climatic analogs for protected areas are in nonprotected locations. Therefore, unprotected landscapes could pose additional threats, beyond climate forcing itself, as sensitive biota may have to migrate farther than what is prescribed by the climate velocity to reach a protected area destination. To mitigate future threats to the conservation capacity of the NAM protected area network, conservation plans will need to capitalize on opportunities provided by the existing availability of natural land-cover types outside the current network of NAM protected areas. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.

Simple rules can guide whether land- or ocean-based conservation will best benefit marine ecosystems.

PubMed

Saunders, Megan I; Bode, Michael; Atkinson, Scott; Klein, Carissa J; Metaxas, Anna; Beher, Jutta; Beger, Maria; Mills, Morena; Giakoumi, Sylvaine; Tulloch, Vivitskaia; Possingham, Hugh P

2017-09-01

Coastal marine ecosystems can be managed by actions undertaken both on the land and in the ocean. Quantifying and comparing the costs and benefits of actions in both realms is therefore necessary for efficient management. Here, we quantify the link between terrestrial sediment runoff and a downstream coastal marine ecosystem and contrast the cost-effectiveness of marine- and land-based conservation actions. We use a dynamic land- and sea-scape model to determine whether limited funds should be directed to 1 of 4 alternative conservation actions-protection on land, protection in the ocean, restoration on land, or restoration in the ocean-to maximise the extent of light-dependent marine benthic habitats across decadal timescales. We apply the model to a case study for a seagrass meadow in Australia. We find that marine restoration is the most cost-effective action over decadal timescales in this system, based on a conservative estimate of the rate at which seagrass can expand into a new habitat. The optimal decision will vary in different social-ecological contexts, but some basic information can guide optimal investments to counteract land- and ocean-based stressors: (1) marine restoration should be prioritised if the rates of marine ecosystem decline and expansion are similar and low; (2) marine protection should take precedence if the rate of marine ecosystem decline is high or if the adjacent catchment is relatively intact and has a low rate of vegetation decline; (3) land-based actions are optimal when the ratio of marine ecosystem expansion to decline is greater than 1:1.4, with terrestrial restoration typically the most cost-effective action; and (4) land protection should be prioritised if the catchment is relatively intact but the rate of vegetation decline is high. These rules of thumb illustrate how cost-effective conservation outcomes for connected land-ocean systems can proceed without complex modelling.

Simple rules can guide whether land- or ocean-based conservation will best benefit marine ecosystems

PubMed Central

Bode, Michael; Atkinson, Scott; Klein, Carissa J.; Metaxas, Anna; Beher, Jutta; Beger, Maria; Mills, Morena; Giakoumi, Sylvaine; Tulloch, Vivitskaia; Possingham, Hugh P.

2017-01-01

Coastal marine ecosystems can be managed by actions undertaken both on the land and in the ocean. Quantifying and comparing the costs and benefits of actions in both realms is therefore necessary for efficient management. Here, we quantify the link between terrestrial sediment runoff and a downstream coastal marine ecosystem and contrast the cost-effectiveness of marine- and land-based conservation actions. We use a dynamic land- and sea-scape model to determine whether limited funds should be directed to 1 of 4 alternative conservation actions—protection on land, protection in the ocean, restoration on land, or restoration in the ocean—to maximise the extent of light-dependent marine benthic habitats across decadal timescales. We apply the model to a case study for a seagrass meadow in Australia. We find that marine restoration is the most cost-effective action over decadal timescales in this system, based on a conservative estimate of the rate at which seagrass can expand into a new habitat. The optimal decision will vary in different social–ecological contexts, but some basic information can guide optimal investments to counteract land- and ocean-based stressors: (1) marine restoration should be prioritised if the rates of marine ecosystem decline and expansion are similar and low; (2) marine protection should take precedence if the rate of marine ecosystem decline is high or if the adjacent catchment is relatively intact and has a low rate of vegetation decline; (3) land-based actions are optimal when the ratio of marine ecosystem expansion to decline is greater than 1:1.4, with terrestrial restoration typically the most cost-effective action; and (4) land protection should be prioritised if the catchment is relatively intact but the rate of vegetation decline is high. These rules of thumb illustrate how cost-effective conservation outcomes for connected land–ocean systems can proceed without complex modelling. PMID:28877168

The Evolution of Gene Regulatory Networks that Define Arthropod Body Plans.

PubMed

Auman, Tzach; Chipman, Ariel D

2017-09-01

Our understanding of the genetics of arthropod body plan development originally stems from work on Drosophila melanogaster from the late 1970s and onward. In Drosophila, there is a relatively detailed model for the network of gene interactions that proceeds in a sequential-hierarchical fashion to define the main features of the body plan. Over the years, we have a growing understanding of the networks involved in defining the body plan in an increasing number of arthropod species. It is now becoming possible to tease out the conserved aspects of these networks and to try to reconstruct their evolution. In this contribution, we focus on several key nodes of these networks, starting from early patterning in which the main axes are determined and the broad morphological domains of the embryo are defined, and on to later stage wherein the growth zone network is active in sequential addition of posterior segments. The pattern of conservation of networks is very patchy, with some key aspects being highly conserved in all arthropods and others being very labile. Many aspects of early axis patterning are highly conserved, as are some aspects of sequential segment generation. In contrast, regional patterning varies among different taxa, and some networks, such as the terminal patterning network, are only found in a limited range of taxa. The growth zone segmentation network is ancient and is probably plesiomorphic to all arthropods. In some insects, it has undergone significant modification to give rise to a more hardwired network that generates individual segments separately. In other insects and in most arthropods, the sequential segmentation network has undergone a significant amount of systems drift, wherein many of the genes have changed. However, it maintains a conserved underlying logic and function. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

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.

Local understandings of conservation in southeastern Mexico and their implications for community-based conservation as an alternative paradigm.

PubMed

Reyes-Garcia, Victoria; Ruiz-Mallen, Isabel; Porter-Bolland, Luciana; Garcia-Frapolli, Eduardo; Ellis, Edward A; Mendez, Maria-Elena; Pritchard, Diana J; Sanchez-Gonzalez, María-Consuelo

2013-08-01

Since the 1990s national and international programs have aimed to legitimize local conservation initiatives that might provide an alternative to the formal systems of state-managed or otherwise externally driven protected areas. We used discourse analysis (130 semistructured interviews with key informants) and descriptive statistics (679 surveys) to compare local perceptions of and experiences with state-driven versus community-driven conservation initiatives. We conducted our research in 6 communities in southeastern Mexico. Formalization of local conservation initiatives did not seem to be based on local knowledge and practices. Although interviewees thought community-based initiatives generated less conflict than state-managed conservation initiatives, the community-based initiatives conformed to the biodiversity conservation paradigm that emphasizes restricted use of and access to resources. This restrictive approach to community-based conservation in Mexico, promoted through state and international conservation organizations, increased the area of protected land and had local support but was not built on locally relevant and multifunctional landscapes, a model that community-based conservation is assumed to advance. © 2013 Society for Conservation Biology.

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.

Achieving open access to conservation science.

PubMed

Fuller, Richard A; Lee, Jasmine R; Watson, James E M

2014-12-01

Conservation science is a crisis discipline in which the results of scientific enquiry must be made available quickly to those implementing management. We assessed the extent to which scientific research published since the year 2000 in 20 conservation science journals is publicly available. Of the 19,207 papers published, 1,667 (8.68%) are freely downloadable from an official repository. Moreover, only 938 papers (4.88%) meet the standard definition of open access in which material can be freely reused providing attribution to the authors is given. This compares poorly with a comparable set of 20 evolutionary biology journals, where 31.93% of papers are freely downloadable and 7.49% are open access. Seventeen of the 20 conservation journals offer an open access option, but fewer than 5% of the papers are available through open access. The cost of accessing the full body of conservation science runs into tens of thousands of dollars per year for institutional subscribers, and many conservation practitioners cannot access pay-per-view science through their workplace. However, important initiatives such as Research4Life are making science available to organizations in developing countries. We urge authors of conservation science to pay for open access on a per-article basis or to choose publication in open access journals, taking care to ensure the license allows reuse for any purpose providing attribution is given. Currently, it would cost $51 million to make all conservation science published since 2000 freely available by paying the open access fees currently levied to authors. Publishers of conservation journals might consider more cost effective models for open access and conservation-oriented organizations running journals could consider a broader range of options for open access to nonmembers such as sponsorship of open access via membership fees. © 2014 The Authors. Conservation Biology published by Wiley Periodicals, Inc., on behalf of the Society for Conservation Biology.

Efficient Low Dissipative High Order Schemes for Multiscale MHD Flows, I: Basic Theory

NASA Technical Reports Server (NTRS)

Sjoegreen, Bjoern; Yee, H. C.

2003-01-01

The objective of this paper is to extend our recently developed highly parallelizable nonlinear stable high order schemes for complex multiscale hydrodynamic applications to the viscous MHD equations. These schemes employed multiresolution wavelets as adaptive numerical dissipation controls t o limit the amount of and to aid the selection and/or blending of the appropriate types of dissipation to be used. The new scheme is formulated for both the conservative and non-conservative form of the MHD equations in curvilinear grids. The four advantages of the present approach over existing MHD schemes reported in the open literature are as follows. First, the scheme is constructed for long-time integrations of shock/turbulence/combustion MHD flows. Available schemes are too diffusive for long-time integrations and/or turbulence/combustion problems. Second, unlike exist- ing schemes for the conservative MHD equations which suffer from ill-conditioned eigen- decompositions, the present scheme makes use of a well-conditioned eigen-decomposition obtained from a minor modification of the eigenvectors of the non-conservative MHD equations t o solve the conservative form of the MHD equations. Third, this approach of using the non-conservative eigensystem when solving the conservative equations also works well in the context of standard shock-capturing schemes for the MHD equations. Fourth, a new approach to minimize the numerical error of the divergence-free magnetic condition for high order schemes is introduced. Numerical experiments with typical MHD model problems revealed the applicability of the newly developed schemes for the MHD equations.

Comparison of Drosophilidae (Diptera) assemblages from two highland Araucaria Forest fragments, with and without environmental conservation policies.

PubMed

Cavasini, R; Buschini, M L T; Machado, L P B; Mateus, R P

2014-11-01

Flies from the Drosophilidae family are model organisms for biological studies and are often suggested as bioindicators of environmental quality. The Araucaria Forest, one of Atlantic Forest phyto-physiognomy, displays a highly fragmented distribution due to the expansion of agriculture and urbanization. Thus, this work aimed to evaluate and compare the drosophilid assemblages from two highland Araucaria Forest fragments, one a conservation unit (PMA - Parque Municipal das Araucárias) and the other a private property without any conservational policy (FBL - Fazenda Brandalise), in space and time, using species abundances and richness, ecological indexes and Neotropical and exotic species proportions as parameters to establish the level of environmental quality of these fragments. Our results showed that the observed diversity in PMA (H' = 2.221) was approximately 40% higher than in FBL (H' = 1.592). This could be due to higher preservation quality and habitat diversity in PMA, indicating the importance of conservation units. However, richness were similar for these areas, with PMA (Dmg = 6.602) only 8% higher than FBL (Dmg = 6.128), which suggest that the larger distance from city limits and the larger size of FBL forested area could be compensating the higher disturbance caused by antrophic extractive exploitation of this fragment. This points out that, besides the quality of presevertion, the size and/or connection with other fragments should be considered for areas destined for biodiversity conservation. In general, both areas presented similar drosophilid assemblages, and the expressive abundance of both Neotropical species (mostly of the subgroup willistoni) and the exotic species D. kikkawai suggests that these areas are in intermediate stages of conservation.

Functional Targets of the Monogenic Diabetes Transcription Factors HNF-1α and HNF-4α Are Highly Conserved Between Mice and Humans

PubMed Central

Boj, Sylvia F.; Servitja, Joan Marc; Martin, David; Rios, Martin; Talianidis, Iannis; Guigo, Roderic; Ferrer, Jorge

2009-01-01

OBJECTIVE The evolutionary conservation of transcriptional mechanisms has been widely exploited to understand human biology and disease. Recent findings, however, unexpectedly showed that the transcriptional regulators hepatocyte nuclear factor (HNF)-1α and -4α rarely bind to the same genes in mice and humans, leading to the proposal that tissue-specific transcriptional regulation has undergone extensive divergence in the two species. Such observations have major implications for the use of mouse models to understand HNF-1α– and HNF-4α–deficient diabetes. However, the significance of studies that assess binding without considering regulatory function is poorly understood. RESEARCH DESIGN AND METHODS We compared previously reported mouse and human HNF-1α and HNF-4α binding studies with independent binding experiments. We also integrated binding studies with mouse and human loss-of-function gene expression datasets. RESULTS First, we confirmed the existence of species-specific HNF-1α and -4α binding, yet observed incomplete detection of binding in the different datasets, causing an underestimation of binding conservation. Second, only a minor fraction of HNF-1α– and HNF-4α–bound genes were downregulated in the absence of these regulators. This subset of functional targets did not show evidence for evolutionary divergence of binding or binding sequence motifs. Finally, we observed differences between conserved and species-specific binding properties. For example, conserved binding was more frequently located near transcriptional start sites and was more likely to involve multiple binding events in the same gene. CONCLUSIONS Despite evolutionary changes in binding, essential direct transcriptional functions of HNF-1α and -4α are largely conserved between mice and humans. PMID:19188435

Glade/woodland restoration in the St. Francis Mountain Bird Conservation Area

Treesearch

David A. Hasenbeck

2007-01-01

The Missouri Department of Conservation (MDC), the Missouri Department of Natural Resources, the U.S. Forest Service, and American Bird Conservancy, share goals to restore and manage high quality glade, savanna, and woodland habitats within the Saint Francis Bird Conservation Area. The partnership endeavors to maintain and enhance an ecosystem with native glade and...

Large-scale conservation planning in a multinational marine environment: cost matters.

PubMed

Mazor, Tessa; Giakoumi, Sylvaine; Kark, Salit; Possingham, Hugh P

2014-07-01

Explicitly including cost in marine conservation planning is essential for achieving feasible and efficient conservation outcomes. Yet, spatial priorities for marine conservation are still often based solely on biodiversity hotspots, species richness, and/or cumulative threat maps. This study aims to provide an approach for including cost when planning large-scale Marine Protected Area (MPA) networks that span multiple countries. Here, we explore the incorporation of cost in the complex setting of the Mediterranean Sea. In order to include cost in conservation prioritization, we developed surrogates that account for revenue from multiple marine sectors: commercial fishing, noncommercial fishing, and aquaculture. Such revenue can translate into an opportunity cost for the implementation of an MPA network. Using the software Marxan, we set conservation targets to protect 10% of the distribution of 77 threatened marine species in the Mediterranean Sea. We compared nine scenarios of opportunity cost by calculating the area and cost required to meet our targets. We further compared our spatial priorities with those that are considered consensus areas by several proposed prioritization schemes in the Mediterranean Sea, none of which explicitly considers cost. We found that for less than 10% of the Sea's area, our conservation targets can be achieved while incurring opportunity costs of less than 1%. In marine systems, we reveal that area is a poor cost surrogate and that the most effective surrogates are those that account for multiple sectors or stakeholders. Furthermore, our results indicate that including cost can greatly influence the selection of spatial priorities for marine conservation of threatened species. Although there are known limitations in multinational large-scale planning, attempting to devise more systematic and rigorous planning methods is especially critical given that collaborative conservation action is on the rise and global financial crisis restricts conservation investments.

The importance of incorporating functional habitats into conservation planning for highly mobile species in dynamic systems.

PubMed

Webb, Matthew H; Terauds, Aleks; Tulloch, Ayesha; Bell, Phil; Stojanovic, Dejan; Heinsohn, Robert

2017-10-01

The distribution of mobile species in dynamic systems can vary greatly over time and space. Estimating their population size and geographic range can be problematic and affect the accuracy of conservation assessments. Scarce data on mobile species and the resources they need can also limit the type of analytical approaches available to derive such estimates. We quantified change in availability and use of key ecological resources required for breeding for a critically endangered nomadic habitat specialist, the Swift Parrot (Lathamus discolor). We compared estimates of occupied habitat derived from dynamic presence-background (i.e., presence-only data) climatic models with estimates derived from dynamic occupancy models that included a direct measure of food availability. We then compared estimates that incorporate fine-resolution spatial data on the availability of key ecological resources (i.e., functional habitats) with more common approaches that focus on broader climatic suitability or vegetation cover (due to the absence of fine-resolution data). The occupancy models produced significantly (P < 0.001) smaller (up to an order of magnitude) and more spatially discrete estimates of the total occupied area than climate-based models. The spatial location and extent of the total area occupied with the occupancy models was highly variable between years (131 and 1498 km 2 ). Estimates accounting for the area of functional habitats were significantly smaller (2-58% [SD 16]) than estimates based only on the total area occupied. An increase or decrease in the area of one functional habitat (foraging or nesting) did not necessarily correspond to an increase or decrease in the other. Thus, an increase in the extent of occupied area may not equate to improved habitat quality or function. We argue these patterns are typical for mobile resource specialists but often go unnoticed because of limited data over relevant spatial and temporal scales and lack of spatial data on the availability of key resources. Understanding changes in the relative availability of functional habitats is crucial to informing conservation planning and accurately assessing extinction risk for mobile resource specialists. © 2017 Society for Conservation Biology.

Conservative management in ureteric hydronephrosis due to deep endometriosis: Could the levonorgestrel-intrauterine device be an option?

PubMed

Simón, Elisa; Tejerizo, Álvaro; Muñoz, José Luis; Álvarez, Carmen; Marqueta, Laura; Jiménez, Jesús S

2017-07-01

Endometriosis can affect up to 10% of women of reproductive age, in a wide range of clinical presentations that vary from mild to severe or deep endometriosis. Deep endometriosis can affect the urinary tract in 1-5% to 15-25% cases. Even though deep endometriosis' surgeries are usually complex with higher rate of complications, conservative management is not always considered as an option because of its high failure rates. This paper describes two cases of deep endometriosis with ureteric involvement (hydronephrosis) treated conservatively with a double-pigtail stent plus a Levonorgestrel intrauterine device, after conservative surgery, who remained symptom free with no evidence of recurrence at 3 years follow-up, avoiding radical high-risk surgery. Impact statement Several treatments have been described for endometriosis. From a symptomatic perspective, conservative medical management has been proposed with a variable response. Concerning deep endometriosis (affecting the urinary or digestive tract), the definitive treatment has always been thought to be radical surgery. However, this can lead to several complications. To illustrate a possible more conservative approach this paper describes two cases of deep infiltrating endometriosis affecting the ureter, treated conservatively with a temporary pigtail ureter stent plus a Levonorgestrel intrauterine device. The management demonstrates that, in a selected population, conservative treatment solves the urinary disease avoiding the surgical complications and, what is more, improving patients' symptoms in a permanent way. Further prospective studies are needed to confirm whether the introduction of this management in clinical practice would reduce the need for surgery thereby, avoiding high-risk surgery and improving the success rate of conservative management.

Assessing conservation relevance of organism-environment relations using predicted changes in response variables

USGS Publications Warehouse

Gutzwiller, Kevin J.; Barrow, Wylie C.; White, Joseph D.; Johnson-Randall, Lori; Cade, Brian S.; Zygo, Lisa M.

2010-01-01

1. Organism–environment models are used widely in conservation. The degree to which they are useful for informing conservation decisions – the conservation relevance of these relations – is important because lack of relevance may lead to misapplication of scarce conservation resources or failure to resolve important conservation dilemmas. Even when models perform well based on model fit and predictive ability, conservation relevance of associations may not be clear without also knowing the magnitude and variability of predicted changes in response variables. 2. We introduce a method for evaluating the conservation relevance of organism–environment relations that employs confidence intervals for predicted changes in response variables. The confidence intervals are compared to a preselected magnitude of change that marks a threshold (trigger) for conservation action. To demonstrate the approach, we used a case study from the Chihuahuan Desert involving relations between avian richness and broad-scale patterns of shrubland. We considered relations for three winters and two spatial extents (1- and 2-km-radius areas) and compared predicted changes in richness to three thresholds (10%, 20% and 30% change). For each threshold, we examined 48 relations. 3. The method identified seven, four and zero conservation-relevant changes in mean richness for the 10%, 20% and 30% thresholds respectively. These changes were associated with major (20%) changes in shrubland cover, mean patch size, the coefficient of variation for patch size, or edge density but not with major changes in shrubland patch density. The relative rarity of conservation-relevant changes indicated that, overall, the relations had little practical value for informing conservation decisions about avian richness. 4. The approach we illustrate is appropriate for various response and predictor variables measured at any temporal or spatial scale. The method is broadly applicable across ecological environments, conservation objectives, types of statistical predictive models and levels of biological organization. By focusing on magnitudes of change that have practical significance, and by using the span of confidence intervals to incorporate uncertainty of predicted changes, the method can be used to help improve the effectiveness of conservation efforts.

On mass and momentum conservation in the variable-parameter Muskingum method

NASA Astrophysics Data System (ADS)

Reggiani, Paolo; Todini, Ezio; Meißner, Dennis

2016-12-01

In this paper we investigate mass and momentum conservation in one-dimensional routing models. To this end we formulate the conservation equations for a finite-dimensional reach and compute individual terms using three standard Saint-Venant (SV) solvers: SOBEK, HEC-RAS and MIKE11. We also employ two different variable-parameter Muskingum (VPM) formulations: the classical Muskingum-Cunge (MC) and the revised, mass-conservative Muskingum-Cunge-Todini (MCT) approach, whereby geometrical cross sections are treated analytically in both cases. We initially compare the three SV solvers for a straight mild-sloping prismatic channel with geometric cross sections and a synthetic hydrograph as boundary conditions against the analytical MC and MCT solutions. The comparison is substantiated by the fact that in this flow regime the conditions for the parabolic equation model solved by MC and MCT are met. Through this intercomparison we show that all approaches have comparable mass and momentum conservation properties, except the MC. Then we extend the MCT to use natural cross sections for a real irregular river channel forced by an observed triple-peak event and compare the results with SOBEK. The model intercomparison demonstrates that the VPM in the form of MCT can be a computationally efficient, fully mass and momentum conservative approach and therefore constitutes a valid alternative to Saint-Venant based flood wave routing for a wide variety of rivers and channels in the world when downstream boundary conditions or hydraulic structures are non-influential.

What's it worth to you? Estimating the public's willingness to pay for biodiversity conservation.

Treesearch

Jonathan Thompson

2005-01-01

Conserving biodiversity in the Oregon Coast Range requires tradeoffs. Policymakers must consider both the costs and benefits of new conservation programs. During this appraisal process, the costs, in terms of economic activity forgone, are often easier to quantify than the benefits. We all know that biodiversity is valuable, but how does its value compare to other...

Organic weed conrol and cover crop residue integration impacts on weed control, quality, and yield and economics in conservation tillage tomato - A case study

USDA-ARS?s Scientific Manuscript database

The increased use of conservation tillage in vegetable production requires more information be developed on the role of cover crops in weed control, tomato quality and yield. Three conservation-tillage systems utilizing crimson clover, brassica and cereal rye as winter cover crops were compared to ...

Constraining Forest Certificate’s Market to Improve Cost-Effectiveness of Biodiversity Conservation in São Paulo State, Brazil

PubMed Central

Blumentrath, Stefan; Barton, David N.; Rusch, Graciela M.; Romeiro, Ademar R.

2016-01-01

The recently launched Brazilian “forest certificates” market is expected to reduce environmental compliance costs for landowners through an offset mechanism, after a long history of conservation laws based in command-and-control and strict rules. In this paper we assessed potential costs and evaluated the cost-effectiveness of the instrument when introducing to this market constraints that aim to address conservation objectives more specifically. Using the conservation planning software Marxan with Zones we simulated different scopes for the “forest certificates” market, and compared their cost-effectiveness with that of existing command-and-control (C&C), i.e. compliance to the Legal Reserve on own property, in the state of São Paulo. The simulations showed a clear potential of the constrained “forest certificates” market to improve conservation effectiveness and increase cost-effectiveness on allocation of Legal Reserves. Although the inclusion of an additional constraint of targeting the BIOTA Conservation Priority Areas doubled the cost (+95%) compared with a “free trade” scenario constrained only by biome, this option was still 50% less costly than the baseline scenario of compliance with Legal Reserve at the property. PMID:27780220

Constraining Forest Certificate's Market to Improve Cost-Effectiveness of Biodiversity Conservation in São Paulo State, Brazil.

PubMed

Bernasconi, Paula; Blumentrath, Stefan; Barton, David N; Rusch, Graciela M; Romeiro, Ademar R

2016-01-01

The recently launched Brazilian "forest certificates" market is expected to reduce environmental compliance costs for landowners through an offset mechanism, after a long history of conservation laws based in command-and-control and strict rules. In this paper we assessed potential costs and evaluated the cost-effectiveness of the instrument when introducing to this market constraints that aim to address conservation objectives more specifically. Using the conservation planning software Marxan with Zones we simulated different scopes for the "forest certificates" market, and compared their cost-effectiveness with that of existing command-and-control (C&C), i.e. compliance to the Legal Reserve on own property, in the state of São Paulo. The simulations showed a clear potential of the constrained "forest certificates" market to improve conservation effectiveness and increase cost-effectiveness on allocation of Legal Reserves. Although the inclusion of an additional constraint of targeting the BIOTA Conservation Priority Areas doubled the cost (+95%) compared with a "free trade" scenario constrained only by biome, this option was still 50% less costly than the baseline scenario of compliance with Legal Reserve at the property.

Oral water soluble contrast for malignant bowel obstruction.

PubMed

Syrmis, William; Richard, Russell; Jenkins-Marsh, Sue; Chia, Siew C; Good, Phillip

2018-03-07

Malignant bowel obstruction (MBO) is a common problem in patients with intra-abdominal cancer. Oral water soluble contrast (OWSC) has been shown to be useful in the management of adhesive small bowel obstruction in identifying patients who will recover with conservative management alone and also in reducing the length of hospital stay. It is not clear whether the benefits of OWSC in adhesive small bowel obstruction are also seen in patients with MBO. To determine the reliability of OWSC media and follow-up abdominal radiographs in predicting the success of conservative treatment in resolving inoperable MBO with conservative management.To determine the efficacy and safety of OWSC media in reducing the duration of obstruction and reducing hospital stay in people with MBO. We identified studies from searching Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE and MEDLINE in Process, Embase, CINAHL, Science Citation Index (Web of Science) and Conference Proceedings Citation Index - Science (Web of Science). We also searched registries of clinical trials and the CareSearch Grey Literature database. The date of the search was the 6 June 2017. Randomised controlled trials (RCTs), or prospective controlled studies, that evaluated the diagnostic potential of OWSC in predicting which malignant bowel obstructions will resolve with conservative treatment.RCTs, or prospective controlled studies, that assessed the therapeutic potential of OWSC in managing MBO at any level compared with placebo, no intervention or usual treatment or supportive care. We used standard methodological procedures expected by Cochrane. We assessed risk of bias and assessed the evidence using GRADE and created a 'Summary of findings' table. We found only one RCT meeting the selection criteria for the second objective (therapeutic potential) of this review. This study recruited nine participants. It compared the use of gastrografin versus placebo in adult patients with MBO with no indication for further intervention (surgery, endoscopy) apart from standardised conservative management.The overall risk of bias for the study was high due to issues with low numbers of participants, selective reporting of outcomes and a high attrition rate for the intervention arm.Primary outcomesThe included trial was a pilot study whose primary outcome was to test the feasibility for a large study. The authors reported specifically on the number of patients screened, the number recruited and reasons for exclusion; this was not the focus of our review.Due to the low number of participants, the authors of the study decided not to report on our primary outcome of assessing the ability of OWSC to predict the likelihood of malignant small bowel obstruction resolving with conservative treatment alone (diagnostic effect). It also did not report on our primary outcome of rate of resolution of MBO in patients receiving OWSC compared with those not receiving it (therapeutic effect).The study reported that no issues regarding safety or tolerability of either gastrografin or placebo were identified. The overall quality of the evidence for the incidence of adverse events with OWSC was very low, downgraded twice for serious limitations to study quality (high risk of selective reporting and attrition bias) and downgraded once for imprecision (sparse data).Secondary outcomesThe study planned to report on this review's secondary outcome measures of length of hospital stay and time from administration of OWSC to resolution of MBO. However the authors of the study decided not to do so due to the low numbers of patients recruited. The study did not report on our secondary outcome measure of survival times from onset of inoperable MBO until death. There is insufficient evidence from RCTs to determine the place of OWSC in predicting which patients with inoperable MBO will respond with conservative treatment alone. There is also insufficient evidence from RCTs to determine the therapeutic effects and safety of OWSC in patients with malignant small bowel obstruction.

Surgery or conservative treatment for rotator cuff tear: a meta-analysis.

PubMed

Ryösä, Anssi; Laimi, Katri; Äärimaa, Ville; Lehtimäki, Kaisa; Kukkonen, Juha; Saltychev, Mikhail

2017-07-01

Comparative evidence on treating rotator cuff tear is inconclusive. The objective of this review was to evaluate the evidence on effectiveness of tendon repair in reducing pain and improving function of the shoulder when compared with conservative treatment of symptomatic rotator cuff tear. Search on CENTRAL, MEDLINE, EMBASE, CINAHL, Web of Science and Pedro databases. Randomised controlled trials (RCT) comparing surgery and conservative treatment of rotator cuff tear. Study selection and extraction based on the Cochrane Handbook for Systematic reviews of Interventions. Random effects meta-analysis. Three identified RCTs involved 252 participants (123 cases and 129 controls). The risk of bias was considered low for all three RCTs. For Constant score, statistically insignificant effect size was 5.6 (95% CI -0.41 to 11.62) points in 1-year follow up favouring surgery and below the level of minimal clinically important difference. The respective difference in pain reduction was -0.93 (95% CI -1.65 to -0.21) cm on a 0-10 pain visual analogue scale favouring surgery. The difference was statistically significant (p = 0.012) in 1-year follow up but below the level of minimal clinically important difference. There is limited evidence that surgery is not more effective in treating rotator cuff tear than conservative treatment alone. Thus, a conservative approach is advocated as the initial treatment modality. Implications for Rehabilitation There is limited evidence that surgery is not more effective in treating rotator cuff tear than conservative treatment alone. There was no clinically significant difference between surgery and active physiotherapy in 1-year follow-up in improving Constant score or reducing pain caused by rotator cuff tear. As physiotherapy is less proneness to complications and less expensive than surgery, a conservative approach is advocated as the initial treatment modality to rotator cuff tears.

Comparing surgical repair with conservative treatment for degenerative rotator cuff tears: a randomized controlled trial.

PubMed

Lambers Heerspink, Frederik O; van Raay, Jos J A M; Koorevaar, Rinco C T; van Eerden, Pepijn J M; Westerbeek, Robin E; van 't Riet, Esther; van den Akker-Scheek, Inge; Diercks, Ronald L

2015-08-01

Good clinical results have been reported for both surgical and conservative treatment of rotator cuff tears. The primary aim of this randomized controlled trial was to compare functional and radiologic improvement after surgical and conservative treatment of degenerative rotator cuff tears. We conducted a randomized controlled trial that included 56 patients with a degenerative full-thickness rotator cuff tear between January 2009 and December 2012; 31 patients were treated conservatively, and rotator cuff repair was performed in 25 patients. Outcome measures, including the Constant-Murley score (CMS), visual analog scale (VAS) pain and VAS disability scores, were assessed preoperatively and after 6 weeks and 3, 6, and 12 months. Magnetic resonance imaging was performed preoperatively and at 12 months postoperatively. At 12 months postoperatively, the mean CMS was 81.9 (standard deviation [SD], 15.6) in the surgery group vs 73.7 (SD, 18.4) in the conservative group (P = .08). VAS pain (P = .04) and VAS disability (P = .02) were significantly lower in the surgery group at the 12-month follow-up. A subgroup analysis showed postoperative CMS results were significantly better in surgically treated patients without a retear compared with conservatively treated patients (88.5 [SD, 6.2] vs 73.7 [SD, 18.4]). In our population of patients with degenerative rotator cuff tears who were randomly treated by surgery or conservative protocol, we did not observe differences in functional outcome as measured with the CMS 1 year after treatment. However, significant differences in pain and disabilities were observed in favor of surgical treatment. The best outcomes in function and pain were seen in patients with an intact rotator cuff postoperatively. Copyright © 2015 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. All rights reserved.

Comparative mtDNA analyses of three sympatric macropodids from a conservation area on the Huon Peninsula, Papua New Guinea.

PubMed

McGreevy, Thomas J; Dabek, Lisa; Husband, Thomas P

2016-07-01

Matschie's tree kangaroo (Dendrolagus matschiei), New Guinea pademelon (Thylogale browni), and small dorcopsis (Dorcopsulus vanheurni) are sympatric macropodid taxa, of conservation concern, that inhabit the Yopno-Urawa-Som (YUS) Conservation Area on the Huon Peninsula, Papua New Guinea. We sequenced three partial mitochondrial DNA (mtDNA) genes from the three taxa to (i) investigate network structure; and (ii) identify conservation units within the YUS Conservation Area. All three taxa displayed a similar pattern in the spatial distribution of their mtDNA haplotypes and the Urawa and Som rivers on the Huon may have acted as a barrier to maternal gene flow. Matschie's tree kangaroo and New Guinea pademelon within the YUS Conservation Area should be managed as single conservation units because mtDNA nucleotides were not fixed for a given geographic area. However, two distinct conservation units were identified for small dorcopsis from the two different mountain ranges within the YUS Conservation Area.

Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms.

PubMed

Sammond, Deanne W; Kastelowitz, Noah; Himmel, Michael E; Yin, Hang; Crowley, Michael F; Bomble, Yannick J

2016-01-01

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions.

Comparing Residue Clusters from Thermophilic and Mesophilic Enzymes Reveals Adaptive Mechanisms

PubMed Central

Sammond, Deanne W.; Kastelowitz, Noah; Himmel, Michael E.; Yin, Hang; Crowley, Michael F.; Bomble, Yannick J.

2016-01-01

Understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. While multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. In this work we compare equivalent clusters of spatially neighboring residues between paired thermophilic and mesophilic homologues to evaluate adaptations under the selective pressure of high temperature. We find the residue clusters in thermophilic enzymes generally display improved atomic packing compared to mesophilic enzymes, in agreement with previous research. Unlike residue clusters from mesophilic enzymes, however, thermophilic residue clusters do not have significant cavities. In addition, anchor residues found in many clusters are highly conserved with respect to atomic packing between both thermophilic and mesophilic enzymes. Thus the improvements in atomic packing observed in thermophilic homologues are not derived from these anchor residues but from neighboring positions, which may serve to expand optimized protein core regions. PMID:26741367

SMED-TLX-1 (NR2E1) is critical for tissue and body plan maintenance in Schmidtea mediterranea in fasting/feeding cycles.

PubMed

Raška, O; Kostrouchová, V; Behenský, F; Yilma, P; Saudek, V; Kostrouch, Z; Kostrouchová, M

2011-01-01

Nuclear receptors (NRs), or nuclear hormone receptors (NHRs), are transcription factors that regulate development and metabolism of most if not all animal species. Their regulatory networks include conserved mechanisms that are shared in-between species as well as mechanisms that are restricted to certain phyla or even species. In search for conserved members of the NHR family in Schmidtea mediterranea, we identified a molecular signature of a class of NRs, NR2E1, in the S. mediterranea genome and cloned its complete cDNA coding sequence. The derived amino acid sequence shows a high degree of conservation of both DNA-binding domain and ligand- binding domain and a remarkably high homology to vertebrate NR2E1 and C. elegans NHR-67. Quantitative PCR detected approximately ten-fold higher expression of Smed-tlx-1 in the proximal part of the head compared to the tail region. The expression of Smed-tlx-1 is higher during fed state than during fasting. Smed-tlx-1 down-regulation by RNA interference affects the ability of the animals to maintain body plan and induces defects of brain, eyes and body shape during fasting and re-growing cycles. These results suggest that SMED-TLX-1 is critical for tissue and body plan maintenance in planaria.

Genetic Diversity and Population Structure: Implications for Conservation of Wild Soybean (Glycine soja Sieb. et Zucc) Based on Nuclear and Chloroplast Microsatellite Variation

PubMed Central

He, Shuilian; Wang, Yunsheng; Volis, Sergei; Li, Dezhu; Yi, Tingshuang

2012-01-01

Wild soybean (Glycine soja Sieb. et Zucc) is the most important germplasm resource for soybean breeding, and is currently subject to habitat loss, fragmentation and population decline. In order to develop successful conservation strategies, a total of 604 wild soybean accessions from 43 locations sampled across its range in China, Japan and Korea were analyzed using 20 nuclear (nSSRs) and five chloroplast microsatellite markers (cpSSRs) to reveal its genetic diversity and population structure. Relatively high nSSR diversity was found in wild soybean compared with other self-pollinated species, and the region of middle and lower reaches of Yangtze River (MDRY) was revealed to have the highest genetic diversity. However, cpSSRs suggested that Korea is a center of diversity. High genetic differentiation and low gene flow among populations were detected, which is consistent with the predominant self-pollination of wild soybean. Two main clusters were revealed by MCMC structure reconstruction and phylogenetic dendrogram, one formed by a group of populations from northwestern China (NWC) and north China (NC), and the other including northeastern China (NEC), Japan, Korea, MDRY, south China (SC) and southwestern China (SWC). Contrib analyses showed that southwestern China makes the greatest contribution to the total diversity and allelic richness, and is worthy of being given conservation priority. PMID:23202917

Land planarian assemblages in protected areas of the interior atlantic forest: implications for conservation.

PubMed

Negrete, Lisandro; Colpo, Karine D; Brusa, Francisco

2014-01-01

Land planarians are an interesting group of free-living flatworms that can be useful as bioindicators because of their high sensitivity to environmental changes and low dispersal capacity. In this study, we describe and compare assemblages of land planarians from areas with different conservation degrees of the Interior Atlantic Forest (Misiones, Argentina), and assess factors that could be related to their abundance and richness. Eight sites were tracked in search of land planarians in Reserva de Vida Silvestre Urugua-í (RVSU) and Campo Anexo Manuel Belgrano (CAMB). Diurnal and nocturnal surveys were performed in each site along nine sampling campaigns. We collected 237 individuals belonging to 18 species of the subfamily Geoplaninae. All sites were dominated by Geoplana sp. 1 and Pasipha hauseri. The richness estimators showed that there would be more species in RVSU than in CAMB. The abundance and richness of land planarians was high during the night and after rainfalls, suggesting an increased activity of flatworms under such conditions. The abundance and richness of land planarians were also related to the conservation condition of the sites. Disturbed sites showed less abundance and richness, and were segregated from non-disturbed ones by nmMDS analysis. Beta diversity between sites was higher than expected, indicating that the species turnover between sites contributed more to the total richness (gamma diversity) than the alpha diversity.

Comparative and Evolutionary Analysis of the Interleukin 17 Gene Family in Invertebrates

PubMed Central

Huang, Xian-De; Zhang, Hua; He, Mao-Xian

2015-01-01

Interleukin 17 (IL-17) is an important pro-inflammatory cytokine and plays critical roles in the immune response to pathogens and in the pathogenesis of inflammatory and autoimmune diseases. Despite its important functions, the origin and evolution of IL-17 in animal phyla have not been characterized. As determined in this study, the distribution of the IL-17 family among 10 invertebrate species and 7 vertebrate species suggests that the IL-17 gene may have originated from Nematoda but is absent from Saccoglossus kowalevskii (Hemichordata) and Insecta. Moreover, the gene number, protein length and domain number of IL-17 differ widely. A comparison of IL-17-containing domains and conserved motifs indicated somewhat low amino acid sequence similarity but high conservation at the motif level, although some motifs were lost in certain species. The third disulfide bond for the cystine knot fold is formed by two cysteine residues in invertebrates, but these have been replaced by two serine residues in Chordata and vertebrates. One third of invertebrate IL-17 proteins were found to have no predicted signal peptide. Furthermore, an analysis of phylogenetic trees and exon–intron structures indicated that the IL-17 family lacks conservation and displays high divergence. These results suggest that invertebrate IL-17 proteins have undergone complex differentiation and that their members may have developed novel functions during evolution. PMID:26218896

Grain-dependent responses of mammalian diversity to land use and the implications for conservation set-aside.

PubMed

Wearn, Oliver R; Carbone, Chris; Rowcliffe, J Marcus; Bernard, Henry; Ewers, Robert M

2016-07-01

Diversity responses to land-use change are poorly understood at local scales, hindering our ability to make forecasts and management recommendations at scales which are of practical relevance. A key barrier in this has been the underappreciation of grain-dependent diversity responses and the role that β-diversity (variation in community composition across space) plays in this. Decisions about the most effective spatial arrangement of conservation set-aside, for example high conservation value areas, have also neglected β-diversity, despite its role in determining the complementarity of sites. We examined local-scale mammalian species richness and β-diversity across old-growth forest, logged forest, and oil palm plantations in Borneo, using intensive camera- and live-trapping. For the first time, we were able to investigate diversity responses, as well as β-diversity, at multiple spatial grains, and across the whole terrestrial mammal community (large and small mammals); β-diversity was quantified by comparing observed β-diversity with that obtained under a null model, in order to control for sampling effects, and we refer to this as the β-diversity signal. Community responses to land use were grain dependent, with large mammals showing reduced richness in logged forest compared to old-growth forest at the grain of individual sampling points, but no change at the overall land-use level. Responses varied with species group, however, with small mammals increasing in richness at all grains in logged forest compared to old-growth forest. Both species groups were significantly depauperate in oil palm. Large mammal communities in old-growth forest became more heterogeneous at coarser spatial grains and small mammal communities became more homogeneous, while this pattern was reversed in logged forest. Both groups, however, showed a significant β-diversity signal at the finest grain in logged forest, likely due to logging-induced environmental heterogeneity. The β-diversity signal in oil palm was weak, but heterogeneity at the coarsest spatial grain was still evident, likely due to variation in landscape forest cover. Our findings suggest that the most effective spatial arrangement of set-aside will involve trade-offs between conserving large and small mammals. Greater consideration in the conservation and management of tropical landscapes needs to be given to β-diversity at a range of spatial grains. © 2016 by the Ecological Society of America.

Interventions for treating chronic ankle instability.

PubMed

de Vries, J S; Krips, R; Sierevelt, I N; Blankevoort, L

2006-10-18

Chronic lateral ankle instability occurs in 10% to 20% of people after an acute ankle sprain. The initial form of treatment is conservative but if this fails and ligament laxity is present, surgical intervention is considered. To compare different treatments, both conservative and surgical, for chronic lateral ankle instability. We searched the Cochrane Bone, Joint and Muscle Trauma Group Specialized Register (to July 2005), the Cochrane Central Register of Controlled Trials (The Cochrane Library 2005, Issue 3), and MEDLINE (1966 to April 2006), EMBASE (1980 to April 2006), CINAHL (1982 to April 2006) and reference lists of articles. All randomised and quasi-randomised controlled trials of interventions for chronic lateral ankle instability were included. Two review authors independently assessed methodological quality and extracted data. Where appropriate, results of comparable studies were pooled. Seven randomised trials were included and divided into three groups: surgical interventions; rehabilitation programs after surgical interventions; and conservative interventions. None of the studies were methodologically flawless. Only one study described an adequate randomisation procedure. Only two studies, both about rehabilitation programs after surgery, had a moderate risk of bias; all other studies had a high risk of bias. Due to clinical and methodological diversity, extensive pooling of the data was not possible. Surgical interventions (four studies): one study showed more complications after the Chrisman-Snook procedure compared to an anatomical reconstruction, whereas another study showed greater mean talar tilt after an anatomical reconstruction. Subjective instability and hindfoot inversion was greater after a dynamic than after a static tenodesis in a third study. The fourth study showed that the operating time for anatomical reconstructions was shorter for the reinsertion technique than for the imbrication method. Rehabilitation after surgical interventions (two studies): both studies provided evidence that early functional mobilization leads to an earlier return to work and sports than immobilisation. Conservative interventions: the only study in this group showed better proprioception and functional outcome with the bi-directional than with the uni-directional pedal technique on a cyclo-ergometer. In view of the low quality methodology of almost all the studies, this review does not provide sufficient evidence to support any specific surgical or conservative intervention for chronic ankle instability. However, after surgical reconstruction, early functional rehabilitation was shown to be superior to six weeks immobilisation regarding time to return to work and sports.

Environmental life cycle assessment of different domestic wastewater streams: policy effectiveness in a tropical urban environment.

PubMed

Ng, Bernard J H; Zhou, Jin; Giannis, Apostolos; Chang, Victor W-C; Wang, Jing-Yuan

2014-07-01

To enhance local water security, the Singapore government promotes two water conservation policies: the use of eco-friendly toilets to reduce yellow water (YW) disposal and the installation of water efficient devices to minimize gray water (GW) discharge. The proposed water conservation policies have different impacts on the environmental performance of local wastewater management. The main purpose of this study is to examine and compare the impacts of different domestic wastewater streams and the effectiveness of two water conservation policies by means of life cycle assessment (LCA). LCA is used to compare three scenarios, including a baseline scenario (BL), YW-reduced scenario (YWR) and GW-reduced scenario (GWR). The BL is designed based on the current wastewater management system, whereas the latter two scenarios are constructed according to the two water conservation policies that are proposed by the Singapore government. The software SIMPARO 7.3 with local data and an eco-invent database is used to build up the model, and the functional unit is defined as the daily wastewater disposal of a Singapore resident. Due to local water supply characteristics, the system boundary is extended to include the sewage sludge management and tap water production processes. The characterization results indicate that the GWR has a significant impact reduction (22-25%) while the YWR has only a 2-4% impact reduction compared with the BL. The contribution analysis reveals that the GW dominates many impact categories except eutrophication potential. The tap water production is identified as the most influential process due to its high embodied energy demand in a local context. Life cycle costing analysis shows that both YWR and GWR are financially favorable. It is also revealed that the current water conservation policies could only achieve Singapore's short-term targets. Therefore, two additional strategies are recommended for achieving long-term goals. This study provides a comprehensive and reliable environmental profile of Singapore's wastewater management with the help of extended system boundary and local data. This work also fills the research gap of previous studies by identifying the contribution of different wastewater streams, which would serve as a good reference for source-separating sanitation system design. Copyright © 2014 Elsevier Ltd. All rights reserved.

Motion of gas in highly rarefied space

NASA Astrophysics Data System (ADS)

Chirkunov, Yu A.

2017-10-01

A model describing a motion of gas in a highly rarefied space received an unlucky number 13 in the list of the basic models of the motion of gas in the three-dimensional space obtained by L.V. Ovsyannikov. For a given initial pressure distribution, a special choice of mass Lagrangian variables leads to the system describing this motion for which the number of independent variables is less by one. Hence, there is a foliation of a highly rarefied gas with respect to pressure. In a strongly rarefied space for each given initial pressure distribution, all gas particles are localized on a two-dimensional surface that moves with time in this space We found some exact solutions of the obtained system that describe the processes taking place inside of the tornado. For this system we found all nontrivial conservation laws of the first order. In addition to the classical conservation laws the system has another conservation law, which generalizes the energy conservation law. With the additional condition we found another one generalized energy conservation law.

Climate Change, Northern Birds of Conservation Concern and Matching the Hotspots of Habitat Suitability with the Reserve Network

PubMed Central

Virkkala, Raimo; Heikkinen, Risto K.; Fronzek, Stefan; Leikola, Niko

2013-01-01

National reserve networks are one of the most important means of species conservation, but their efficiency may be diminished due to the projected climatic changes. Using bioclimatic envelope models and spatial data on habitats and conservation areas, we studied how efficient the reserve network will be in preserving 100 forest, mire, marshland, and alpine bird species of conservation concern in Finland in 2051–2080 under three different climate scenarios. The occurrences of the studied bird species were related to the amount of habitat preferred by each species in the different boreal zones. We employed a novel integrated habitat suitability index that takes into account both the species’ probability of occurrence from the bioclimatic models and the availability of suitable habitat. Using this suitability index, the distribution of the topmost 5% suitability squares (“hotspots”) in the four bird species groups in the period 1971–2000 and under the three scenarios were compared with the location of reserves with the highest amounts of the four habitats to study the efficiency of the network. In species of mires, marshlands, and Arctic mountains, a high proportion of protected habitat was included in the 5% hotspots in the scenarios in 2051–2080, showing that protected areas cover a high proportion of occurrences of bird species. In contrast, in forests in the southern and middle boreal zones, only a small proportion of the protected habitat was included in the 5% hotspots, indicating that the efficiency of the protected area network will be insufficient for forest birds in the future. In the northern boreal zone, the efficiency of the reserve network in forests was highly dependent on the strength of climate change varying between the scenarios. Overall, there is no single solution to preserving biodiversity in a changing climate, but several future pathways should be considered. PMID:23700420

Climate change, northern birds of conservation concern and matching the hotspots of habitat suitability with the reserve network.

PubMed

Virkkala, Raimo; Heikkinen, Risto K; Fronzek, Stefan; Leikola, Niko

2013-01-01

National reserve networks are one of the most important means of species conservation, but their efficiency may be diminished due to the projected climatic changes. Using bioclimatic envelope models and spatial data on habitats and conservation areas, we studied how efficient the reserve network will be in preserving 100 forest, mire, marshland, and alpine bird species of conservation concern in Finland in 2051-2080 under three different climate scenarios. The occurrences of the studied bird species were related to the amount of habitat preferred by each species in the different boreal zones. We employed a novel integrated habitat suitability index that takes into account both the species' probability of occurrence from the bioclimatic models and the availability of suitable habitat. Using this suitability index, the distribution of the topmost 5% suitability squares ("hotspots") in the four bird species groups in the period 1971-2000 and under the three scenarios were compared with the location of reserves with the highest amounts of the four habitats to study the efficiency of the network. In species of mires, marshlands, and Arctic mountains, a high proportion of protected habitat was included in the 5% hotspots in the scenarios in 2051-2080, showing that protected areas cover a high proportion of occurrences of bird species. In contrast, in forests in the southern and middle boreal zones, only a small proportion of the protected habitat was included in the 5% hotspots, indicating that the efficiency of the protected area network will be insufficient for forest birds in the future. In the northern boreal zone, the efficiency of the reserve network in forests was highly dependent on the strength of climate change varying between the scenarios. Overall, there is no single solution to preserving biodiversity in a changing climate, but several future pathways should be considered.

More hostile dyslipidaemia in chronic kidney disease patients on maintenance haemodialysis than on conservative management.

PubMed

Rathi, Teerath Kumar; Dhrolia, Murtaza Fakhruddin; Imtiaz, Salman

2016-08-01

To study the pattern of dyslipidaemia in patients with stage-V chronic kidney disease on conservative management and those on maintenance haemodialysis. This comparative observational study was conducted at the Jinnah Postgraduate Medical Centre, Karachi, from February to July, 2008, and comprised stage-V chronic kidney disease patients. The patients were divided in two groups. Those who were on conservative management were placed in Group A, and those who were on maintenance haemodialysis were in Group B. Serum total lipid, cholesterol, triglycerides and high-density lipoprotein for both groups were assayed on chemical analyser and low-density lipoprotein was calculated by Friedwald equation. SPSS 17 was used for data analysis. Of the 120 patients, there were 60(50%) in each group. The mean age of patients in Group A was 46.33±14.56 years and in Group B was 43.4±14.1years. Of all, 64(53.3%) were men and 56(46.7%) were women. Mean systolic and diastolic blood pressure was 134±19.58mmHg and 83.6±14.14mmHg in Group A and 129±19.7mmHg and 79.7±12.1mmHg in Group B. Mean serum total lipid was significantly higher (p<0.01) whereas mean serum cholesterol was significantly lower (p<0.01) in Group B. Comparison of mean serum triglycerides between the groups was also statistically significant (p<0.01) and was high in Group B. Mean serum high-density lipoprotein was lower in Group B (p<0.01). The difference between serum low-density lipoprotein levels was statistically insignificant between the groups (p=0.11). Pattern of dyslipidaemia in patients on maintenance haemodialysis was more hostile than those on conservative management, and posed increased risk of coronary heart disease.

Species distribution modeling in regions of high need and limited data: waterfowl of China

USGS Publications Warehouse

Prosser, Diann J.; Ding, Changqing; Erwin, R. Michael; Mundkur, Taej; Sullivan, Jeffery D.; Ellis, Erle C.

2018-01-01

BackgroundA number of conservation and societal issues require understanding how species are distributed on the landscape, yet ecologists are often faced with a lack of data to develop models at the resolution and extent desired, resulting in inefficient use of conservation resources. Such a situation presented itself in our attempt to develop waterfowl distribution models as part of a multi-disciplinary team targeting the control of the highly pathogenic H5N1 avian influenza virus in China.MethodsFaced with limited data, we built species distribution models using a habitat suitability approach for China’s breeding and non-breeding (hereafter, wintering) waterfowl. An extensive review of the literature was used to determine model parameters for habitat modeling. Habitat relationships were implemented in GIS using land cover covariates. Wintering models were validated using waterfowl census data, while breeding models, though developed for many species, were only validated for the one species with sufficient telemetry data available.ResultsWe developed suitability models for 42 waterfowl species (30 breeding and 39 wintering) at 1 km resolution for the extent of China, along with cumulative and genus level species richness maps. Breeding season models showed highest waterfowl suitability in wetlands of the high-elevation west-central plateau and northeastern China. Wintering waterfowl suitability was highest in the lowland regions of southeastern China. Validation measures indicated strong performance in predicting species presence. Comparing our model outputs to China’s protected areas indicated that breeding habitat was generally better covered than wintering habitat, and identified locations for which additional research and protection should be prioritized.ConclusionsThese suitability models are the first available for many of China’s waterfowl species, and have direct utility to conservation and habitat planning and prioritizing management of critically important areas, providing an example of how this approach may aid others faced with the challenge of addressing conservation issues with little data to inform decision making.

Environmentalism as a trait: gauging people's prosocial personality in terms of environmental engagement.

PubMed

Kaiser, Florian G; Byrka, Katarzyna

2011-02-01

According to Hardin (1968), environmental deterioration stems from self-interest undermining people's resource conservation in the collective interest. Not surprisingly, selfless prosocial motives, such as personal feelings of moral obligation, have often been recognized as a key force behind people's environmentalism. In our research, we anticipated that environmentalists-people with an inclination for pro-environmental engagement-would possess a propensity to generally act prosocially. In an extension of previous work, we expected that a well-established self-report measure of past conservation behavior would predict people's active participation in a psychological experiment. Based on subjects' degree of environmental engagement, originally established in 2003, we re-contacted a sample of 502 persons in 2005. Of these 502 (68.5% low, 31.5% high in environmentalism), 131 showed up for the announced experiment. Among those participants, we found that environmentalists' prosocial personalities were additionally reflected in their social value orientations. Ninety percent of the environmentalists turned out to be prosocials, whereas only 65% of the less environmentally engaged subjects were prosocials. Overall, our findings lend credit to a notion of environmentalism as an indicator of even subtle quantitative differences in a person's prosocial trait level. By and large, environmentalists acted more prosocially even in mundane activities unrelated to environmental conservation. Additional evidence comes from the commons dilemma experiment in which the participants partook. There, we generally found comparatively more cooperation with others for the collective good from people high in environmentalism. Our findings represent circumstantial evidence for a prosocial propensity dimension along which people differ, and which is also reflected in people's pro-environmental behavioral performance. If, however, environmentalism has to be regarded as indicative of a prosocial trait rather than a state-like motive, high hopes for moral norms and other prosocial motives in environmental conservation do not seem warranted.

Conserving the Birds of Uganda’s Banana-Coffee Arc: Land Sparing and Land Sharing Compared

PubMed Central

Hulme, Mark F.; Vickery, Juliet A.; Green, Rhys E.; Phalan, Ben; Chamberlain, Dan E.; Pomeroy, Derek E.; Nalwanga, Dianah; Mushabe, David; Katebaka, Raymond; Bolwig, Simon; Atkinson, Philip W.

2013-01-01

Reconciling the aims of feeding an ever more demanding human population and conserving biodiversity is a difficult challenge. Here, we explore potential solutions by assessing whether land sparing (farming for high yield, potentially enabling the protection of non-farmland habitat), land sharing (lower yielding farming with more biodiversity within farmland) or a mixed strategy would result in better bird conservation outcomes for a specified level of agricultural production. We surveyed forest and farmland study areas in southern Uganda, measuring the population density of 256 bird species and agricultural yield: food energy and gross income. Parametric non-linear functions relating density to yield were fitted. Species were identified as “winners” (total population size always at least as great with agriculture present as without it) or “losers” (total population sometimes or always reduced with agriculture present) for a range of targets for total agricultural production. For each target we determined whether each species would be predicted to have a higher total population with land sparing, land sharing or with any intermediate level of sparing at an intermediate yield. We found that most species were expected to have their highest total populations with land sparing, particularly loser species and species with small global range sizes. Hence, more species would benefit from high-yield farming if used as part of a strategy to reduce forest loss than from low-yield farming and land sharing, as has been found in Ghana and India in a previous study. We caution against advocacy for high-yield farming alone as a means to deliver land sparing if it is done without strong protection for natural habitats, other ecosystem services and social welfare. Instead, we suggest that conservationists explore how conservation and agricultural policies can be better integrated to deliver land sparing by, for example, combining land-use planning and agronomic support for small farmers. PMID:23390501

The Druggable Pocketome of Corynebacterium diphtheriae: A New Approach for in silico Putative Druggable Targets

PubMed Central

Hassan, Syed S.; Jamal, Syed B.; Radusky, Leandro G.; Tiwari, Sandeep; Ullah, Asad; Ali, Javed; Behramand; de Carvalho, Paulo V. S. D.; Shams, Rida; Khan, Sabir; Figueiredo, Henrique C. P.; Barh, Debmalya; Ghosh, Preetam; Silva, Artur; Baumbach, Jan; Röttger, Richard; Turjanski, Adrián G.; Azevedo, Vasco A. C.

2018-01-01

Diphtheria is an acute and highly infectious disease, previously regarded as endemic in nature but vaccine-preventable, is caused by Corynebacterium diphtheriae (Cd). In this work, we used an in silico approach along the 13 complete genome sequences of C. diphtheriae followed by a computational assessment of structural information of the binding sites to characterize the “pocketome druggability.” To this end, we first computed the “modelome” (3D structures of a complete genome) of a randomly selected reference strain Cd NCTC13129; that had 13,763 open reading frames (ORFs) and resulted in 1,253 (∼9%) structure models. The amino acid sequences of these modeled structures were compared with the remaining 12 genomes and consequently, 438 conserved protein sequences were obtained. The RCSB-PDB database was consulted to check the template structures for these conserved proteins and as a result, 401 adequate 3D models were obtained. We subsequently predicted the protein pockets for the obtained set of models and kept only the conserved pockets that had highly druggable (HD) values (137 across all strains). Later, an off-target host homology analyses was performed considering the human proteome using NCBI database. Furthermore, the gene essentiality analysis was carried out that gave a final set of 10-conserved targets possessing highly druggable protein pockets. To check the target identification robustness of the pipeline used in this work, we crosschecked the final target list with another in-house target identification approach for C. diphtheriae thereby obtaining three common targets, these were; hisE-phosphoribosyl-ATP pyrophosphatase, glpX-fructose 1,6-bisphosphatase II, and rpsH-30S ribosomal protein S8. Our predicted results suggest that the in silico approach used could potentially aid in experimental polypharmacological target determination in C. diphtheriae and other pathogens, thereby, might complement the existing and new drug-discovery pipelines. PMID:29487617

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

PubMed Central

Ezkurdia, Iakes; del Pozo, Angela; Frankish, Adam; Rodriguez, Jose Manuel; Harrow, Jennifer; Ashman, Keith; Valencia, Alfonso; Tress, Michael L.

2012-01-01

Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of “novel” and “putative” protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is remarkable and strongly suggests that the translation of alternative transcripts may be subject to selective constraints. PMID:22446687

Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase

PubMed Central

Lucas, James E; Siegel, Justin B

2015-01-01

Enzyme active site residues are often highly conserved, indicating a significant role in function. In this study we quantitate the functional contribution for all conserved molecular interactions occurring within a Michaelis complex for mannitol 2-dehydrogenase derived from Pseudomonas fluorescens (pfMDH). Through systematic mutagenesis of active site residues, we reveal that the molecular interactions in pfMDH mediated by highly conserved residues not directly involved in reaction chemistry can be as important to catalysis as those directly involved in the reaction chemistry. This quantitative analysis of the molecular interactions within the pfMDH active site provides direct insight into the functional role of each molecular interaction, several of which were unexpected based on canonical sequence conservation and structural analyses. PMID:25752240

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

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.

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.

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.

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 generalize to any place where high species richness overlaps with hazardous wildland vegetation.

Conservation planning under uncertainty in urban development and vegetation dynamics

PubMed Central

Carmel, Yohay

2018-01-01

Systematic conservation planning is a framework for optimally locating and prioritizing areas for conservation. An often-noted shortcoming of most conservation planning studies is that they do not address future uncertainty. The selection of protected areas that are intended to ensure the long-term persistence of biodiversity is often based on a snapshot of the current situation, ignoring processes such as climate change. Scenarios, in the sense of being accounts of plausible futures, can be utilized to identify conservation area portfolios that are robust to future uncertainty. We compared three approaches for utilizing scenarios in conservation area selection: considering a full set of scenarios (all-scenarios portfolio), assuming the realization of specific scenarios, and a reference strategy based on the current situation (current distributions portfolio). Our objective was to compare the robustness of these approaches in terms of their relative performance across future scenarios. We focused on breeding bird species in Israel’s Mediterranean region. We simulated urban development and vegetation dynamics scenarios 60 years into the future using DINAMICA-EGO, a cellular-automata simulation model. For each scenario, we mapped the target species’ available habitat distribution, identified conservation priority areas using the site-selection software MARXAN, and constructed conservation area portfolios using the three aforementioned strategies. We then assessed portfolio performance based on the number of species for which representation targets were met in each scenario. The all-scenarios portfolio consistently outperformed the other portfolios, and was more robust to ‘errors’ (e.g., when an assumed specific scenario did not occur). On average, the all-scenarios portfolio achieved representation targets for five additional species compared with the current distributions portfolio (approximately 33 versus 28 species). Our findings highlight the importance of considering a broad and meaningful set of scenarios, rather than relying on the current situation, the expected occurrence of specific scenarios, or the worst-case scenario. PMID:29621330

Conservation planning under uncertainty in urban development and vegetation dynamics.

PubMed

Troupin, David; Carmel, Yohay

2018-01-01

Systematic conservation planning is a framework for optimally locating and prioritizing areas for conservation. An often-noted shortcoming of most conservation planning studies is that they do not address future uncertainty. The selection of protected areas that are intended to ensure the long-term persistence of biodiversity is often based on a snapshot of the current situation, ignoring processes such as climate change. Scenarios, in the sense of being accounts of plausible futures, can be utilized to identify conservation area portfolios that are robust to future uncertainty. We compared three approaches for utilizing scenarios in conservation area selection: considering a full set of scenarios (all-scenarios portfolio), assuming the realization of specific scenarios, and a reference strategy based on the current situation (current distributions portfolio). Our objective was to compare the robustness of these approaches in terms of their relative performance across future scenarios. We focused on breeding bird species in Israel's Mediterranean region. We simulated urban development and vegetation dynamics scenarios 60 years into the future using DINAMICA-EGO, a cellular-automata simulation model. For each scenario, we mapped the target species' available habitat distribution, identified conservation priority areas using the site-selection software MARXAN, and constructed conservation area portfolios using the three aforementioned strategies. We then assessed portfolio performance based on the number of species for which representation targets were met in each scenario. The all-scenarios portfolio consistently outperformed the other portfolios, and was more robust to 'errors' (e.g., when an assumed specific scenario did not occur). On average, the all-scenarios portfolio achieved representation targets for five additional species compared with the current distributions portfolio (approximately 33 versus 28 species). Our findings highlight the importance of considering a broad and meaningful set of scenarios, rather than relying on the current situation, the expected occurrence of specific scenarios, or the worst-case scenario.

The alignment of agricultural and nature conservation policies in the European Union.

PubMed

Hodge, Ian; Hauck, Jennifer; Bonn, Aletta

2015-08-01

Europe is a region of relatively high population density and productive agriculture subject to substantial government intervention under the Common Agricultural Policy (CAP). Many habitats and species of high conservation interest have been created by the maintenance of agricultural practices over long periods. These practices are often no longer profitable, and nature conservation initiatives require government support to cover the cost for them to be continued. The CAP has been reformed both to reduce production of agricultural commodities at costs in excess of world prices and to establish incentives for landholders to adopt voluntary conservation measures. A separate nature conservation policy has established an extensive series of protected sites (Natura 2000) that has, as yet, failed to halt the loss of biodiversity. Additional broader scale approaches have been advocated for conservation in the wider landscape matrix, including the alignment of agricultural and nature conservation policies, which remains a challenge. Possibilities for alignment include further shifting of funds from general support for farmers toward targeted payments for biodiversity goals at larger scales and adoption of an ecosystem approach. The European response to the competing demands for land resources may offer lessons globally as demands on rural land increase. © 2015 Society for Conservation Biology.

Membership in conservation groups and outdoor clubs

Treesearch

John C. Hendee

1971-01-01

Conservation groups and outdoor clubs are a major influence on natural resource policy through their articulate members. Different kinds of groups are described - their membership, representativeness, potential growth, multiple memberships, and comparability with other voluntary organizations.

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 preceded) periods of high expenditure on land conservation projects, identifying one mechanism conservation organizations could explore to seed greater activity in priority locations. Our results demonstrate how limitations on the ability of conservation organizations to reallocate their funding across space can impede organizational effectiveness and elucidate ways conservation planning tools could be more useful if they quantified and incorporated these constraints. © 2015 Society for Conservation Biology.

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

PubMed Central

Nelson, William C.; Stegen, James C.

2015-01-01

Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. “Housekeeping” genes and genes for biosynthesis of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle, or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest that the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum. PMID:26257709

Diversity of secretion systems associated with virulence characteristics of the classical bordetellae.

PubMed

Park, Jihye; Zhang, Ying; Chen, Chun; Dudley, Edward G; Harvill, Eric T

2015-12-01

Secretion systems are key virulence factors, modulating interactions between pathogens and the host's immune response. Six potential secretion systems (types 1-6; T1SS-T6SS) have been discussed in classical bordetellae, respiratory commensals/pathogens of mammals. The prototypical Bordetella bronchiseptica strain RB50 genome seems to contain all six systems, whilst two human-restricted subspecies, Bordetella parapertussis and Bordetella pertussis, have lost different subsets of these. This implicates secretion systems in the divergent evolutionary histories that have led to their success in different niches. Based on our previous work demonstrating that changes in secretion systems are associated with virulence characteristics, we hypothesized there would be substantial divergence of the loci encoding each amongst sequenced strains. Here, we describe extensive differences in secretion system loci; 10 of the 11 sequenced strains had lost subsets of genes or one entire secretion system locus. These loci contained genes homologous to those present in the respective loci in distantly related organisms, as well as genes unique to bordetellae, suggesting novel and/or auxiliary functions. The high degree of conservation of the T3SS locus, a complex machine with interdependent parts that must be conserved, stands in dramatic contrast to repeated loss of T5aSS 'autotransporters', which function as an autonomous unit. This comparative analysis provided insights into critical aspects of each pathogen's adaptation to its different niche, and the relative contributions of recombination, mutation and horizontal gene transfer. In addition, the relative conservation of various secretion systems is an important consideration in the ongoing search for more highly conserved protective antigens for the next generation of pertussis vaccines.

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

DOE PAGES

Nelson, William C.; Stegen, James C.

2015-07-21

Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in a broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. “Housekeeping” genes and genes for biosynthesismore » of peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides, and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle, or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest that the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum.« less

The reduced genomes of Parcubacteria (OD1) contain signatures of a symbiotic lifestyle

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

Nelson, William C.; Stegen, James C.

2015-07-21

Candidate phylum OD1 bacteria (also referred to as Parcubacteria) have been identified in broad range of anoxic environments through community survey analysis. Although none of these species have been isolated in the laboratory, several genome sequences have been reconstructed from metagenomic sequence data and single-cell sequencing. The organisms have small (generally <1 Mb) genomes with severely reduced metabolic capabilities. We have reconstructed 8 partial to near-complete OD1 genomes from oxic groundwater samples, and compared them against existing genomic data. The conserved core gene set comprises 202 genes, or ~28% of the genomic complement. ‘Housekeeping’ genes and genes for biosynthesis ofmore » peptidoglycan and Type IV pilus production are conserved. Gene sets for biosynthesis of cofactors, amino acids, nucleotides and fatty acids are absent entirely or greatly reduced. The only aspects of energy metabolism conserved are the non-oxidative branch of the pentose-phosphate shunt and central glycolysis. These organisms also lack some activities conserved in almost all other known bacterial genomes, including signal recognition particle, pseudouridine synthase A, and FAD synthase. Pan-genome analysis indicates a broad genotypic diversity and perhaps a highly fluid gene complement, indicating historical adaptation to a wide range of growth environments and a high degree of specialization. The genomes were examined for signatures suggesting either a free-living, streamlined lifestyle or a symbiotic lifestyle. The lack of biosynthetic capabilities and DNA repair, along with the presence of potential attachment and adhesion proteins suggest the Parcubacteria are ectosymbionts or parasites of other organisms. The wide diversity of genes that potentially mediate cell-cell contact suggests a broad range of partner/prey organisms across the phylum.« less

Comparative analysis of the L, M, and S RNA segments of Crimean-Congo haemorrhagic fever virus isolates from southern Africa.

PubMed

Goedhals, Dominique; Bester, Phillip A; Paweska, Janusz T; Swanepoel, Robert; Burt, Felicity J

2015-05-01

Crimean-Congo haemorrhagic fever virus (CCHFV) is a member of the Bunyaviridae family with a tripartite, negative sense RNA genome. This study used predictive software to analyse the L (large), M (medium), and S (small) segments of 14 southern African CCHFV isolates. The OTU-like cysteine protease domain and the RdRp domain of the L segment are highly conserved among southern African CCHFV isolates. The M segment encodes the structural glycoproteins, GN and GC, and the non-structural glycoproteins which are post-translationally cleaved at highly conserved furin and subtilase SKI-1 cleavage sites. All of the sites previously identified were shown to be conserved among southern African CCHFV isolates. The heavily O-glycosylated N-terminal variable mucin-like domain of the M segment shows the highest sequence variability of the CCHFV proteins. Five transmembrane domains are predicted in the M segment polyprotein resulting in three regions internal to and three regions external to the membrane across the G(N), NS(M) and G(C) glycoproteins. The corroboration of conserved genome domains and sequence identity among geographically diverse isolates may assist in the identification of protein function and pathogenic mechanisms, as well as the identification of potential targets for antiviral therapy and vaccine design. As detailed functional studies are lacking for many of the CCHFV proteins, identification of functional domains by prediction of protein structure, and identification of amino acid level similarity to functionally characterised proteins of related viruses or viruses with similar pathogenic mechanisms are a necessary step for selection of areas for further study. © 2015 Wiley Periodicals, Inc.

Myxobolus cerebralis internal transcribed spacer 1 (ITS-1) sequences support recent spread of the parasite to North America and within Europe

USGS Publications Warehouse

Whipps, Christopher M.; El-Matbouli, M.; Hedrick, R.P.; Blazer, V.; Kent, M.L.

2004-01-01

Molecular approaches for resolving relationships among the Myxozoa have relied mainly on small subunit (SSU) ribosomal DNA (rDNA) sequence analysis. This region of the gene is generally used for higher phylogenetic studies, and the conservative nature of this gene may make it inadequate for intraspecific comparisons. Previous intraspecific studies of Myxobolus cerebralis based on molecular analyses reported that the sequence of SSU rDNA and the internal transcribed spacer (ITS) were highly conserved in representatives of the parasite from North America and Europe. Considering that the ITS is usually a more variable region than the SSU, we reanalyzed available sequences on GenBank and obtained sequences from other M. cerebralis representatives from the states of California and West Virginia in the USA and from Germany and Russia. With the exception of 7 base pairs, most of the sequence designated as ITS-1 in GenBank was a highly conserved portion of the rDNA near the 3-prime end of the SSU region. Nonetheless, the additional ITS-1 sequences obtained from the available geographic representatives were well conserved. It is unlikely that we would have observed virtually identical ITS-1 sequences between European and American M. cerebralis samples had it spread naturally over time, particularly when compared to the variation seen between isolates of another myxozoan (Kudoa thyrsites) that has most likely spread naturally. These data further support the hypothesis that the current distribution of M. cerebralis in North America is a result of recent introductions followed by dispersal via anthropogenic means, largely through the stocking of infected trout for sport fishing.

Amphibian diversity and threatened species in a severely transformed neotropical region in Mexico.

PubMed

Meza-Parral, Yocoyani; Pineda, Eduardo

2015-01-01

Many regions around the world concentrate a large number of highly endangered species that have very restricted distributions. The mountainous region of central Veracruz, Mexico, is considered a priority area for amphibian conservation because of its high level of endemism and the number of threatened species. The original tropical montane cloud forest in the region has been dramatically reduced and fragmented and is now mainly confined to ravines and hillsides. We evaluated the current situation of amphibian diversity in the cloud forest fragments of this region by analyzing species richness and abundance, comparing assemblage structure and species composition, examining the distribution and abundance of threatened species, and identifying the local and landscape variables associated with the observed amphibian diversity. From June to October 2012 we sampled ten forest fragments, investing 944 person-hours of sampling effort. A total of 895 amphibians belonging to 16 species were recorded. Notable differences in species richness, abundance, and assemblage structure between forest fragments were observed. Species composition between pairs of fragments differed by an average of 53%, with the majority (58%) resulting from species replacement and the rest (42%) explained by differences in species richness. Half of the species detected are under threat of extinction according to the International Union for Conservation of Nature, and although their distribution and abundance varied markedly, there were also ubiquitous and abundant species, along with rare species of restricted distribution. The evident heterogeneity of the ten study sites indicates that to conserve amphibians in a mountainous region such as this one it is necessary to protect groups of fragments which represent the variability of the system. Both individually and together cloud forest fragments are very important to conservation because each remnant is inhabited by several threatened species, some of them at imminent risk of extinction.

Targeting ecosystem features for conservation: Standing crops in the Florida Everglades

USGS Publications Warehouse

Turner, A.M.; Trexler, J.C.; Jordan, C.F.; Slack, S.J.; Geddes, P.; Chick, J.H.; Loftus, W.F.

1999-01-01

The Everglades in southern Florida, U.S.A., is a major focus of conservation activities. The freshwater wetlands of the Everglades do not have high species richness, and no species of threatened aquatic animals or plants live there. We have, however, identified a distinctive ecological feature of the Everglades that is threatened by canal construction, draining, and nutrient enrichment from agricultural runoff compared to values reported from other freshwater systems, standing stocks of periphyton in relatively undisturbed areas of the Everglades were unusually high, and standing stocks of invertebrates and fish were unusually low. Averaging data gathered from nine sites and five sampling periods spanning I year, we found that periphyton standing crop was 88.2 g/m2 (ash-free dry mass), invertebrate standing stock was 0.64 g/m2 (dry mass), and fish standing stock was 1.2 g/m2 (dry mass of large and small species combined). We found that fish standing stocks were much higher in phosphorus-enriched sites than in nearby reference sites but that invertebrate standing stocks were similar in enriched and reference sites. Our results support the notion that oligotrophy is at least partially responsible for the low standing stocks of fish, but they also suggest that species interactions and a paucity of deep-water refugia are important. Anthropogenic eutrophication in Everglades marshes will lead to the loss of distinctive ecosystem features. A focus on species richness and 'hot spots' of threatened species provides no basis for conservation of ecosystems like the Everglades. If oligotrophic ecosystems often have low species richness, they will be underrepresented in preservation networks based on some common criteria for establishing conservation priorities.