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Sample records for identify species suitable

  1. Identifying plant traits: a key aspect for suitable species selection in ecological restoration of semiarid slopes

    Science.gov (United States)

    Bochet, Esther; García-Fayos, Patricio

    2017-04-01

    In the context of ecological restoration, one of the greatest challenges for practitioners and scientists is to select suitable species for revegetation purposes. In semiarid environments where restoration projects often fail, little attention has been paid so far to the contribution of plant traits to species success. The objective of this study was to (1) identify plant traits associated with species success on four roadside situations along an erosion-productivity gradient, and (2) to provide an ecological framework for selecting suitable species on the basis of their morphological and functional traits, applied to semiarid environments. We analyzed the association of 10 different plant traits with species success of 296 species surveyed on the four roadside situations in a semiarid region (Valencia, Spain). Plant traits included general plant traits (longevity, woodiness) and more specific root-, seed- and leaf-related traits (root type, sprouting ability, seed mucilage, seed mass, seed susceptibility to removal, specific leaf area and leaf dry matter content). All of them were selected according to the prevailing limiting ecogeomorphological processes acting along the erosion-productivity gradient. We observed strong shifts along the erosion-productivity gradient in the traits associated to species success. At the harshest end of the gradient, the most intensely eroded and driest one, species success was mainly associated to seed resistance to removal by runoff and to resistance to drought. At the opposite end of the gradient, the most productive one, species success was associated to a competitive-ruderal plant strategy (herbaceous successful species with high specific leaf area and low leaf dry matter content). Our study provides an ecologically-based approach for selecting suitable native species on the basis or their morphological and functional traits and supports a differential trait-based selection of species as regards roadslope type and aspect. In

  2. Multi-locus DNA barcoding identifies matK as a suitable marker for species identification in Hibiscus L.

    Science.gov (United States)

    Poovitha, Sundar; Stalin, Nithaniyal; Balaji, Raju; Parani, Madasamy

    2016-12-01

    The genus Hibiscus L. includes several taxa of medicinal value and species used for the extraction of natural dyes. These applications require the use of authentic plant materials. DNA barcoding is a molecular method for species identification, which helps in reliable authentication by using one or more DNA barcode marker. In this study, we have collected 44 accessions, representing 16 species of Hibiscus, distributed in the southern peninsular India, to evaluate the discriminatory power of the two core barcodes rbcLa and matK together with the suggested additional regions trnH-psbA and ITS2. No intraspecies divergence was observed among the accessions studied. Interspecies divergence was 0%-9.6% with individual markers, which increased to 0%-12.5% and 0.8%-20.3% when using two- and three-marker combinations, respectively. Differentiation of all the species of Hibiscus was possible with the matK DNA barcode marker. Also, in two-marker combinations, only those combinations with matK differentiated all the species. Though all the three-marker combinations showed 100% species differentiation, species resolution was consistently better when the matK marker formed part of the combination. These results clearly showed that matK is more suitable when compared to rbcLa, trnH-psbA, and ITS2 for species identification in Hibiscus.

  3. Identifying suitable sites for Florida panther reintroduction

    Science.gov (United States)

    Thatcher, Cindy A.; van Manen, Frank T.; Clark, Joseph D.

    2006-01-01

    A major objective of the 1995 Florida Panther (Puma concolor cory) Recovery Plan is the establishment of 2 additional panther populations within the historic range. Our goal was to identify prospective sites for Florida panther reintroduction within the historic range based on quantitative landscape assessments. First, we delineated 86 panther home ranges using telemetry data collected from 1981 to 2001 in south Florida to develop a Mahalanobis distance (D2) habitat model, using 4 anthropogenic variables and 3 landscape variables mapped at a 500-m resolution. From that analysis, we identified 9 potential reintroduction sites of sufficient size to support a panther population. We then developed a similar D2 model at a higher spatial resolution to quantify the area of favorable panther habitat at each site. To address potential for the population to expand, we calculated the amount of favorable habitat adjacent to each prospective reintroduction site within a range of dispersal distances of female panthers. We then added those totals to the contiguous patches to estimate the total amount of effective panther habitat at each site. Finally, we developed an expert-assisted model to rank and incorporate potentially important habitat variables that were not appropriate for our empirical analysis (e.g., area of public lands, livestock density). Anthropogenic factors heavily influenced both the landscape and the expert-assisted models. Of the 9 areas we identified, the Okefenokee National Wildlife Refuge, Ozark National Forest, and Felsenthal National Wildlife Refuge regions had the highest combination of effective habitat area and expert opinion scores. Sensitivity analyses indicated that variability among key model parameters did not affect the high ranking of those sites. Those sites should be considered as starting points for the field evaluation of potential reintroduction sites.

  4. Using habitat suitability models to target invasive plant species surveys.

    Science.gov (United States)

    Crall, Alycia W; Jarnevich, Catherine S; Panke, Brendon; Young, Nick; Renz, Mark; Morisette, Jeffrey

    2013-01-01

    Managers need new tools for detecting the movement and spread of nonnative, invasive species. Habitat suitability models are a popular tool for mapping the potential distribution of current invaders, but the ability of these models to prioritize monitoring efforts has not been tested in the field. We tested the utility of an iterative sampling design (i.e., models based on field observations used to guide subsequent field data collection to improve the model), hypothesizing that model performance would increase when new data were gathered from targeted sampling using criteria based on the initial model results. We also tested the ability of habitat suitability models to predict the spread of invasive species, hypothesizing that models would accurately predict occurrences in the field, and that the use of targeted sampling would detect more species with less sampling effort than a nontargeted approach. We tested these hypotheses on two species at the state scale (Centaurea stoebe and Pastinaca sativa) in Wisconsin (USA), and one genus at the regional scale (Tamarix) in the western United States. These initial data were merged with environmental data at 30-m2 resolution for Wisconsin and 1-km2 resolution for the western United States to produce our first iteration models. We stratified these initial models to target field sampling and compared our models and success at detecting our species of interest to other surveys being conducted during the same field season (i.e., nontargeted sampling). Although more data did not always improve our models based on correct classification rate (CCR), sensitivity, specificity, kappa, or area under the curve (AUC), our models generated from targeted sampling data always performed better than models generated from nontargeted data. For Wisconsin species, the model described actual locations in the field fairly well (kappa = 0.51, 0.19, P guiding invasive species monitoring, and we support the use of an iterative sampling design for

  5. Suitability

    NARCIS (Netherlands)

    Bokdam, J.; Braeckel, van A.

    2002-01-01

    The suitability of grazing, burning, mowing and cutting as tools for succession control in peatland was assessed and expressed on a scale from 0 - 1. All management tools are suitable, but their effects are conditional. The suitability depends on the targeted vegetation transition and on their

  6. Identifying Areas Suitable for the Occurrence of Rift Valley Fever in North Africa: Implications for Surveillance.

    Science.gov (United States)

    Arsevska, E; Hellal, J; Mejri, S; Hammami, S; Marianneau, P; Calavas, D; Hénaux, V

    2016-12-01

    Rift Valley fever (RVF) is a vector-borne zoonotic disease that has caused widespread outbreaks throughout Africa and the Arabian Peninsula, with serious consequences for livestock-based economies and public health. Although there have never been any reports of RVF in Morocco, Algeria, Tunisia and Libya, it is a priority disease in the Maghreb, due to the threat of introduction of the virus through transboundary livestock movements or infected mosquito vectors. However, the implementation of surveillance activities and early warning contingency plans requires better knowledge of the epidemiological situation. We conducted a multicriteria decision analysis, integrating host distribution with a combination of important ecological factors that drive mosquito abundance, to identify hotspots and suitable time periods for RVF enzootic circulation (i.e. stable transmission at a low to moderate level for an extended period of time) and an RVF epizootic event (i.e. a sudden occurrence of a large number of infected animals over a large geographic area) in the Maghreb. We also modelled vector species distribution using available information on vector presence and habitat preference. We found that the northern regions of the Maghreb were moderately suitable for RVF enzootics, but highly suitable for RVF epizootics. The vector species distribution model identified these regions as the most favourable mosquito habitats. Due to the low density of animal hosts and arid conditions, the desert region showed low RVF suitability, except in oases. However, the presence of competent vectors in putative unsuitable areas underlines the need for further assessments of mosquito habitat preference. This study produced monthly RVF suitability maps useful for animal health managers and veterinary services involved in designing risk-based surveillance programmes. The suitability maps can be further enhanced using existing country-specific sources of information and by incorporating knowledge

  7. Identifying suitable piercement salt domes for nuclear waste storage sites

    International Nuclear Information System (INIS)

    Kehle, R.; e.

    1980-08-01

    Piercement salt domes of the northern interior salt basins of the Gulf of Mexico are being considered as permanent storage sites for both nuclear and chemically toxic wastes. The suitable domes are stable and inactive, having reached their final evolutionary configuration at least 30 million years ago. They are buried to depths far below the level to which erosion will penetrate during the prescribed storage period and are not subject to possible future reactivation. The salt cores of these domes are themselves impermeable, permitting neither the entry nor exit of ground water or other unwanted materials. In part, a stable dome may be recognized by its present geometric configuration, but conclusive proof depends on establishing its evolutionary state. The evolutionary state of a dome is obtained by reconstructing the growth history of the dome as revealed by the configuration of sedimentary strata in a large area (commonly 3,000 square miles or more) surrounding the dome. A high quality, multifold CDP reflection seismic profile across a candidate dome will provide much of the necessary information when integrated with available subsurface control. Additional seismic profiles may be required to confirm an apparent configuration of the surrounding strata and an interpreted evolutionary history. High frequency seismic data collected in the near vicinity of a dome are also needed as a supplement to the CDP data to permit accurate depiction of the configuration of shallow strata. Such data must be tied to shallow drill hole control to confirm the geologic age at which dome growth ceased. If it is determined that a dome reached a terminal configuration many millions of years ago, such a dome is incapable of reactivation and thus constitutes a stable storage site for nuclear wastes

  8. Predicting habitat suitability for rare plants at local spatial scales using a species distribution model.

    Science.gov (United States)

    Gogol-Prokurat, Melanie

    2011-01-01

    were not available at large extents. No single model met all habitat prioritization criteria, and the best models were overlaid to identify consensus areas of high suitability. Although the four species modeled here co-occur and are treated together for conservation planning, model accuracy and predicted suitable areas varied among species.

  9. The right tree for the job? perceptions of species suitability for the provision of ecosystem services.

    Science.gov (United States)

    Smaill, Simeon J; Bayne, Karen M; Coker, Graham W R; Paul, Thomas S H; Clinton, Peter W

    2014-04-01

    Stakeholders in plantation forestry are increasingly aware of the importance of the ecosystem services and non-market values associated with forests. In New Zealand, there is significant interest in establishing species other than Pinus radiata D. Don (the dominant plantation species) in the belief that alternative species are better suited to deliver these services. Significant risk is associated with this position as there is little objective data to support these views. To identify which species were likely to be planted to deliver ecosystem services, a survey was distributed to examine stakeholder perceptions. Stakeholders were asked which of 15 tree attributes contributed to the provision of five ecosystem services (amenity value, bioenergy production, carbon capture, the diversity of native habitat, and erosion control/water quality) and to identify which of 22 candidate tree species possessed those attributes. These data were combined to identify the species perceived most suitable for the delivery of each ecosystem service. Sequoia sempervirens (D.Don) Endl. closely matched the stakeholder derived ideotypes associated with all five ecosystem services. Comparisons to data from growth, physiological and ecological studies demonstrated that many of the opinions held by stakeholders were inaccurate, leading to erroneous assumptions regarding the suitability of most candidate species. Stakeholder perceptions substantially influence tree species selection, and plantations established on the basis of inaccurate opinions are unlikely to deliver the desired outcomes. Attitudinal surveys associated with engagement campaigns are essential to improve stakeholder knowledge, advancing the development of fit-for-purpose forest management that provides the required ecosystem services.

  10. Suitability of Selected Coral Species for Culture in the Ornamental ...

    African Journals Online (AJOL)

    Eldoret, Kenya; 3Kenya Tropical Sea Life, PO Box 10570-80101 Bamburi, Kenya. Keywords: ..... temperatures to rise above that of the open sea during the NEM ... At the species level, A. humilis exhibited the highest survival ..... in Florida. Proceedings of the 11th. International Coral Reef Symposium,. Ft Lauderdale, Florida ...

  11. Identifying ambassador species for conservation marketing

    Directory of Open Access Journals (Sweden)

    E.A. Macdonald

    2017-10-01

    Full Text Available Conservation relies heavily on external funding, much of it from a supportive public. Therefore it is important to know which species are most likely to catalyse such funding. Whilst previous work has looked at the physical attributes that contribute to a species' appeal, no previous studies have tried to examine the extent to which a species' sympatriots might contribute to it's potential as flagship for wider conservation. Therefore, here we estimate ‘flexibility’ and ‘appeal’ scores for all terrestrial mammals (n = 4320 and identify which of these might serve as ambassadors (defined as both highly appealing and flexible. Relatively few mammals (between 240 and 331 emerged as ambassadors, with carnivores featuring heavily in this group (representing 5% of terrestrial mammals but 39% of ambassadors. ‘Top ambassadors’ were defined as those with both flexibility and appeal scores greater than 1 standard deviation above the mean. Less than a quarter of the 20 most endangered and evolutionary distinct species in this study were classed as ambassadors, highlighting the need for surrogate species to catalyse conservation effort in areas with such priority species. This is the first global analysis bringing together flexibility and appeal for all terrestrial mammals, and demonstrates an approach for determining how best to market species in order to achieve maximal conservation gain in a world with urgent conservation need but limited resources.

  12. IDENTIFYING OPERATIONAL REQUIREMENTS TO SELECT SUITABLE DECISION MODELS FOR A PUBLIC SECTOR EPROCUREMENT DECISION SUPPORT SYSTEM

    Directory of Open Access Journals (Sweden)

    Mohamed Adil

    2014-10-01

    Full Text Available Public sector procurement should be a transparent and fair process. Strict legal requirements are enforced on public sector procurement to make it a standardised process. To make fair decisions on selecting suppliers, a practical method which adheres to legal requirements is important. The research that is the base for this paper aimed at identifying a suitable Multi-Criteria Decision Analysis (MCDA method for the specific legal and functional needs of the Maldivian Public Sector. To identify such operational requirements, a set of focus group interviews were conducted in the Maldives with public officials responsible for procurement decision making. Based on the operational requirements identified through focus groups, criteria-based evaluation is done on published MCDA methods to identify the suitable methods for e-procurement decision making. This paper describes the identification of the operational requirements and the results of the evaluation to select suitable decision models for the Maldivian context.

  13. Increase in quantity and quality of suitable areas for invasive species as climate changes.

    Science.gov (United States)

    Bertelsmeier, Cleo; Luque, Gloria M; Courchamp, Franck

    2013-12-01

    As climatically suitable range projections become increasingly used to assess distributions of species, we recommend systematic assessments of the quality of habitat in addition to the classical binary classification of habitat. We devised a method to assess occurrence probability, captured by a climatic suitability index, through which we could determine variations in the quality of potential habitat. This relative risk assessment circumvents the use of an arbitrary suitability threshold. We illustrated our method with 2 case studies on invasive ant species. We estimated invasion potential of the destroyer ant (Monomorium destructor) and the European fire ant (Myrmica rubra) on a global scale currently and by 2080 with climate change. We found that 21.1% of the world's landmass currently has a suitable climate for the destroyer ant and 16% has a suitable climate for European fire ant. Our climatic suitability index showed that both ant species would benefit from climate change, but in different ways. The size of the potential distribution increased by 35.8% for the destroyer ant. Meanwhile, the total area of potential distribution remained the same for the European fire ant (>0.05%), but the level of climatic suitability within this range increased greatly and led to an improvement in habitat quality (i.e., of invasive species' establishment likelihood). Either through quantity or quality of suitable areas, both invasive ant species are likely to increase the extent of their invasion in the future, following global climate change. Our results show that species may increase their range if either more areas become suitable or if the available areas present improved suitability. Studies in which an arbitrary suitability threshold was used may overlook changes in area quality within climatically suitable areas and as a result reach incorrect predictions. Incremento de la Cantidad y Calidad de Áreas Idóneas para Especies Invasoras a Medida que Cambia el Clima.

  14. The suitability of selected wood species in the production of turned ...

    African Journals Online (AJOL)

    The study investigated the suitability of selected wood species in the production of turned glue-laminated products. Five different wood species of high quality grades which were sourced from Bodija market Ibadan, south western Nigeria were thoroughly examined where the moisture content, density and shrinkage ...

  15. Suitable woody species for a land application alternative to pulp and paper mill wastewater disposal

    International Nuclear Information System (INIS)

    Aw, M.; Wagner, M.R.

    1993-01-01

    Saline pulp and paper wastewater produced by Stone Container Corporation in Snowflake, Arizona was used to irrigate 32 different species/genotypes/hybrids of woody plants to test their suitability as an alternative treatment to the current wastewater disposal method. Suitability was measured in terms of survival and height growth. Among the 32 species, six were found to be a very good choice for wastewater treatment and biomass production. Their suitability is further justified by the fact that some have salt tolerance and others fix nitrogen. These species are Tamarix ramosissima, Atriplex canescens, Robinia pseudoacacia, Eleagnus angustifoliz, Ulmus pumila, and Populus deltoides x Populus nigra. Three other species are possible candidates. These include Caragana arborescens, Gleditsia triacanthos and Populus deltoides var. siouxland. In general, conifers performed poorly because of the harsh environment and other silvicultural problems

  16. Predicting Environmental Suitability for a Rare and Threatened Species (Lao Newt, Laotriton laoensis) Using Validated Species Distribution Models

    Science.gov (United States)

    Chunco, Amanda J.; Phimmachak, Somphouthone; Sivongxay, Niane; Stuart, Bryan L.

    2013-01-01

    The Lao newt (Laotriton laoensis) is a recently described species currently known only from northern Laos. Little is known about the species, but it is threatened as a result of overharvesting. We integrated field survey results with climate and altitude data to predict the geographic distribution of this species using the niche modeling program Maxent, and we validated these predictions by using interviews with local residents to confirm model predictions of presence and absence. The results of the validated Maxent models were then used to characterize the environmental conditions of areas predicted suitable for L. laoensis. Finally, we overlaid the resulting model with a map of current national protected areas in Laos to determine whether or not any land predicted to be suitable for this species is coincident with a national protected area. We found that both area under the curve (AUC) values and interview data provided strong support for the predictive power of these models, and we suggest that interview data could be used more widely in species distribution niche modeling. Our results further indicated that this species is mostly likely geographically restricted to high altitude regions (i.e., over 1,000 m elevation) in northern Laos and that only a minute fraction of suitable habitat is currently protected. This work thus emphasizes that increased protection efforts, including listing this species as endangered and the establishment of protected areas in the region predicted to be suitable for L. laoensis, are urgently needed. PMID:23555808

  17. Identifying Farm Pond Habitat Suitability for the Common Moorhen (Gallinula chloropus: A Conservation-Perspective Approach

    Directory of Open Access Journals (Sweden)

    Chun-Hsien Lai

    2018-04-01

    Full Text Available The purpose of this study was to establish a habitat-suitability assessment model for Gallinula chloropus, or the Common Moorhen, to be applied to the selection of the most suitable farm pond for habitat conservation in Chiayi County, Taiwan. First, the fuzzy Delphi method was employed to evaluate habitat selection factors and calculate the weights of these factors. The results showed that the eight crucial factors, by importance, in descending order, were (1 area ratio of farmlands within 200 m of the farm pond; (2 pond area; (3 pond perimeter; (4 aquatic plant coverage of the pond surface; (5 drought period; (6 coverage of high and low shrubs around the pond bank; (7 bank type; and (8 water-surface-to-bank distance. Subsequently, field evaluations of 75 farm ponds in Chiayi County were performed. The results indicated that 15 farm ponds had highly-suitable habitats and were inhabited by unusually high numbers of Common Moorhens; these habitats were most in need of conservation. A total of two farm ponds were found to require habitat-environment improvements, and Common Moorhens with typical reproductive capacity could be appropriately introduced into 22 farm ponds to restore the ecosystem of the species. Additionally, the habitat suitability and number of Common Moorhens in 36 farm ponds were lower than average; these ponds could be used for agricultural irrigation, detention basins, or for recreational use by community residents. Finally, the total habitat suitability scores and occurrence of Common Moorhens in each farm pond were used to verify the accuracy of the habitat-suitability assessment model for the Common Moorhen. The overall accuracy was 0.8, and the Kappa value was 0.60, which indicates that the model established in this study exhibited high credibility. To sum up, this is an applicable framework not only to assess the habitat suitability of farm ponds for Common Moorhens, but also to determine whether a particular location may

  18. Determination of the suitability of certain deciduous species for production of furfural and charcoal

    Energy Technology Data Exchange (ETDEWEB)

    Piotrowski, P.

    1979-01-01

    Determination of the suitability of chips of certain deciduous species for production of furfural and charcoal is discussed. The results of determination of suitability of unpeeled chips from cut branches (beech, birch, alder) and oak chips from wastes of production of furfural and also the suitability of cellolignin obtained from these chips for the production of charcoal are cited. An industrial unit of Swedish make equipped with a continuous hydrolyzer was used in hydrolysis tests of the deciduous chips. Unstripped birch, beech, and alder chips and oak chips from the wastes of wood processing contained 17-20 percent pentozanes and are suitable for industrial production of furfural. The content of substances soluble in an alcohol-benzene mixture in cellolignin from this feedstock was 21.1-30.5 percent. The amount of cellolignin obtained from chips of these species satisfied the demands of charcoal production. The charcoal yield was approximately 20 percent relative to the dry mass of carbonized cellolignin.

  19. Edible insects - species suitable for entomophagy under condition of Czech Republic

    Directory of Open Access Journals (Sweden)

    Martina Bednářová

    2013-01-01

    Full Text Available Since 2002, when the first lecture on entomophagy took place at Mendel University in Brno, till today, participants of these educational lectures were asked to fill questionnaires in order to evaluate interest in entomophagy in Czech Republic and pick suitable species. Analyses of nutritional value of selected species were also performed during this time. The questionnaire was divided into several parts - suitable species, sensory properties, difficulty of breeding and processing and respondents own attitude to the consumption of insect species. For the purpose of this study the questionnaire was evaluated using the semantic differential, so to create a comprehensive picture of each insect species. Based on evaluation of more than 5,000 questionnaires, certain developmental stages of seven species of insect were selected for further evaluation: Tenebrio molitor (TM larvae, Zophobas morio (ZM larvae, Gryllus assimillis (GA nymphs, Locusta migratoria (LM nymphs, Galleria mellonella (GM larvae, Bombyx mori (BM Pupa, Apis mellifera (AM bee brood, while cockroaches were completely excluded for use in entomophagy. Although they are easy to breed and are available all year-round, consumers showed relatively great disgust. For all of these species, basic nutritional values were analysed, as well as content of amino acids and fattty acids. All parameters were statistically evaluated using ANOVA-1. Each species appears to be suitable for entomophagy for a different reason. Generally speaking, AM, TM and GA were best accepted considering the sensory aspect, nutritional values are interesting especially in BM and GM and TM wins with simplicity of its breeding.

  20. Global estimation of areas with suitable environmental conditions for mariculture species.

    Directory of Open Access Journals (Sweden)

    Muhammed A Oyinlola

    Full Text Available Aquaculture has grown rapidly over the last three decades expanding at an average annual growth rate of 5.8% (2005-2014, down from 8.8% achieved between 1980 and 2010. The sector now produces 44% of total food fish production. Increasing demand and consumption from a growing global population are driving further expansion of both inland and marine aquaculture (i.e., mariculture, including marine species farmed on land. However, the growth of mariculture is dependent on the availability of suitable farming areas for new facilities, particularly for open farming practices that rely on the natural oceanic environmental parameters such as temperature, oxygen, chlorophyll etc. In this study, we estimated the marine areas within the exclusive economic zones of all countries that were suitable for potential open ocean mariculture activities. To this end, we quantify the environmental niche and inferred the global habitat suitability index (HSI of the 102 most farmed marine species using four species distribution models. The average weighted HSI across the four models suggests that 72,000,000 km2 of ocean are to be environmentally suitable to farm one or more species. About 92% of the predicted area (66,000,000 km2 is environmentally suitable for farming finfish, 43% (31,000,000 km2 for molluscs and 54% (39,000,000 km2 for crustaceans. These predictions do not consider technological feasibility that can limit crustaceans farming in open waters. Suitable mariculture areas along the Atlantic coast of South America and West Africa appear to be most under-utilized for farming. Our results suggest that factors other than environmental considerations such as the lack of socio-economic and technological capacity, as well as aqua feed supply are currently limiting the potential for mariculture expansion in many areas.

  1. Shaken but not stirred: Multiscale habitat suitability modeling of sympatric marten species (Martes martes and Martes foina) in the northern Iberian Peninsula

    Science.gov (United States)

    Maria Vergara; Samuel A. Cushman; Fermin Urra; Aritz Ruiz-Gonzalez

    2016-01-01

    Multispecies and multiscale habitat suitability models (HSM) are important to identify the environmental variables and scales influencing habitat selection and facilitate the comparison of closely related species with different ecological requirements. Objectives This study explores the multiscale relationships of habitat suitability for the pine (Martes...

  2. CENTRAL KALIMANTAN’S FAST GROWING SPECIES: SUITABILITY FOR PULP AND PAPER

    Directory of Open Access Journals (Sweden)

    Danang Sudarwoko Adi

    2015-04-01

    Full Text Available Recent studies of fast growing species grown in PT. Sari Bumi Kusuma, Central Kalimantan, show that based on their fiber dimensions there are five species, namely Endospermum diadenum, Dillenia spp., Adinandra dumosa, Adiandra sp., and Nauclea junghuhnii with good potential for pulp and paper production. The fiber length of those five wood species are was more than 2,200 µm on average. This paper studies the physical properties, fiber dimensions and their chemical contents to predict the paper and pulp quality. The result shows that all of the species were classified in the medium to high density category. All species were classified into the first class quality for pulp and paper. Based on chemical contents, Dillenia sp. is the most suitable species due to its high value of holocellulose and a-cellulose, low lignin content, and its fiber length is about 3,119 µm on average. A. dumosa also has good opportunities because it had the longest fiber lengths (3,137 µm on average and high value of holocellulose, even though it has the highest lignin content. While Nuclea junghuhnii is less suitable due to low values of holocellulose and a-cellulose.

  3. High Resolution Habitat Suitability Modelling For Restricted-Range Hawaiian Alpine Arthropod Species

    Science.gov (United States)

    Stephenson, N. M.

    2016-12-01

    Mapping potentially suitable habitat is critical for effective species conservation and management but can be challenging in areas exhibiting complex heterogeneity. An approach that combines non-intrusive spatial data collection techniques and field data can lead to a better understanding of landscapes and species distributions. Nysius wekiuicola, commonly known as the wēkiu bug, is the most studied arthropod species endemic to the Maunakea summit in Hawai`i, yet details about its geographic distribution and habitat use remain poorly understood. To predict the geographic distribution of N. wekiuicola, MaxEnt habitat suitability models were generated from a diverse set of input variables, including fifteen years of species occurrence data, high resolution digital elevation models, surface mineralogy maps derived from hyperspectral remote sensing, and climate data. Model results indicate that elevation (78.2 percent), and the presence of nanocrystalline hematite surface minerals (13.7 percent) had the highest influence, with lesser contributions from aspect, slope, and other surface mineral classes. Climatic variables were not included in the final analysis due to auto-correlation and coarse spatial resolution. Biotic factors relating to predation and competition also likely dictate wēkiu bug capture patterns and influence our results. The wēkiu bug range and habitat suitability models generated as a result of this study will be directly incorporated into management and restoration goals for the summit region and can also be adapted for other arthropod species present, leading to a more holistic understanding of metacommunity dynamics. Key words: Microhabitat, Structure from Motion, Lidar, MaxEnt, Habitat Suitability

  4. Comparative study of the suitability of two lichen species for trace element atmospheric monitoring

    Energy Technology Data Exchange (ETDEWEB)

    Saiki, Mitiko; Alves, Edson R.; Genezini, Frederico A., E-mail: mitiko@ipen.br, E-mail: eralves@ipen.br, E-mail: fredzini@ipen.br [Instituto de Pesquisas Energeticas e Nucleares (IPEN-CNEN-SP), Sao Paulo, SP (Brazil); Saldiva, Paulo H.N., E-mail: pepino@usp.br [Universidade de Sao Paulo (USP), Sao Paulo, SP (Brazil). Faculdade de Medicina

    2013-07-01

    Lichens have been widely used in monitoring studies. Consequently, it is very useful to study the suitability of lichen species to monitor pollutants allowing in this way the best choice. The aim of this study was to compare the accumulation of trace elements by two epiphytic lichen species Canoparmelia texana (Tuck) Elix and Hale and Usnea amblyoclada (Mull. Arg.) Zahlbr. Five samples of each species were collected during the period from November 2010 in a same site far from downtown Sao Paulo city. Lichens collected from tree barks were cleaned, freeze-dried, ground and analyzed by neutron activation analysis. Aliquots of lichen samples and synthetic elemental standards were irradiated at the IEA-R1 nuclear research reactor. The induced gamma activities were measured using a hyperpure Ge detector coupled to a digital spectrum analyzer. Concentrations of As, Ba, Cd, Cr, Cs, Fe, Mg, Mn, Na, Rb, V and Zn were determined in both lichen species. The results demonstrated that both species can be used for evaluating air quality. The element concentrations showed difference between lichen species and also among their sampling periods. These differences may be attributed to the distinct mechanisms of element absorption by lichens as well as various other factors that affect their element accumulation. The comparative evaluation made calculating the ratios between C. texana species sample and that in Usnea amblyoclada for elemental concentrations indicated that, in general, foliose C. texana present similar or higher concentrations than those presented by fruticose Usnea. (author)

  5. Insights into the CuO nanoparticle ecotoxicity with suitable marine model species.

    Science.gov (United States)

    Rotini, A; Gallo, A; Parlapiano, I; Berducci, M T; Boni, R; Tosti, E; Prato, E; Maggi, C; Cicero, A M; Migliore, L; Manfra, L

    2018-01-01

    Metal oxide nanoparticles, among them copper oxide nanoparticles (CuO NPs), are widely used in different applications (e.g. batteries, gas sensors, superconductors, plastics and metallic coatings), increasing their potential release in the environment. In aquatic matrix, the behavior of CuO NPs may strongly change, depending on their surface charge and some physical-chemical characteristics of the medium (e.g. ionic strength, salinity, pH and natural organic matter content). Ecotoxicity of CuO NPs to aquatic organisms was mainly studied on freshwater species, few tests being performed on marine biota. The aim of this study was to assess the toxicity of CuO NPs on suitable indicator species, belonging to the ecologically relevant level of consumers. The selected bioassays use reference protocols to identify Effect/Lethal Concentrations (E(L)C), by assessing lethal and sub-lethal endpoints. Mortality tests were performed on rotifer (Brachionus plicatilis), shrimp (Artemia franciscana) and copepod (Tigriopus fulvus). While moult release failure and fertilization rate were studied, as sub-lethal endpoints, on T. fulvus and sea urchin (Paracentrotus lividus), respectively. The size distribution and sedimentation rates of CuO NPs, together with the copper dissolution, were also analyzed in the exposure media. The CuO NP ecotoxicity assessment showed a concentration-dependent response for all species, indicating similar mortality for B. plicatilis (48hLC 50 = 16.94 ± 2.68mg/l) and T. fulvus (96hLC 50 = 12.35 ± 0.48mg/l), followed by A. franciscana (48hLC 50 = 64.55 ± 3.54mg/l). Comparable EC 50 values were also obtained for the sub-lethal endpoints in P. lividus (EC 50 = 2.28 ± 0.06mg/l) and T. fulvus (EC 50 = 2.38 ± 0.20mg/l). Copper salts showed higher toxicity than CuO NPs for all species, with common sensitivity trend as follows: P. lividus ≥ T. fulvus (sublethal endpoint) ≥ B. plicatilis >T. fulvus (lethal endpoint) >A. franciscana. CuO NP micrometric

  6. Identifying Suitable Locations for Mesophotic Hard Corals Offshore of Maui, Hawai'i.

    Directory of Open Access Journals (Sweden)

    Bryan Costa

    Full Text Available Mesophotic hard corals (MHC are increasingly threatened by a growing number of anthropogenic stressors, including impacts from fishing, land-based sources of pollution, and ocean acidification. However, little is known about their geographic distributions (particularly around the Pacific islands because it is logistically challenging and expensive to gather data in the 30 to 150 meter depth range where these organisms typically live. The goal of this study was to begin to fill this knowledge gap by modelling and predicting the spatial distribution of three genera of mesophotic hard corals offshore of Maui in the Main Hawaiian Islands. Maximum Entropy modeling software was used to create separate maps of predicted probability of occurrence and uncertainty for: (1 Leptoseris, (2 Montipora, and (3 Porites. Genera prevalence was derived from the in situ presence/absence data, and used to convert relative habitat suitability to probability of occurrence values. Approximately 1,300 georeferenced records of the occurrence of MHC, and 34 environmental predictors were used to train the model ensembles. Receiver Operating Characteristic (ROC Area Under the Curve (AUC values were between 0.89 and 0.97, indicating excellent overall model performance. Mean uncertainty and mean absolute error for the spatial predictions ranged from 0.006% to 0.05% and 3.73% to 17.6%, respectively. Depth, distance from shore, euphotic depth (mean and standard deviation and sea surface temperature (mean and standard deviation were identified as the six most influential predictor variables for partitioning habitats among the three genera. MHC were concentrated between Hanaka'ō'ō and Papawai Points offshore of western Maui most likely because this area hosts warmer, clearer and calmer water conditions almost year round. While these predictions helped to fill some knowledge gaps offshore of Maui, many information gaps remain in the Hawaiian Archipelago and Pacific Islands. This

  7. Modelling seasonal habitat suitability for wide-ranging species: Invasive wild pigs in northern Australia.

    Directory of Open Access Journals (Sweden)

    Jens G Froese

    Full Text Available Invasive wildlife often causes serious damage to the economy and agriculture as well as environmental, human and animal health. Habitat models can fill knowledge gaps about species distributions and assist planning to mitigate impacts. Yet, model accuracy and utility may be compromised by small study areas and limited integration of species ecology or temporal variability. Here we modelled seasonal habitat suitability for wild pigs, a widespread and harmful invader, in northern Australia. We developed a resource-based, spatially-explicit and regional-scale approach using Bayesian networks and spatial pattern suitability analysis. We integrated important ecological factors such as variability in environmental conditions, breeding requirements and home range movements. The habitat model was parameterized during a structured, iterative expert elicitation process and applied to a wet season and a dry season scenario. Model performance and uncertainty was evaluated against independent distributional data sets. Validation results showed that an expert-averaged model accurately predicted empirical wild pig presences in northern Australia for both seasonal scenarios. Model uncertainty was largely associated with different expert assumptions about wild pigs' resource-seeking home range movements. Habitat suitability varied considerably between seasons, retracting to resource-abundant rainforest, wetland and agricultural refuge areas during the dry season and expanding widely into surrounding grassland floodplains, savanna woodlands and coastal shrubs during the wet season. Overall, our model suggested that suitable wild pig habitat is less widely available in northern Australia than previously thought. Mapped results may be used to quantify impacts, assess risks, justify management investments and target control activities. Our methods are applicable to other wide-ranging species, especially in data-poor situations.

  8. Rigorous Screening Technology for Identifying Suitable CO2 Storage Sites II

    Energy Technology Data Exchange (ETDEWEB)

    George J. Koperna Jr.; Vello A. Kuuskraa; David E. Riestenberg; Aiysha Sultana; Tyler Van Leeuwen

    2009-06-01

    This report serves as the final technical report and users manual for the 'Rigorous Screening Technology for Identifying Suitable CO2 Storage Sites II SBIR project. Advanced Resources International has developed a screening tool by which users can technically screen, assess the storage capacity and quantify the costs of CO2 storage in four types of CO2 storage reservoirs. These include CO2-enhanced oil recovery reservoirs, depleted oil and gas fields (non-enhanced oil recovery candidates), deep coal seems that are amenable to CO2-enhanced methane recovery, and saline reservoirs. The screening function assessed whether the reservoir could likely serve as a safe, long-term CO2 storage reservoir. The storage capacity assessment uses rigorous reservoir simulation models to determine the timing, ultimate storage capacity, and potential for enhanced hydrocarbon recovery. Finally, the economic assessment function determines both the field-level and pipeline (transportation) costs for CO2 sequestration in a given reservoir. The screening tool has been peer reviewed at an Electrical Power Research Institute (EPRI) technical meeting in March 2009. A number of useful observations and recommendations emerged from the Workshop on the costs of CO2 transport and storage that could be readily incorporated into a commercial version of the Screening Tool in a Phase III SBIR.

  9. Assessment of suitability of tree species for the production of biomass on trace element contaminated soils

    International Nuclear Information System (INIS)

    Evangelou, Michael W.H.; Deram, Annabelle; Gogos, Alexander; Studer, Björn; Schulin, Rainer

    2012-01-01

    Highlights: ► Birch: lowest metal concentrations in foliage, wood and bark. ► Bark proportion does not have to decline with increasing age of tree. ► Long harvest rotation (>25 y) reduces metal concentrations in stem. ► Birch: most suitable tree for BCL. - Abstract: To alleviate the demand on fertile agricultural land for production of bioenergy, we investigated the possibility of producing biomass for bioenergy on trace element (TE) contaminated land. Soil samples and plant tissues (leaves, wood and bark) of adult willow (Salix sp.), poplar (Populus sp.), and birch (Betula pendula) trees were collected from five contaminated sites in France and Germany and analysed for Zn, Cd, Pb, Cu, Ca, and K. Cadmium concentration in tree leaves were correlated with tree species, whereas Zn concentration in leaves was site correlated. Birch revealed significantly lower leaf Cd concentrations (1.2–8.9 mg kg −1 ) than willow and poplar (5–80 mg kg −1 ), thus posing the lowest risk for TE contamination of surrounding areas. Birch displayed the lowest bark concentrations for Ca (2300–6200 mg kg −1 ) and K (320–1250 mg kg −1 ), indicating that it would be the most suitable tree species for fuel production, as high concentrations of K and Ca decrease the ash melting point which results in a reduced plant lifetime. Due to higher TE concentrations in bark compared to wood a small bark proportion in relation to the trunk is desirable. In general the bark proportion was reduced with the tree age. In summary, birch was amongst the investigated species the most suitable for biomass production on TE contaminated land.

  10. Aporrectodea caliginosa, a suitable earthworm species for field based genotoxicity assessment?

    International Nuclear Information System (INIS)

    Klobucar, Goeran I.V.; Stambuk, Anamaria; Srut, Maja; Husnjak, Ivana; Merkas, Martina; Traven, Luka; Cvetkovic, Zelimira

    2011-01-01

    There is a growing interest for the application of biomakers to field-collected earthworms. Therefore we have evaluated the usability of native populations of endogeic, widely distributed earthworm Aporrectodea caliginosa in the assessment of soil genotoxicity using the Comet assay. Validation of the Comet assay on earthworm coelomocytes has been established using commercially available Eisenia fetida exposed to copper, cadmium, and pentachlorophenol, along with A. caliginosa exposed to copper in a filter paper contact test. Neutral red retention time (NRRT) assay was conducted on copper exposed and field-collected earthworms. Significant DNA and lysosomal damage was measured using Comet and NRRT assays in native populations of A. caliginosa sampled from the polluted soils in the urban area in comparison to the earthworms from the reference site. The results of this study confirm the employment of A. caliginosa as a suitable species for the in situ soil toxicity and genotoxicity field surveys. - Research highlights: → Native A. caliginosa has shown significant biological effect measured by the Comet and NRRT assays. → The Comet assay on A. caliginosa and E. fetida has shown to be of similar sensitivity as the NRRT assay. → A. caliginosa is a suitable species for the in situ soil toxicity and genotoxicity field surveys. - Native populations of endogeic earthworm Aporrectodea caliginosa can be successfully applied in the genotoxicity field surveys using Comet assay.

  11. Aporrectodea caliginosa, a suitable earthworm species for field based genotoxicity assessment?

    Energy Technology Data Exchange (ETDEWEB)

    Klobucar, Goeran I.V., E-mail: gklobuca@zg.biol.pmf.hr [Department of Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb (Croatia); Stambuk, Anamaria; Srut, Maja [Department of Zoology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb (Croatia); Husnjak, Ivana [Ministry of Environmental Protection, Physical Planning and Construction, Ulica Republike Austrije 14, Zagreb (Croatia); Merkas, Martina [Croatian Institute for Brain Research, School of Medicine, University of Zagreb, Salata 12, 10000 Zagreb (Croatia); Traven, Luka [Department of Environmental Medicine, Medical Faculty, University of Rijeka, Brace Branchetta 20a, 51000 Rijeka (Croatia); Teaching Institute of Public Health of the Primorsko-goranska County, Kresimirova 52a, 51000 Rijeka (Croatia); Cvetkovic, Zelimira [Department of Ecology, Institute of Public Health, Mirogojska c. 16, 10000 Zagreb (Croatia)

    2011-04-15

    There is a growing interest for the application of biomakers to field-collected earthworms. Therefore we have evaluated the usability of native populations of endogeic, widely distributed earthworm Aporrectodea caliginosa in the assessment of soil genotoxicity using the Comet assay. Validation of the Comet assay on earthworm coelomocytes has been established using commercially available Eisenia fetida exposed to copper, cadmium, and pentachlorophenol, along with A. caliginosa exposed to copper in a filter paper contact test. Neutral red retention time (NRRT) assay was conducted on copper exposed and field-collected earthworms. Significant DNA and lysosomal damage was measured using Comet and NRRT assays in native populations of A. caliginosa sampled from the polluted soils in the urban area in comparison to the earthworms from the reference site. The results of this study confirm the employment of A. caliginosa as a suitable species for the in situ soil toxicity and genotoxicity field surveys. - Research highlights: > Native A. caliginosa has shown significant biological effect measured by the Comet and NRRT assays. > The Comet assay on A. caliginosa and E. fetida has shown to be of similar sensitivity as the NRRT assay. > A. caliginosa is a suitable species for the in situ soil toxicity and genotoxicity field surveys. - Native populations of endogeic earthworm Aporrectodea caliginosa can be successfully applied in the genotoxicity field surveys using Comet assay.

  12. RAPD-PCR – still a suitable Method for Genetically Underexplored Species?

    Directory of Open Access Journals (Sweden)

    Konstanze Ursula Behrmann

    2015-11-01

    Full Text Available Saithe (Pollachius virens is a commercially important fish species; the annual catch quota in the Northeast Atlantic exceeds 100.000 t. Despite that saithe is underexplored from a fish population genetically view. Because saithe is a highly migratory species, which undergoes a long larval drift, the population structure of saithe within the Northeast Atlantic is not fully understood. Models used as a basis for the management plan are based on tagging studies, which have been carried out in the 1960th. But still there are doubts regarding the numbers of stocks living in the Northeast Atlantic. Migration routes are affected by salmon farming, growing steadily from the 1990th. In the last years a hyperstability of the saithe stock in the North Sea had been detected underlining the need to have a closer look on the saithe stocks in the Northeast Atlantic. Random amplified polymorphic DNA (RAPD - PCR is a DNA fingerprinting technique often used in species identification and population genetic research for species, whose genome has not been sequenced very extensive as being the case for most of the food fishes. We applied RAPD-PCR in a study of saithe populations from the North Atlantic. The suitability of RAPD-PCR was improved by optimisations for enhanced reproducibility. The “classical” protocol for RAPD-PCR was modified by increasing the annealing temperature and shortening the time of annealing, providing a much better reproducibility. Thus, RAPD-PCR was found to be a straightforward and low-cost way, compared to other population genetic tools, to get a first insight into the population structure of less sequenced fish species within a very short time, being useful for preliminary studies or laboratories without large capacities for DNA sequencing.

  13. Suitability of cuticular pores and sensilla for harpacticoid copepod species delineation and phylogenetic reconstruction.

    Science.gov (United States)

    Karanovic, Tomislav; Kim, Kichoon

    2014-11-01

    Cuticular organs have not been described systematically in harpacticoids until recently, and they haven ever been used as characters for reconstructing phylogenetic relationships in any crustacean group. We survey cuticular pores and sensilla on somites in ten Miraciidae species, belonging to six genera, from Korea, Australia, and Russia. Nine species belong to the subfamily Stenheliinae, while the outgroup belongs to the subfamily Diosaccinae. We aim to compare phylogenetic trees reconstructed for these harpactioids based on: 1) cuticular organs (with 76 characters scored, 71% of them phylogenetically informative); 2) traditionally used macro-morphological characters (66 scored, 77% of them informative);and 3) mtCOI DNA data. All analyses suggest that cuticular organs are useful characters for harpacticoid species delineation, although not as sensitive as some fast-evolving molecular markers. Reconstructed cladograms based on all three datasets show very high bootstrap values for clades representing distinct genera, suggesting that cuticular organs are suitable characters for studying phylogenetic relationships. Bootstrap values for the more basal nodes differ among the different cladograms,as do the sister-group relationships they suggest, indicating that cuticular organs probably have different evolutionary constraints from macro-morphological characters. Cuticular organs could be quite useful in the study of old museum specimens and fossil crustaceans.

  14. Connecting infrared spectra with plant traits to identify species

    Science.gov (United States)

    Buitrago, Maria F.; Skidmore, Andrew K.; Groen, Thomas A.; Hecker, Christoph A.

    2018-05-01

    Plant traits are used to define species, but also to evaluate the health status of forests, plantations and crops. Conventional methods of measuring plant traits (e.g. wet chemistry), although accurate, are inefficient and costly when applied over large areas or with intensive sampling. Spectroscopic methods, as used in the food industry and mineralogy, are nowadays applied to identify plant traits, however, most studies analysed visible to near infrared, while infrared spectra of longer wavelengths have been little used for identifying the spectral differences between plant species. This study measured the infrared spectra (1.4-16.0 μm) on individual, fresh leaves of 19 species (from herbaceous to woody species), as well as 14 leaf traits for each leaf. The results describe at which wavelengths in the infrared the leaves' spectra can differentiate most effectively between these plant species. A Quadratic Discrimination Analysis (QDA) shows that using five bands in the SWIR or the LWIR is enough to accurately differentiate these species (Kappa: 0.93, 0.94 respectively), while the MWIR has a lower classification accuracy (Kappa: 0.84). This study also shows that in the infrared spectra of fresh leaves, the identified species-specific features are correlated with leaf traits as well as changes in their values. Spectral features in the SWIR (1.66, 1.89 and 2.00 μm) are common to all species and match the main features of pure cellulose and lignin spectra. The depth of these features varies with changes of cellulose and leaf water content and can be used to differentiate species in this region. In the MWIR and LWIR, the absorption spectra of leaves are formed by key species-specific traits including lignin, cellulose, water, nitrogen and leaf thickness. The connection found in this study between leaf traits, features and spectral signatures are novel tools to assist when identifying plant species by spectroscopy and remote sensing.

  15. A comparative study to identify a suitable model of ownership for Iran football pro league clubs

    Directory of Open Access Journals (Sweden)

    Saeed Amirnejad

    2018-01-01

    Full Text Available Today the government ownership of the professional football clubs is absolutely illogical view point. Most of sports clubs are conducted by private sector using different models of ownership all over the world. In Iran, government credits benefit was main reason that the professional sport was firstly developed by government firms and organizations. Therefore, the sports team ownership is without the professionalization standards. The present comparative study was to examine the different football club ownership structures of the top leagues and the current condition of Iran football pro league ownership and then present a suitable ownership structure of Iran football clubs to leave behind the government club ownership. Among the initial 120 scientific texts, the thirty two cases including papers, books and reports were found relevant to this study. We studied the ownership prominence and several football club models of ownership focused on stock listing model of ownership, private investor model of ownership, supporter trust model of ownership and Japan partnership model of ownership; theoretical concepts, empirical studies, main findings, strengths and weaknesses were covered in analysis procedure. According to various models of ownership in leagues and the models’ productivity in football clubs, each model of ownership considering national environmental, economic, social conditions has strengths and weaknesses. So, we cannot present a definite model of ownership for Iran football pro league clubs due to different micro-environments of Iran clubs. We need a big planning to provide a supporter-investor mixed model of ownership to Iranian clubs. Considering strengths and weaknesses in the models of ownership as well as the micro and macro environment of Iran football clubs, German model and Japan partnership model are offered as suitable ones to probable new model of ownership in Iran pro league clubs. Consequently, more studies are required

  16. Restoration Plan for Degraded Forest in The Democratic People’s Republic of Korea Considering Suitable Tree Species and Spatial Distribution

    Directory of Open Access Journals (Sweden)

    Sle-gee Lee

    2018-03-01

    Full Text Available The ecosystem across the Democratic People’s Republic of Korea (DPRK is threatened by deforestation. However, there is very little attention being given to government efforts for afforestation and rehabilitation plan. The most significant barriers to addressing this problem are technique limitations, availability of information, and lack of a stepwise forest management plan. This study identifies spatially suitable tree species, and establishes a stepwise restoration plan to support decision making for restoring degraded forest in the DPRK throughout a suitable restoration map. First off, target species were chosen from reference data, and spatial distribution maps for each tree species were prepared based on social needs as well as natural conditions in the DPRK. The suitable restoration map was calculated by two priorities in a weighting method; suitable priority, and distributional clustering level. Finally, the 23 afforestation species were selected for the suitable restoration map, including 11 coniferous and 12 deciduous tree species. We introduced a stepwise afforestation/restoration plan of degraded forest in the DPRK; general (long-term, detailed (medium-term, implementation (short-term plans. Maps with different spatial resolutions were prepared for each of the plans. A restoration map with 12.5 km spatial resolution can be used for the general plan at the national level, and maps with 5 km and 1 km spatial resolutions can be used for detailed plan at the local level and implementation plan at the site level, respectively.

  17. Identifying suitable substrates for high-quality graphene-based heterostructures

    Science.gov (United States)

    Banszerus, L.; Janssen, H.; Otto, M.; Epping, A.; Taniguchi, T.; Watanabe, K.; Beschoten, B.; Neumaier, D.; Stampfer, C.

    2017-06-01

    We report on a scanning confocal Raman spectroscopy study investigating the strain-uniformity and the overall strain and doping of high-quality chemical vapour deposited (CVD) graphene-based heterostuctures on a large number of different substrate materials, including hexagonal boron nitride (hBN), transition metal dichalcogenides, silicon, different oxides and nitrides, as well as polymers. By applying a hBN-assisted, contamination free, dry transfer process for CVD graphene, high-quality heterostructures with low doping densities and low strain variations are assembled. The Raman spectra of these pristine heterostructures are sensitive to substrate-induced doping and strain variations and are thus used to probe the suitability of the substrate material for potential high-quality graphene devices. We find that the flatness of the substrate material is a key figure for gaining, or preserving high-quality graphene.

  18. Can suitable candidates for levodopa/carbidopa intestinal gel therapy be identified using current evidence?

    Directory of Open Access Journals (Sweden)

    Maria José Catalán

    2017-09-01

    In recent years, strong evidence has supported the use of LCIG in treating motor fluctuations associated with APD, and several clinical studies provide emerging evidence for additional benefits of LCIG treatment in certain patients. This article provides an overview of the published literature on the benefits, limitations, and drawbacks of LCIG in relation to PD symptoms, the psychosocial impact of the disease, and the quality of life of patients, with the aim of determining candidates for whom treatment with LCIG would be beneficial. According to current evidence, patients with APD (defined as inability to achieve optimal control of the disease with conventional oral treatment, a relatively well-preserved cognitive-behavioral status, and good family/caregiver would count as suitable candidates for LCIG treatment. Contraindications in the opinion of the authors are severe dementia and active psychosis.

  19. Is the climate right for pleistocene rewilding? Using species distribution models to extrapolate climatic suitability for mammals across continents.

    Directory of Open Access Journals (Sweden)

    Orien M W Richmond

    Full Text Available Species distribution models (SDMs are increasingly used for extrapolation, or predicting suitable regions for species under new geographic or temporal scenarios. However, SDM predictions may be prone to errors if species are not at equilibrium with climatic conditions in the current range and if training samples are not representative. Here the controversial "Pleistocene rewilding" proposal was used as a novel example to address some of the challenges of extrapolating modeled species-climate relationships outside of current ranges. Climatic suitability for three proposed proxy species (Asian elephant, African cheetah and African lion was extrapolated to the American southwest and Great Plains using Maxent, a machine-learning species distribution model. Similar models were fit for Oryx gazella, a species native to Africa that has naturalized in North America, to test model predictions. To overcome biases introduced by contracted modern ranges and limited occurrence data, random pseudo-presence points generated from modern and historical ranges were used for model training. For all species except the oryx, models of climatic suitability fit to training data from historical ranges produced larger areas of predicted suitability in North America than models fit to training data from modern ranges. Four naturalized oryx populations in the American southwest were correctly predicted with a generous model threshold, but none of these locations were predicted with a more stringent threshold. In general, the northern Great Plains had low climatic suitability for all focal species and scenarios considered, while portions of the southern Great Plains and American southwest had low to intermediate suitability for some species in some scenarios. The results suggest that the use of historical, in addition to modern, range information and randomly sampled pseudo-presence points may improve model accuracy. This has implications for modeling range shifts of

  20. Identifying the Species Threat Hotspots from Global Supply Chains

    OpenAIRE

    Moran, Daniel; Kanemoto, Keiichiro

    2016-01-01

    Identifying species threat hotspots has been a successful approach for setting conservation priorities. One major challenge in conservation is that in many hotspots export industries continue to drive overexploitation. Conservation measures must consider not just the point of impact, but also the consumer demand that ultimately drives resource use. To understand which species threat hotspots are driven by which consumers, we have developed a new approach to link a set of biodiversity footprin...

  1. Using Risk Assessment and Habitat Suitability Models to Prioritise Invasive Species for Management in a Changing Climate.

    Science.gov (United States)

    Chai, Shauna-Lee; Zhang, Jian; Nixon, Amy; Nielsen, Scott

    2016-01-01

    Accounting for climate change in invasive species risk assessments improves our understanding of potential future impacts and enhances our preparedness for the arrival of new non-native species. We combined traditional risk assessment for invasive species with habitat suitability modeling to assess risk to biodiversity based on climate change. We demonstrate our method by assessing the risk for 15 potentially new invasive plant species to Alberta, Canada, an area where climate change is expected to facilitate the poleward expansion of invasive species ranges. Of the 15 species assessed, the three terrestrial invasive plant species that could pose the greatest threat to Alberta's biodiversity are giant knotweed (Fallopia sachalinensis), tamarisk (Tamarix chinensis), and alkali swainsonpea (Sphaerophysa salsula). We characterise giant knotweed as 'extremely invasive', with 21 times the suitable habitat between baseline and future projected climate. Tamarisk is 'extremely invasive' with a 64% increase in suitable habitat, and alkali swainsonpea is 'highly invasive' with a 21% increase in suitable habitat. Our methodology can be used to predict and prioritise potentially new invasive species for their impact on biodiversity in the context of climate change.

  2. Using Risk Assessment and Habitat Suitability Models to Prioritise Invasive Species for Management in a Changing Climate.

    Directory of Open Access Journals (Sweden)

    Shauna-Lee Chai

    Full Text Available Accounting for climate change in invasive species risk assessments improves our understanding of potential future impacts and enhances our preparedness for the arrival of new non-native species. We combined traditional risk assessment for invasive species with habitat suitability modeling to assess risk to biodiversity based on climate change. We demonstrate our method by assessing the risk for 15 potentially new invasive plant species to Alberta, Canada, an area where climate change is expected to facilitate the poleward expansion of invasive species ranges. Of the 15 species assessed, the three terrestrial invasive plant species that could pose the greatest threat to Alberta's biodiversity are giant knotweed (Fallopia sachalinensis, tamarisk (Tamarix chinensis, and alkali swainsonpea (Sphaerophysa salsula. We characterise giant knotweed as 'extremely invasive', with 21 times the suitable habitat between baseline and future projected climate. Tamarisk is 'extremely invasive' with a 64% increase in suitable habitat, and alkali swainsonpea is 'highly invasive' with a 21% increase in suitable habitat. Our methodology can be used to predict and prioritise potentially new invasive species for their impact on biodiversity in the context of climate change.

  3. Predicting Potential Changes in Suitable Habitat and Distribution by 2100 for Tree Species of the Eastern United States

    Science.gov (United States)

    Louis R Iverson; Anantha M. Prasad; Mark W. Schwartz; Mark W. Schwartz

    2005-01-01

    We predict current distribution and abundance for tree species present in eastern North America, and subsequently estimate potential suitable habitat for those species under a changed climate with 2 x CO2. We used a series of statistical models (i.e., Regression Tree Analysis (RTA), Multivariate Adaptive Regression Splines (MARS), Bagging Trees (...

  4. Identifying applicants suitable to a career in nursing: a value-based approach to undergraduate selection.

    Science.gov (United States)

    Traynor, Marian; Galanouli, Despina; Roberts, Martin; Leonard, Lawrence; Gale, Thomas

    2017-06-01

    The aim of this study was to complement existing evidence on the suitability of Multiple Mini Interviews as a potential tool for the selection of nursing candidates on to a BSc (Hons) nursing programme. This study aimed to trial the Multiple Mini Interview approach to recruitment with a group of first year nursing students (already selected using traditional interviews). Cross-sectional validation study. This paper reports on the evaluation of the participants' detailed scores from the Multiple Mini Interview stations; their original interview scores and their end of year results. This study took place in March 2015. Scores from the seven Multiple Mini Interview stations were analysed to show the internal structure, reliability and generalizability of the stations. Original selection scores from interviews and in-course assessment were correlated with the MMI scores and variation by students' age, gender and disability status was explored. Reliability of the Multiple Mini Interview score was moderate (G = 0·52). The Multiple Mini Interview score provided better differentiation between more able students than did the original interview score but neither score was correlated with the module results. Multiple Mini Interview scores were positively associated with students' age but not their gender or disability status. The Multiple Mini Interview reported in this study offers a selection process that is based on the values and personal attributes regarded as desirable for a career in nursing and does not necessarily predict academic success. Its moderate reliability indicates the need for further improvement but it is capable of discriminating between candidates and shows little evidence of bias. © 2016 John Wiley & Sons Ltd.

  5. Identifying species threat hotspots from global supply chains.

    Science.gov (United States)

    Moran, Daniel; Kanemoto, Keiichiro

    2017-01-04

    Identifying hotspots of species threat has been a successful approach for setting conservation priorities. One important challenge in conservation is that, in many hotspots, export industries continue to drive overexploitation. Conservation measures must consider not just the point of impact, but also the consumer demand that ultimately drives resource use. To understand which species threat hotspots are driven by which consumers, we have developed a new approach to link a set of biodiversity footprint accounts to the hotspots of threatened species on the IUCN Red List of Threatened Species. The result is a map connecting consumption to spatially explicit hotspots driven by production on a global scale. Locating biodiversity threat hotspots driven by consumption of goods and services can help to connect conservationists, consumers, companies and governments in order to better target conservation actions.

  6. Development of computational fluid dynamics--habitat suitability (CFD-HSI) models to identify potential passage--Challenge zones for migratory fishes in the Penobscot River

    Science.gov (United States)

    Haro, Alexander J.; Dudley, Robert W.; Chelminski, Michael

    2012-01-01

    A two-dimensional computational fluid dynamics-habitat suitability (CFD–HSI) model was developed to identify potential zones of shallow depth and high water velocity that may present passage challenges for five anadromous fish species in the Penobscot River, Maine, upstream from two existing dams and as a result of the proposed future removal of the dams. Potential depth-challenge zones were predicted for larger species at the lowest flow modeled in the dam-removal scenario. Increasing flows under both scenarios increased the number and size of potential velocity-challenge zones, especially for smaller species. This application of the two-dimensional CFD–HSI model demonstrated its capabilities to estimate the potential effects of flow and hydraulic alteration on the passage of migratory fish.

  7. Landscape Metrics to Assess Habitat Suitability for Conversation Bird Species in the Southeastern United States

    National Research Council Canada - National Science Library

    Dove, Linda

    2001-01-01

    .... The degree to which a given species is affected by habitat fragmentation is dependent on the complex interaction of the habitat requirements of the species and the shape, size, and makeup of the fragmented habitat...

  8. Estimating suitable environments for invasive plant species across large landscapes: a remote sensing strategy using Landsat 7 ETM+

    Science.gov (United States)

    Young, Kendal E.; Abbott, Laurie B.; Caldwell, Colleen A.; Schrader, T. Scott

    2013-01-01

    The key to reducing ecological and economic damage caused by invasive plant species is to locate and eradicate new invasions before they threaten native biodiversity and ecological processes. We used Landsat Enhanced Thematic Mapper Plus imagery to estimate suitable environments for four invasive plants in Big Bend National Park, southwest Texas, using a presence-only modeling approach. Giant reed (Arundo donax), Lehmann lovegrass (Eragrostis lehmanniana), horehound (Marrubium vulgare) and buffelgrass (Pennisteum ciliare) were selected for remote sensing spatial analyses. Multiple dates/seasons of imagery were used to account for habitat conditions within the study area and to capture phenological differences among targeted species and the surrounding landscape. Individual species models had high (0.91 to 0.99) discriminative ability to differentiate invasive plant suitable environments from random background locations. Average test area under the receiver operating characteristic curve (AUC) ranged from 0.91 to 0.99, indicating that plant predictive models exhibited high discriminative ability to differentiate suitable environments for invasive plant species from random locations. Omission rates ranged from <1.0 to 18%. We demonstrated that useful models estimating suitable environments for invasive plants may be created with <50 occurrence locations and that reliable modeling using presence-only datasets can be powerful tools for land managers.

  9. Suitability of seven species of soil-inhabiting invertebrates for testing toxicity of pesticides in soil pore water

    NARCIS (Netherlands)

    Ronday, R.; Houx, N.W.H.

    1996-01-01

    This study assessed the suitability of seven species of soil invertebrates for toxicologically testing pesticides in water. Requirements were that the organisms must survive in water, be easy to handle, be easy to breed, be sensitive to pesticides, and show unambiguous toxicological effects. The

  10. Estimating suitable environments for invasive plant species across large landscapes: A remote sensing strategy using Landsat 7 ETM+

    Science.gov (United States)

    The key to reducing ecological and economic damage caused by invasive plant species is to locate and eradicate new invasions before they threaten native biodiversity and ecological processes. We used Landsat Enhanced Thematic Mapper Plus imagery to estimate suitable environments for four invasive pl...

  11. Application of the Analytic Hierarchy Process to Identify the Most Suitable Lessor of Freight Car Finance Leasing

    Directory of Open Access Journals (Sweden)

    Lei Lei

    2017-01-01

    Full Text Available Finance leasing (also “equipment leasing” saves the cost, improves the efficiency and benefit, larger the manufacture supply channels, which is an optimal solution for equipment supply with uncertain freight demand. The article collects the definitions of Finance Leasing based on the four pillars theory of finance leasing, also divides the lessors in Freight Car finance leasing into three categories according to their major business: manufacturers, banks as the representative financial institutions, firms that specialized in finance leasing. To identify the most suitable lessor for each railway department, an indicator system is built and operated by Yaahp (a software based on Analytic Hierarchy Process.

  12. Richness of Ancient Forest Plant Species Indicates Suitable Habitats for Macrofungi

    Czech Academy of Sciences Publication Activity Database

    Hofmeister, J.; Hošek, J.; Brabec, Marek; Dvořák, D.; Beran, M.; Deckerová, H.; Burel, J.; Kříž, M.; Borovička, Jan; Běťák, J.; Vašutová, Martina

    2014-01-01

    Roč. 23, č. 8 (2014), s. 2015-2031 ISSN 0960-3115 Grant - others:GA MŽP(CZ) SP/2D1/146/08 Institutional support: RVO:67985807 ; RVO:67985831 ; RVO:67179843 Keywords : diversity * forest continuity * forest management * Herb-layer plant species * red-listed species * species richness * surrogacy Subject RIV: BB - Applied Statistics, Operational Research; EH - Ecology, Behaviour (GLU-S); EH - Ecology, Behaviour (UEK-B) Impact factor: 2.365, year: 2014

  13. Plant species potentially suitable for cover on low-level solid nuclear waste disposal sites: a literature review

    International Nuclear Information System (INIS)

    Brenkert, A.L.; Parr, P.D.; Taylor, F.G.

    1984-09-01

    This report reviews available literature on soil conditions, hydrology, and climatological data and suggests plant species suitable for covering the low-level nuclear waste disposal areas in the White Oak Creek Watershed within the Oak Ridge Reservation. Literature on naturally invading species and secondary succession, on plant species used for reclamation of coal spoils and roadsides, and on horticultural species is reviewed. The potential of plant species to take up, or mine, the waste through deep rooting is assessed. The effects of vegetation cover on the water balance in a watershed are reviewed. Several conclusions are presented concerning the management of vegetation cover on low-level solid waste disposal areas. 163 references, 2 figures, 9 tables

  14. Plant species potentially suitable for cover on low-level solid nuclear waste disposal sites: a literature review

    Energy Technology Data Exchange (ETDEWEB)

    Brenkert, A.L.; Parr, P.D.; Taylor, F.G.

    1984-09-01

    This report reviews available literature on soil conditions, hydrology, and climatological data and suggests plant species suitable for covering the low-level nuclear waste disposal areas in the White Oak Creek Watershed within the Oak Ridge Reservation. Literature on naturally invading species and secondary succession, on plant species used for reclamation of coal spoils and roadsides, and on horticultural species is reviewed. The potential of plant species to take up, or mine, the waste through deep rooting is assessed. The effects of vegetation cover on the water balance in a watershed are reviewed. Several conclusions are presented concerning the management of vegetation cover on low-level solid waste disposal areas. 163 references, 2 figures, 9 tables.

  15. Meiotic behavior of wild Caricaceae species potentially suitable for papaya improvement

    Directory of Open Access Journals (Sweden)

    Emanuelli Narducci da Silva

    2012-01-01

    Full Text Available The purpose of this study was to evaluate the meiotic behavior and determine the meiotic index and pollen viability of representative plants of the wild species V. goudotiana, V. quercifolia and J. spinosa. Meiotic analysis confirmed that the species are diploid and have 18 chromosomes. Meiosis was partially normal, since some abnormalities, e.g, sticky and lagging chromosomes, precocious segregation, lack of synchrony, and disturbances in the spindle fibers were observed. These abnormalities resulted in post-meiotic products (monads, dyads, triads, and polyads that probably contributed to the meiotic index of 85.7 % (V. goudotiana to 95.9 % (J. spinosa; significant variation was observed in the species V. goudotiana. The pollen viability of 68.0% (V. goudotiana to 96.0 % (J. spinosa was reasonably good in these wild species. Crossings in breeding programs involving V. goudotiana should therefore be carefully planned, since part of the gametes of this species is unviable.

  16. Identifying ozone-sensitive communities of (semi-)natural vegetation suitable for mapping exceedance of critical levels

    International Nuclear Information System (INIS)

    Mills, G.; Hayes, F.; Jones, M.L.M.; Cinderby, S.

    2007-01-01

    Using published data on the responses of individual species to ozone, 54 EUNIS (European Nature Information System) level 4 communities with six or more ozone-sensitive species (%OS) and c. 20% or more species tested for ozone sensitivity, were identified as potentially ozone-sensitive. The largest number of these communities (23) was associated with Grasslands, with Heathland, scrub and tundra, and Mires, bogs and fens having the next highest representation at 11 and 8 level 4 communities each respectively. Within the grasslands classification, E4 (Alpine and sub-alpine grasslands), E5 (Woodland fringes and clearings) and E1 (Dry grasslands) were the most sensitive with 68.1, 51.6 and 48.6%OS respectively. It is feasible to map the land-cover for these and other communities at level 2, but it may not be currently possible to map the land-cover for all communities identified to be ozone-sensitive at levels 3 and 4. - Grassland communities such as alpine and sub-alpine grasslands have the highest potential sensitivity ozone, based on the responses of their component species

  17. Predicting Species Distributions Using Record Centre Data: Multi-Scale Modelling of Habitat Suitability for Bat Roosts.

    Science.gov (United States)

    Bellamy, Chloe; Altringham, John

    2015-01-01

    Conservation increasingly operates at the landscape scale. For this to be effective, we need landscape scale information on species distributions and the environmental factors that underpin them. Species records are becoming increasingly available via data centres and online portals, but they are often patchy and biased. We demonstrate how such data can yield useful habitat suitability models, using bat roost records as an example. We analysed the effects of environmental variables at eight spatial scales (500 m - 6 km) on roost selection by eight bat species (Pipistrellus pipistrellus, P. pygmaeus, Nyctalus noctula, Myotis mystacinus, M. brandtii, M. nattereri, M. daubentonii, and Plecotus auritus) using the presence-only modelling software MaxEnt. Modelling was carried out on a selection of 418 data centre roost records from the Lake District National Park, UK. Target group pseudoabsences were selected to reduce the impact of sampling bias. Multi-scale models, combining variables measured at their best performing spatial scales, were used to predict roosting habitat suitability, yielding models with useful predictive abilities. Small areas of deciduous woodland consistently increased roosting habitat suitability, but other habitat associations varied between species and scales. Pipistrellus were positively related to built environments at small scales, and depended on large-scale woodland availability. The other, more specialist, species were highly sensitive to human-altered landscapes, avoiding even small rural towns. The strength of many relationships at large scales suggests that bats are sensitive to habitat modifications far from the roost itself. The fine resolution, large extent maps will aid targeted decision-making by conservationists and planners. We have made available an ArcGIS toolbox that automates the production of multi-scale variables, to facilitate the application of our methods to other taxa and locations. Habitat suitability modelling has the

  18. Species distribution models and ecological suitability analysis for potential tick vectors of lyme disease in Mexico.

    Science.gov (United States)

    Illoldi-Rangel, Patricia; Rivaldi, Chissa-Louise; Sissel, Blake; Trout Fryxell, Rebecca; Gordillo-Pérez, Guadalupe; Rodríguez-Moreno, Angel; Williamson, Phillip; Montiel-Parra, Griselda; Sánchez-Cordero, Víctor; Sarkar, Sahotra

    2012-01-01

    Species distribution models were constructed for ten Ixodes species and Amblyomma cajennense for a region including Mexico and Texas. The model was based on a maximum entropy algorithm that used environmental layers to predict the relative probability of presence for each taxon. For Mexico, species geographic ranges were predicted by restricting the models to cells which have a higher probability than the lowest probability of the cells in which a presence record was located. There was spatial nonconcordance between the distributions of Amblyomma cajennense and the Ixodes group with the former restricted to lowlands and mainly the eastern coast of Mexico and the latter to montane regions with lower temperature. The risk of Lyme disease is, therefore, mainly present in the highlands where some Ixodes species are known vectors; if Amblyomma cajennense turns out to be a competent vector, the area of risk also extends to the lowlands and the east coast.

  19. Species Distribution Models and Ecological Suitability Analysis for Potential Tick Vectors of Lyme Disease in Mexico

    Directory of Open Access Journals (Sweden)

    Patricia Illoldi-Rangel

    2012-01-01

    Full Text Available Species distribution models were constructed for ten Ixodes species and Amblyomma cajennense for a region including Mexico and Texas. The model was based on a maximum entropy algorithm that used environmental layers to predict the relative probability of presence for each taxon. For Mexico, species geographic ranges were predicted by restricting the models to cells which have a higher probability than the lowest probability of the cells in which a presence record was located. There was spatial nonconcordance between the distributions of Amblyomma cajennense and the Ixodes group with the former restricted to lowlands and mainly the eastern coast of Mexico and the latter to montane regions with lower temperature. The risk of Lyme disease is, therefore, mainly present in the highlands where some Ixodes species are known vectors; if Amblyomma cajennense turns out to be a competent vector, the area of risk also extends to the lowlands and the east coast.

  20. Plant species dispersed by Galapagos tortoises surf the wave of habitat suitability under anthropogenic climate change.

    Science.gov (United States)

    Ellis-Soto, Diego; Blake, Stephen; Soultan, Alaaeldin; Guézou, Anne; Cabrera, Fredy; Lötters, Stefan

    2017-01-01

    Native biodiversity on the Galapagos Archipelago is severely threatened by invasive alien species. On Santa Cruz Island, the abundance of introduced plant species is low in the arid lowlands of the Galapagos National Park, but increases with elevation into unprotected humid highlands. Two common alien plant species, guava (Psidium guajava) and passion fruit (Passiflora edulis) occur at higher elevations yet their seeds are dispersed into the lowlands by migrating Galapagos tortoises (Chelonoidis spp.). Tortoises transport large quantities of seeds over long distances into environments in which they have little or no chance of germination and survival under current climate conditions. However, climate change is projected to modify environmental conditions on Galapagos with unknown consequences for the distribution of native and introduced biodiversity. We quantified seed dispersal of guava and passion fruit in tortoise dung piles and the distribution of adult plants along two elevation gradients on Santa Cruz to assess current levels of 'wasted' seed dispersal. We computed species distribution models for both taxa under current and predicted future climate conditions. Assuming that tortoise migratory behaviour continues, current levels of "wasted" seed dispersal in lowlands were projected to decline dramatically in the future for guava but not for passion fruit. Tortoises will facilitate rapid range expansion for guava into lowland areas within the Galapagos National Park where this species is currently absent. Coupled with putative reduction in arid habitat for native species caused by climate change, tortoise driven guava invasion will pose a serious threat to local plant communities.

  1. Plant species dispersed by Galapagos tortoises surf the wave of habitat suitability under anthropogenic climate change.

    Directory of Open Access Journals (Sweden)

    Diego Ellis-Soto

    Full Text Available Native biodiversity on the Galapagos Archipelago is severely threatened by invasive alien species. On Santa Cruz Island, the abundance of introduced plant species is low in the arid lowlands of the Galapagos National Park, but increases with elevation into unprotected humid highlands. Two common alien plant species, guava (Psidium guajava and passion fruit (Passiflora edulis occur at higher elevations yet their seeds are dispersed into the lowlands by migrating Galapagos tortoises (Chelonoidis spp.. Tortoises transport large quantities of seeds over long distances into environments in which they have little or no chance of germination and survival under current climate conditions. However, climate change is projected to modify environmental conditions on Galapagos with unknown consequences for the distribution of native and introduced biodiversity. We quantified seed dispersal of guava and passion fruit in tortoise dung piles and the distribution of adult plants along two elevation gradients on Santa Cruz to assess current levels of 'wasted' seed dispersal. We computed species distribution models for both taxa under current and predicted future climate conditions. Assuming that tortoise migratory behaviour continues, current levels of "wasted" seed dispersal in lowlands were projected to decline dramatically in the future for guava but not for passion fruit. Tortoises will facilitate rapid range expansion for guava into lowland areas within the Galapagos National Park where this species is currently absent. Coupled with putative reduction in arid habitat for native species caused by climate change, tortoise driven guava invasion will pose a serious threat to local plant communities.

  2. Wastewater Reuse: An Economic Perspective to Identify Suitable Areas for Poplar Vegetation Filter Systems for Energy Production

    Directory of Open Access Journals (Sweden)

    Mauro Viccaro

    2017-11-01

    Full Text Available The increasing interest towards climate change, water and energy saving, and soil protection has led the research community to consider non-conventional water as a sustainable source for irrigation of energy crops. Vegetation filter systems are considered a reliable technique for sustainable biomass cultivation, enabling the use of reclaimed wastewater as water and nutrients sources during irrigation periods. In this study, a geographic information system (GIS-based spatial model was developed to identify areas potentially suitable for creating vegetation filter systems with poplars to size the plants of energy production. An economic assessment allowed us to identify the cost-effectiveness areas for biomass production that can be fertigated by reclaimed wastewater. Considering the Basilicata region as the test region, a surface area of 258,512 ha was investigated, identifying 73,331 ha of SRF soils sited downstream of 45 wastewater treatment plants (WWTPs. However, considering only areas that have positive net present value and are economically attractive, results indicate 1606 ha of SRF falling within the areas of influence of 39 WWTPs. The results show that the sector of dedicated crops, adjacent and linked with WWTPs, expresses a total capacity of 50.56 MW for thermal, 8.25 MW for electricity, and 31 MW for cogeneration (25.07 MWt and 5.94 MWe plants.

  3. Suitability of native and ornamental oak species in California for Agrilus auroguttatus

    Science.gov (United States)

    L.J. Haavik; A.D. Graves; T.W. Coleman; F.L. Flint; R.C. Venette; S.J. Seybold

    2014-01-01

    Goldspotted oak borer, Agrilus auroguttatus Schaeffer (Coleoptera: Buprestidae), is a new invasive species in southern California, USA. The extent of the host range of this insect is not known, but this knowledge will have a major impact on assessment of the risks that this pest poses to oaks [Quercus spp. (Fagaceae)]. We...

  4. Validation of the ITS2 region as a novel DNA barcode for identifying medicinal plant species.

    Science.gov (United States)

    Chen, Shilin; Yao, Hui; Han, Jianping; Liu, Chang; Song, Jingyuan; Shi, Linchun; Zhu, Yingjie; Ma, Xinye; Gao, Ting; Pang, Xiaohui; Luo, Kun; Li, Ying; Li, Xiwen; Jia, Xiaocheng; Lin, Yulin; Leon, Christine

    2010-01-07

    The plant working group of the Consortium for the Barcode of Life recommended the two-locus combination of rbcL+matK as the plant barcode, yet the combination was shown to successfully discriminate among 907 samples from 550 species at the species level with a probability of 72%. The group admits that the two-locus barcode is far from perfect due to the low identification rate, and the search is not over. Here, we compared seven candidate DNA barcodes (psbA-trnH, matK, rbcL, rpoC1, ycf5, ITS2, and ITS) from medicinal plant species. Our ranking criteria included PCR amplification efficiency, differential intra- and inter-specific divergences, and the DNA barcoding gap. Our data suggest that the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA represents the most suitable region for DNA barcoding applications. Furthermore, we tested the discrimination ability of ITS2 in more than 6600 plant samples belonging to 4800 species from 753 distinct genera and found that the rate of successful identification with the ITS2 was 92.7% at the species level. The ITS2 region can be potentially used as a standard DNA barcode to identify medicinal plants and their closely related species. We also propose that ITS2 can serve as a novel universal barcode for the identification of a broader range of plant taxa.

  5. A novel diagnostic protocol to identify patients suitable for discharge after a single high-sensitivity troponin

    Science.gov (United States)

    Carlton, Edward W; Cullen, Louise; Than, Martin; Gamble, James; Khattab, Ahmed; Greaves, Kim

    2015-01-01

    Objective To establish whether a novel accelerated diagnostic protocol (ADP) for suspected acute coronary syndrome (ACS) could successfully identify low-risk patients suitable for discharge after a single high-sensitivity troponin T (hs-cTnT) taken at presentation to the emergency department. We also compared the diagnostic accuracy of this ADP with strategies using initial undetectable hs-cTnT. Methods This prospective observational study evaluated the ability of the Triage Rule-out Using high-Sensitivity Troponin (TRUST) ADP to identify low-risk patients with suspected ACS. The ADP incorporated a single presentation hs-cTnT of <14 ng/L, a non-ischaemic ECG and a modified Goldman risk score. Diagnostic performance of the ADP was compared with the detection limit cut-offs of hs-cTnT (<5 ng/L and <3 ng/L). The primary end point was fatal/non-fatal acute myocardial infarction (AMI) within 30 days. Results 960 participants were recruited, mean age 58.0 years, 80 (8.3%) had an AMI. The TRUST ADP classified 382 (39.8%) as low-risk with a sensitivity for identifying AMI of 98.8% (95% CI 92.5% to 99.9%). hs-cTnT detection limits (<5 ng/L and <3 ng/L) had a sensitivity of 100% (94.3 to 100) and 100% (94.4 to 100), respectively. The TRUST ADP identified more patients suitable for early discharge at 39.8% vs 29.3% (<5 ng/L) and 7.9% (<3 ng/L) (p<0.001) with a lower false-positive rate for AMI detection; specificity 43.3% (95% CI 42.7% to 43.4%) vs 32.0% (95% CI 31.5% to 32.0%) and 8.6% (95% CI 8.1% to 8.6%), respectively. Conclusions The TRUST ADP, which incorporates structured risk-assessment and a single presentation hs-cTnT blood draw, has potential to allow early discharge in 40% of patients with suspected ACS and has greater clinical utility than undetectable hs-cTnT strategies. Trial registration number ISRCTN No. 21109279. PMID:25691511

  6. Tree Species Suitability to Bioswales and Impact on the Urban Water Budget.

    Science.gov (United States)

    Scharenbroch, Bryant C; Morgenroth, Justin; Maule, Brian

    2016-01-01

    Water movement between soil and the atmosphere is restricted by hardscapes in the urban environment. Some green infrastructure is intended to increase infiltration and storage of water, thus decreasing runoff and discharge of urban stormwater. Bioswales are a critical component of a water-sensitive urban design (or a low-impact urban design), and incorporation of trees into these green infrastructural components is believed to be a novel way to return stored water to the atmosphere via transpiration. This research was conducted in The Morton Arboretum's main parking lot, which is one of the first and largest green infrastructure installations in the midwestern United States. The parking lot is constructed of permeable pavers and tree bioswales. Trees in bioswales were evaluated for growth and condition and for their effects on water cycling via transpiration. Our data indicate that trees in bioswales accounted for 46 to 72% of total water outputs via transpiration, thereby reducing runoff and discharge from the parking lot. By evaluating the stomatal conductance, diameter growth, and condition of a variety of tree species in these bioswales, we found that not all species are equally suited for bioswales and that not all are equivalent in their transpiration and growth rates, thereby contributing differentially to the functional capacity of bioswales. We conclude that species with high stomatal conductance and large mature form are likely to contribute best to bioswale function. Copyright © by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, Inc.

  7. Native plant species suitable as bioindicators and biomonitors for airborne fluoride

    International Nuclear Information System (INIS)

    Weinstein, Leonard H.; Davison, Alan W.

    2003-01-01

    The strengths and limitations of techniques for biomonitoring and bioindicating fluorides are reviewed. - For 30-40 years airborne fluoride, usually in the form of HF or SiF 4 , was one of the most important and damaging air pollutants affecting forests, crops and natural vegetation. It is much more toxic than most other air pollutants such as O 3 or SO 2 because injury to the most sensitive species begins when they are exposed to a concentration below 1 ppb (ca. 0.8 μg m -3 ) for a 1- to 3-day period. The long-term threshold concentration is around 0.25-0.30 μg m -3 . Higher concentrations and longer durations of exposure induce much more rapid and extensive injury. However, there is a difference in sensitivity between the most and least sensitive species of around 2-3 orders of magnitude and most species possess a degree of resistance. Dramatic improvements in engineering technology have greatly reduced emissions but because of the high toxicity, cases of vegetation injury are still common, even in developed countries, and cases involving litigation still occur. Therefore there is a continuing need for bioindicators and biomonitoring of fluorides, so this paper reviews the subject, drawing attention to the strengths and limitations of the techniques. Visible symptoms are described and illustrated and tables of relative sensitivity are given and their limitations discussed. Finally, examples of biomonitoring in Europe and the USA are presented

  8. A COMBINED FUZZY MCDM APPROACH FOR IDENTIFYING THE SUITABLE LANDS FOR URBAN DEVELOPMENT: AN EXAMPLE FROM BANDAR ABBS, IRAN

    Directory of Open Access Journals (Sweden)

    Mohsen Dadras

    2014-01-01

    Full Text Available This study aims at identifying the suitable lands for urban dev elopment in Bandar Abbas city based on its real world use regarding specific crite ria and sub-criteria. The city of Bandar Abbas is considered as the most important commer cial and economic city of Iran. It is also considered as one of the major cities of Iran which has played a pivotal role in the country's development and progress in recen t years especially after the end of Iran-Iraq war owing to its embracing the country's m ain commercial ports. This process has caused the immigration rate into the city to rise significantly over the past 20 years. Thus, the development of the city is meanwhile c onsidered as a high priority. Bandar Abbas city does not have a rich capacity for g rowth and development due to its special geographical situation being located in coastal border. Among the limitations placed in the city's development way, natural limit ations (heights and sea shore in the northern and southern parts of the city and struc tural limitations (military centers in the east and west sides of the city may be referred . Therefore, identifying the suitable lands for urban development within Bandar Abbas city l imits is becoming an essential priority. Therefore, d ifferent quantitative and quali tative criteria have been studied in order to select and identify these lands. The struct ures of qualitative criteria for most parts involve ambiguities and vagueness. This leads us to use Fuzzy logic in this study as a natural method for determining the solutions fo r problems of Multi- criteria decision making (MCDM. In the current research, a com bination of MCDM methods has been presented for analysis. To assignee weights of the criteria Fuzzy AHP (analytic hierarchy process is used for land selection and Fuzzy TOPSIS (method for order priority by similarity to ideal solution is utilized to choose the alternative that is the most appropriate through these criteria weights. The

  9. A novel enterovirus species identified from severe diarrheal goats

    OpenAIRE

    Wang, Mingyue; He, Jia; Lu, Haibing; Liu, Yajing; Deng, Yingrui; Zhu, Lisai; Guo, Changming; Tu, Changchun; Wang, Xinping

    2017-01-01

    Backgrounds The Enterovirus genus of the family of Picornaviridae consists of 9 species of Enteroviruses and 3 species of Rhinoviruses based on the latest virus taxonomy. Those viruses contribute significantly to respiratory and digestive disorders in human and animals. Out of 9 Enterovirus species, Enterovirus E-G are closely related to diseases affecting on livestock industry. While enterovirus infection has been increasingly reported in cattle and swine, the enterovirus infections in small...

  10. A rapid method for selecting suitable animal species for studying pathogen interactions with plasma protein ligands in vivo.

    Science.gov (United States)

    Naudin, Clément; Schumski, Ariane; Salo-Ahen, Outi M H; Herwald, Heiko; Smeds, Emanuel

    2017-05-01

    Species tropism constitutes a serious problem for developing relevant animal models of infection. Human pathogens can express virulence factors that show specific selectivity to human proteins, while their affinity for orthologs from other species can vary significantly. Suitable animal species must be used to analyse whether virulence factors are potential targets for drug development. We developed an assay that rapidly predicts applicable animal species for studying virulence factors binding plasma proteins. We used two well-characterized Staphylococcus aureus proteins, SSL7 and Efb, to develop an ELISA-based inhibition assay using plasma from different animal species. The interaction between SSL7 and human C5 and the binding of Efb to human fibrinogen and human C3 was studied. Affinity experiments and Western blot analyses were used to validate the assay. Human, monkey and cat plasma interfered with binding of SSL7 to human C5. Binding of Efb to human fibrinogen was blocked in human, monkey, gerbil and pig plasma, while human, monkey, gerbil, rabbit, cat and guinea pig plasma inhibited the binding of Efb to human C3. These results emphasize the importance of choosing correct animal models, and thus, our approach is a rapid and cost-effective method that can be used to prevent unnecessary animal experiments. © 2017 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

  11. Identifying biodiversity hotspots for threatened mammal species in Iran

    NARCIS (Netherlands)

    Farashi, Azita; Shariati Najafabadi, Mitra; Hosseini, Mahshid

    2017-01-01

    Conservation biology has much more attention for biodiversity hot spots than before. In order to recognize the hotspots for Iranian terrestrial mammal species that are listed in any red list, nationally or globally, ten Species Distribution Models (SDMs) have been applied. The SDMs evaluation

  12. Assess suitability of hydroaeroponic culture to establish tripartite symbiosis between different AMF species, beans, and rhizobia

    Directory of Open Access Journals (Sweden)

    Jansa Jan

    2009-06-01

    Full Text Available Abstract Background Like other species of the Phaseoleae tribe, common bean (Phaseolus vulgaris L. has the potential to establish symbiosis with rhizobia and to fix the atmospheric dinitrogen (N2 for its N nutrition. Common bean has also the potential to establish symbiosis with arbuscular mycorrhizal fungi (AMF that improves the uptake of low mobile nutrients such as phosphorus, from the soil. Both rhizobial and mycorrhizal symbioses can act synergistically in benefits on plant. Results The tripartite symbiosis of common bean with rhizobia and arbuscular mycorrhizal fungi (AMF was assessed in hydroaeroponic culture with common bean (Phaseolus vulgaris L., by comparing the effects of three fungi spp. on growth, nodulation and mycorrhization of the roots under sufficient versus deficient P supplies, after transfer from initial sand culture. Although Glomus intraradices Schenck & Smith colonized intensely the roots of common bean in both sand and hydroaeroponic cultures, Gigaspora rosea Nicolson & Schenck only established well under sand culture conditions, and no root-colonization was found with Acaulospora mellea Spain & Schenck under either culture conditions. Interestingly, mycorrhization by Glomus was also obtained by contact with mycorrhized Stylosanthes guianensis (Aubl. sw in sand culture under deficient P before transfer into hydroaeroponic culture. The effect of bean genotype on both rhizobial and mycorrhizal symbioses with Glomus was subsequently assessed with the common bean recombinant inbreed line 7, 28, 83, 115 and 147, and the cultivar Flamingo. Significant differences among colonization and nodulation of the roots and growth among genotypes were found. Conclusion The hydroaeroponic culture is a valuable tool for further scrutinizing the physiological interactions and nutrient partitioning within the tripartite symbiosis.

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

    Science.gov (United States)

    Lachat, Thibault; Bütler, Rita

    2009-07-01

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

  14. The meaning and classification of tattoos in the context of their suitability to identify corpses of unknown identity.

    Science.gov (United States)

    Sadowski, Wojciech A; Borowska-Solonynko, Aleksandra B

    2017-01-01

    To present the most popular types of tattoos, their meaning and classification, and to assess the suitability of different forms of tattoos in the process of identification of corpses of unknown identity. The tattoos found on 729 cadavers who underwent post mortem examinations at the Department of Forensic Medicine in Warsaw in the years 2012-2015 were analyzed. The tattoos were photographed and identified in terms of their meaning domain and classified into groups. Tattoos belonging to all groups were found, according to the most popular tattoo classification, which is based on their nature and includes: criminal and prison tattoos (defining the prison hierarchy, criminal profession as well as intentions and goals, erotic tattoos, environmental, penitentiary), military and artistic. The novel classification, focusing on the utility of certain kinds of tattoos for identyfying corpses of unknown identity, was also developed. According to the above mentioned classification the following kinds of tattoos are distinguished: individual (artistic), group (e.g. penitentiary - indicating the fact of being imprisoned in a penitentiary institution or belonging to a "prison kites" subculture, or presenting criminal profession; group confined tattoo (indicating a staying in a specific penitentiary institution), group tattoo with individual data (indicating the fact of staying in a penitentiary institution as well as dates of imprisonment), and others (e.g. names of relatives, military tattoo, etc.). Analysis of individual types of tattoo can accelerate the process of identification of the cadavers. The proposed classification allows to quickly determine whether a particular tattoo can be helpful in initial individual identification (in the case of individual tattoos) or whether it can be used to reduce the group of people considered (in cases of different types of group tattoos).

  15. Habitat suitability of Anopheles vector species and association with human malaria in the Atlantic Forest in south-eastern Brazil.

    Science.gov (United States)

    Laporta, Gabriel Zorello; Ramos, Daniel Garkauskas; Ribeiro, Milton Cezar; Sallum, Maria Anice Mureb

    2011-08-01

    Every year, autochthonous cases of Plasmodium vivax malaria occur in low-endemicity areas of Vale do Ribeira in the south-eastern part of the Atlantic Forest, state of São Paulo, where Anopheles cruzii and Anopheles bellator are considered the primary vectors. However, other species in the subgenus Nyssorhynchus of Anopheles (e.g., Anopheles marajoara) are abundant and may participate in the dynamics of malarial transmission in that region. The objectives of the present study were to assess the spatial distribution of An. cruzii, An. bellator and An. marajoara and to associate the presence of these species with malaria cases in the municipalities of the Vale do Ribeira. Potential habitat suitability modelling was applied to determine both the spatial distribution of An. cruzii, An. bellator and An. marajoara and to establish the density of each species. Poisson regression was utilized to associate malaria cases with estimated vector densities. As a result, An. cruzii was correlated with the forested slopes of the Serra do Mar, An. bellator with the coastal plain and An. marajoara with the deforested areas. Moreover, both An. marajoara and An. cruzii were positively associated with malaria cases. Considering that An. marajoara was demonstrated to be a primary vector of human Plasmodium in the rural areas of the state of Amapá, more attention should be given to the species in the deforested areas of the Atlantic Forest, where it might be a secondary vector.

  16. A novel enterovirus species identified from severe diarrheal goats.

    Science.gov (United States)

    Wang, Mingyue; He, Jia; Lu, Haibing; Liu, Yajing; Deng, Yingrui; Zhu, Lisai; Guo, Changming; Tu, Changchun; Wang, Xinping

    2017-01-01

    The Enterovirus genus of the family of Picornaviridae consists of 9 species of Enteroviruses and 3 species of Rhinoviruses based on the latest virus taxonomy. Those viruses contribute significantly to respiratory and digestive disorders in human and animals. Out of 9 Enterovirus species, Enterovirus E-G are closely related to diseases affecting on livestock industry. While enterovirus infection has been increasingly reported in cattle and swine, the enterovirus infections in small ruminants remain largely unknown. Virology, molecular and bioinformatics methods were employed to characterize a novel enterovirus CEV-JL14 from goats manifesting severe diarrhea with morbidity and mortality respectively up to 84% and 54% in China. CEV-JL14 was defined and proposed as a new Enterovirus species L within the genus of Enterovirus of the family Picornaviridae. CEV-JL14 had a complete genome sequence of 7461 nucleotides with an ORF encoding 2172 amino acids, and shared 77.1% of genomic sequence identity with TB4-OEV, an ovine enterovirus. Comparison of 5'-UTR and structural genes of CEV-JL14 with known Enterovirus species revealed highly genetic variations among CEV-JL14 with known Enterovirus species. VP1 nucleotide sequence identities of CEV-14 were 51.8%-53.5% with those of Enterovirus E and F, 30.9%-65.3% with Enterovirus G, and 43.8-51. 5% with Enterovirus A-D, respectively. CEV-JL14 was proposed as a novel species within the genus of Enterovirus according to the current ICTV demarcation criteria of enteroviruses. CEV-JL14 clustered phylogenetically to neither Enterovirus E and F, nor to Enterovirus G. It was defined and proposed as novel species L within the genus of Enterovirus. This is the first report of caprine enterovirus in China, the first complete genomic sequence of a caprine enterovirus revealed, and the unveiling of significant genetic variations between ovine enterovirus and caprine enterovirus, thus broadening the current understanding of enteroviruses.

  17. Assessing future suitability of tree species under climate change by multiple methods: a case study in southern Germany

    Directory of Open Access Journals (Sweden)

    Helge Walentowski

    2017-07-01

    Full Text Available We compared results derived using three different approaches to assess the suitability of common tree species on the Franconian Plateau in southern Germany under projected warmer and drier climate conditions in the period 2061-2080. The study area is currently a relatively warm and dry region of Germany. We calculated species distribution models (SDMs using information on species’ climate envelopes to predict regional species spectra under 63 different climate change scenarios. We complemented this with fine-scale ecological niche analysis using data from 51 vegetation surveys in seven forest reserves in the study area, and tree-ring analysis (TRA from local populations of five tree species to quantify their sensitivity to climatic extreme years. The SDMs showed that predicted future climate change in the region remains within the climate envelope of certain species (e.g. Quercus petraea, whilst for e.g. Fagus sylvatica, future climate conditions in one third of the scenarios are too warm and dry. This was confirmed by the TRA: sensitivity to drought periods is lower for Q. petraea than for F. sylvatica. The niche analysis shows that the local ecological niches of Quercus robur and Fraxinus excelsior are mainly characterized by soils providing favorable water supply than by climate, and Pinus sylvestris (planted is strongly influenced by light availability. The best adapted species for a warmer and potentially drier climate in the study region are Acer campestre, Sorbus torminalis, S. aria, Ulmus minor, and Tilia platyphyllos, which should therefore play a more prominent role in future climate-resilient mixed forest ecosystems.

  18. A novel enterovirus species identified from severe diarrheal goats.

    Directory of Open Access Journals (Sweden)

    Mingyue Wang

    Full Text Available The Enterovirus genus of the family of Picornaviridae consists of 9 species of Enteroviruses and 3 species of Rhinoviruses based on the latest virus taxonomy. Those viruses contribute significantly to respiratory and digestive disorders in human and animals. Out of 9 Enterovirus species, Enterovirus E-G are closely related to diseases affecting on livestock industry. While enterovirus infection has been increasingly reported in cattle and swine, the enterovirus infections in small ruminants remain largely unknown.Virology, molecular and bioinformatics methods were employed to characterize a novel enterovirus CEV-JL14 from goats manifesting severe diarrhea with morbidity and mortality respectively up to 84% and 54% in China.CEV-JL14 was defined and proposed as a new Enterovirus species L within the genus of Enterovirus of the family Picornaviridae. CEV-JL14 had a complete genome sequence of 7461 nucleotides with an ORF encoding 2172 amino acids, and shared 77.1% of genomic sequence identity with TB4-OEV, an ovine enterovirus. Comparison of 5'-UTR and structural genes of CEV-JL14 with known Enterovirus species revealed highly genetic variations among CEV-JL14 with known Enterovirus species. VP1 nucleotide sequence identities of CEV-14 were 51.8%-53.5% with those of Enterovirus E and F, 30.9%-65.3% with Enterovirus G, and 43.8-51. 5% with Enterovirus A-D, respectively. CEV-JL14 was proposed as a novel species within the genus of Enterovirus according to the current ICTV demarcation criteria of enteroviruses.CEV-JL14 clustered phylogenetically to neither Enterovirus E and F, nor to Enterovirus G. It was defined and proposed as novel species L within the genus of Enterovirus. This is the first report of caprine enterovirus in China, the first complete genomic sequence of a caprine enterovirus revealed, and the unveiling of significant genetic variations between ovine enterovirus and caprine enterovirus, thus broadening the current understanding of

  19. A novel enterovirus species identified from severe diarrheal goats

    Science.gov (United States)

    Liu, Yajing; Deng, Yingrui; Zhu, Lisai; Guo, Changming; Tu, Changchun; Wang, Xinping

    2017-01-01

    Backgrounds The Enterovirus genus of the family of Picornaviridae consists of 9 species of Enteroviruses and 3 species of Rhinoviruses based on the latest virus taxonomy. Those viruses contribute significantly to respiratory and digestive disorders in human and animals. Out of 9 Enterovirus species, Enterovirus E-G are closely related to diseases affecting on livestock industry. While enterovirus infection has been increasingly reported in cattle and swine, the enterovirus infections in small ruminants remain largely unknown. Methods Virology, molecular and bioinformatics methods were employed to characterize a novel enterovirus CEV-JL14 from goats manifesting severe diarrhea with morbidity and mortality respectively up to 84% and 54% in China. Results CEV-JL14 was defined and proposed as a new Enterovirus species L within the genus of Enterovirus of the family Picornaviridae. CEV-JL14 had a complete genome sequence of 7461 nucleotides with an ORF encoding 2172 amino acids, and shared 77.1% of genomic sequence identity with TB4-OEV, an ovine enterovirus. Comparison of 5’-UTR and structural genes of CEV-JL14 with known Enterovirus species revealed highly genetic variations among CEV-JL14 with known Enterovirus species. VP1 nucleotide sequence identities of CEV-14 were 51.8%-53.5% with those of Enterovirus E and F, 30.9%-65.3% with Enterovirus G, and 43.8–51. 5% with Enterovirus A-D, respectively. CEV-JL14 was proposed as a novel species within the genus of Enterovirus according to the current ICTV demarcation criteria of enteroviruses. Conclusions CEV-JL14 clustered phylogenetically to neither Enterovirus E and F, nor to Enterovirus G. It was defined and proposed as novel species L within the genus of Enterovirus. This is the first report of caprine enterovirus in China, the first complete genomic sequence of a caprine enterovirus revealed, and the unveiling of significant genetic variations between ovine enterovirus and caprine enterovirus, thus broadening the

  20. High-resolution assessment of land use impacts on biodiversity in life cycle assessment using species habitat suitability models.

    Science.gov (United States)

    de Baan, Laura; Curran, Michael; Rondinini, Carlo; Visconti, Piero; Hellweg, Stefanie; Koellner, Thomas

    2015-02-17

    Agricultural land use is a main driver of global biodiversity loss. The assessment of land use impacts in decision-support tools such as life cycle assessment (LCA) requires spatially explicit models, but existing approaches are either not spatially differentiated or modeled at very coarse scales (e.g., biomes or ecoregions). In this paper, we develop a high-resolution (900 m) assessment method for land use impacts on biodiversity based on habitat suitability models (HSM) of mammal species. This method considers potential land use effects on individual species, and impacts are weighted by the species' conservation status and global rarity. We illustrate the method using a case study of crop production in East Africa, but the underlying HSMs developed by the Global Mammals Assessment are available globally. We calculate impacts of three major export crops and compare the results to two previously developed methods (focusing on local and regional impacts, respectively) to assess the relevance of the methodological innovations proposed in this paper. The results highlight hotspots of product-related biodiversity impacts that help characterize the links among agricultural production, consumption, and biodiversity loss.

  1. Antimicrobial susceptibility among clinical Nocardia species identified by multilocus sequence analysis.

    Science.gov (United States)

    McTaggart, Lisa R; Doucet, Jennifer; Witkowska, Maria; Richardson, Susan E

    2015-01-01

    Antimicrobial susceptibility patterns of 112 clinical isolates, 28 type strains, and 9 reference strains of Nocardia were determined using the Sensititre Rapmyco microdilution panel (Thermo Fisher, Inc.). Isolates were identified by highly discriminatory multilocus sequence analysis and were chosen to represent the diversity of species recovered from clinical specimens in Ontario, Canada. Susceptibility to the most commonly used drug, trimethoprim-sulfamethoxazole, was observed in 97% of isolates. Linezolid and amikacin were also highly effective; 100% and 99% of all isolates demonstrated a susceptible phenotype. For the remaining antimicrobials, resistance was species specific with isolates of Nocardia otitidiscaviarum, N. brasiliensis, N. abscessus complex, N. nova complex, N. transvalensis complex, N. farcinica, and N. cyriacigeorgica displaying the traditional characteristic drug pattern types. In addition, the antimicrobial susceptibility profiles of a variety of rarely encountered species isolated from clinical specimens are reported for the first time and were categorized into four additional drug pattern types. Finally, MICs for the control strains N. nova ATCC BAA-2227, N. asteroides ATCC 19247(T), and N. farcinica ATCC 23826 were robustly determined to demonstrate method reproducibility and suitability of the commercial Sensititre Rapmyco panel for antimicrobial susceptibility testing of Nocardia spp. isolated from clinical specimens. The reported values will facilitate quality control and standardization among laboratories. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  2. Identifying of meat species using polymerase chain reaction (PCR)

    International Nuclear Information System (INIS)

    Foong, Chow Ming; Sani, Norrakiah Abdullah

    2013-01-01

    Meat has been widely consumed as an important protein source in daily life of human. Furthermore, with busy and intense urban lifestyle, processed food is now one of the main protein sources of one’s diet. Consumers rely on the food labeling to decide if the meat product purchased is safe and reliable. Therefore, it is important to ensure the food labeling is done in a correct manner to avoid consumer fraud. More consumers are now concern about the food quality and safety as compared to before. This study described the meat species identification and detection method using Polymerase Chain Reaction (PCR) in 8 types of meats (cattle, buffalo, goat, sheep, chicken, duck, pork and horse). The objective of this study is to decide on the specificity of oligonucleotide sequences obtained from previous study. There were 5 proposed oligonucleotide primer in this study. The main important finding in this work is the specificity of oligonucleotide primers to raw meats. It if found that the oligonucleotide primers proposed were not specific to the local raw meat species. Therefore, further study is needed to obtain a species-specific oligonucletide primers for PCR, in order to be applied in food product testing

  3. Identifying of meat species using polymerase chain reaction (PCR)

    Energy Technology Data Exchange (ETDEWEB)

    Foong, Chow Ming; Sani, Norrakiah Abdullah [School of Chemical Sciences and Food Technology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor (Malaysia)

    2013-11-27

    Meat has been widely consumed as an important protein source in daily life of human. Furthermore, with busy and intense urban lifestyle, processed food is now one of the main protein sources of one’s diet. Consumers rely on the food labeling to decide if the meat product purchased is safe and reliable. Therefore, it is important to ensure the food labeling is done in a correct manner to avoid consumer fraud. More consumers are now concern about the food quality and safety as compared to before. This study described the meat species identification and detection method using Polymerase Chain Reaction (PCR) in 8 types of meats (cattle, buffalo, goat, sheep, chicken, duck, pork and horse). The objective of this study is to decide on the specificity of oligonucleotide sequences obtained from previous study. There were 5 proposed oligonucleotide primer in this study. The main important finding in this work is the specificity of oligonucleotide primers to raw meats. It if found that the oligonucleotide primers proposed were not specific to the local raw meat species. Therefore, further study is needed to obtain a species-specific oligonucletide primers for PCR, in order to be applied in food product testing.

  4. The Invasive Species Forecasting System (ISFS): An iRODS-Based, Cloud-Enabled Decision Support System for Invasive Species Habitat Suitability Modeling

    Science.gov (United States)

    Gill, Roger; Schnase, John L.

    2012-01-01

    The Invasive Species Forecasting System (ISFS) is an online decision support system that allows users to load point occurrence field sample data for a plant species of interest and quickly generate habitat suitability maps for geographic regions of interest, such as a national park, monument, forest, or refuge. Target customers for ISFS are natural resource managers and decision makers who have a need for scientifically valid, model- based predictions of the habitat suitability of plant species of management concern. In a joint project involving NASA and the Maryland Department of Natural Resources, ISFS has been used to model the potential distribution of Wavyleaf Basketgrass in Maryland's Chesapeake Bay Watershed. Maximum entropy techniques are used to generate predictive maps using predictor datasets derived from remotely sensed data and climate simulation outputs. The workflow to run a model is implemented in an iRODS microservice using a custom ISFS file driver that clips and re-projects data to geographic regions of interest, then shells out to perform MaxEnt processing on the input data. When the model completes, all output files and maps from the model run are registered in iRODS and made accessible to the user. The ISFS user interface is a web browser that uses the iRODS PHP client to interact with the ISFS/iRODS- server. ISFS is designed to reside in a VMware virtual machine running SLES 11 and iRODS 3.0. The ISFS virtual machine is hosted in a VMware vSphere private cloud infrastructure to deliver the online service.

  5. Cyanobacteria species identified in the Weija and Kpong reservoirs ...

    African Journals Online (AJOL)

    The Kpong and Weija reservoirs supply drinking water to Accra, Ghana. This study was conducted to identify the cyanobacteria present in these reservoirs and to ascertain whether current treatment processes remove whole cyanobacteria cells from the drinking water produced. Cyanotoxins are mostly cell bound and could ...

  6. Integration of Remote Sensing and other public GIS data source to identify suitable zones for groundwater exploitation by manual drilling

    Science.gov (United States)

    Fussi, Fabio; Fava, Francesco; Di Mauro, Biagio; Bonomi, Tullia; Fumagalli, Letizia; DI Leo, Margherita; Hamidou Kane, Cheik; Faye, Gayane; Niang, Magatte; Wade, Souleye; Hamidou, Barry; Colombo, Roberto

    2015-04-01

    In several countries of the world the situation of water supply is still critical, far from the international target defined by United Nations for 2015 (Millenium Development Goals) and producing a huge impact on health and living condition of the population. Manual drilling (it means techniques to drill boreholes for water using human or animal power) is well known and practiced for centuries in many countries. In recent years, it has been considered a potential strategy to increase water access in poor countries and has raised the attention of national governments and international organizations. Manual drilling is applicable only where hydrogeological context is suitable, according to the following conditions: thick layers of unconsolidated sediments and shallow water table. Mapping of zones with suitable hydrogeological context has been carried out in several countries in Africa, but the results have evident limitations; previous methods are based on existing direct data and qualitative experience, leading to unreliable interpretation when direct data are limited. This research aims to develop a methodology to estimate shallow hydrogeological features and asses the distribution of suitable zones for manual drilling through the integration of indirect information obtained from remote sensing and other existing source of data. The research is carried out in two different study areas, in Senegal and Guinea (Western Africa), with semi-arid climate, moderate vegetation cover, unconsolidated sandy and clay deposits overlaying sedimentary and igneous rocks A set of variables have been obtained through processing of three categories of data, listed below: - geology, geomorphology, soil and land cover, obtained from existing thematic maps; - vegetation phenology, apparent thermal inertia, and soil moisture, obtained from analysis of multitemporal optical (MOD13Q1), thermal (MOD11A1), and radar (ASAR) remotely sensed data: -morphometric parameters, obtained from public

  7. Proteomics approach to identify unique xylem sap proteins in Pierce's disease-tolerant Vitis species.

    Science.gov (United States)

    Basha, Sheikh M; Mazhar, Hifza; Vasanthaiah, Hemanth K N

    2010-03-01

    Pierce's disease (PD) is a destructive bacterial disease of grapes caused by Xylella fastidiosa which is xylem-confined. The tolerance level to this disease varies among Vitis species. Our research was aimed at identifying unique xylem sap proteins present in PD-tolerant Vitis species. The results showed wide variation in the xylem sap protein composition, where a set of polypeptides with pI between 4.5 and 4.7 and M(r) of 31 kDa were present in abundant amount in muscadine (Vitis rotundifolia, PD-tolerant), in reduced levels in Florida hybrid bunch (Vitis spp., PD-tolerant) and absent in bunch grapes (Vitis vinifera, PD-susceptible). Liquid chromatography/mass spectrometry/mass spectrometry analysis of these proteins revealed their similarity to beta-1, 3-glucanase, peroxidase, and a subunit of oxygen-evolving enhancer protein 1, which are known to play role in defense and oxygen generation. In addition, the amount of free amino acids and soluble sugars was found to be significantly lower in xylem sap of muscadine genotypes compared to V. vinifera genotypes, indicating that the higher nutritional value of bunch grape sap may be more suitable for Xylella growth. These data suggest that the presence of these unique proteins in xylem sap is vital for PD tolerance in muscadine and Florida hybrid bunch grapes.

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

    Science.gov (United States)

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

    2018-01-01

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

  9. Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent.

    Science.gov (United States)

    Allman, Elizabeth S; Degnan, James H; Rhodes, John A

    2011-06-01

    Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals-each with many genes-splitting into new populations or species. The coalescent process, which models ancestry of gene copies within populations, is often used to model the probability distribution of gene trees given a fixed species tree. This multispecies coalescent model provides a framework for phylogeneticists to infer species trees from gene trees using maximum likelihood or Bayesian approaches. Because the coalescent models a branching process over time, all trees are typically assumed to be rooted in this setting. Often, however, gene trees inferred by traditional phylogenetic methods are unrooted. We investigate probabilities of unrooted gene trees under the multispecies coalescent model. We show that when there are four species with one gene sampled per species, the distribution of unrooted gene tree topologies identifies the unrooted species tree topology and some, but not all, information in the species tree edges (branch lengths). The location of the root on the species tree is not identifiable in this situation. However, for 5 or more species with one gene sampled per species, we show that the distribution of unrooted gene tree topologies identifies the rooted species tree topology and all its internal branch lengths. The length of any pendant branch leading to a leaf of the species tree is also identifiable for any species from which more than one gene is sampled.

  10. Identifying suitable sanitary landfill locations in the state of Morelos, México, using a Geographic Information System

    Science.gov (United States)

    Marín, Luis E.; Torres, Vicente; Bolongaro, Andrea; Reyna, José A.; Pohle, O.; Hernández-Espriú, A.; Chavarría, Jerónimo; García-Barrios, R.; Tabla, Hugo Francisco Parra

    GIS is a powerful tool that may help to better manage natural resources. In this paper, we present a GIS model developed for the state of Morelos as an aid to determine whether a potential site, Loma de Mejia, met the Mexican Federal Guidelines. The Mexican Government has established federal guidelines for sanitary landfill site selection (NOM-083-SERMARNAT-2003). These guidelines were translated into a water-based Geographic Information System and applied to the state of Morelos, Mexico. For these examples, we used the SIGAM® (Sistema de Información Geográfico del Agua en México; a water-based GIS for Mexico) which has at least 60 layers from the National Water Commission (CONAGUA), the national mapping agency (INEGI; Instituto Nacional de Estadística, Geografía e Informática), NASA, and academic institutions. Results show that a GIS is a powerful tool that may allow federal, state and municipal policy makers to conduct an initial regional site reconnaissance rapidly. Once potential sites are selected, further characterization must be carried out in order to determine if proposed locations are suitable or not for a sanitary landfill. Based on the SIGAM© software, the Loma de Mejia would not comply with the Mexican Federal Guidelines.

  11. Selection of the most suitable method for the extraction of DNA from foods and feeds for species identification

    Directory of Open Access Journals (Sweden)

    Michaela Nesvadbová

    2010-01-01

    Full Text Available High quality and purity of DNA isolated from food and feed is essential for species identification and has unpredictable influences an effect of analysis. In this study, the efficiency of eight different methods for DNA isolation was investigated. For DNA extraction, the raw chicken meet, ham, sausages, tinned lunch meat, pate, tinned feeds for dogs, complete granulated feeds for dogs and chicken flour were used. Kits of several different producers, i.e.: NucleoSpin Food (Marchery-Nagel, Wizard Genomic DNA Purification Kit (Promega, Invisorb Spin Food Kit I (Invitek, Wizard SV Genomic DNA Purification System (Promega, JetQuick Tissue DNA Spin Kit (Genomed, RNA Blue (Top-Bio, JetQuick Blood & Cell Culture Kit (Genomed, QIAamp DNA Mini Kit and QIAamp DNA Blood Mini Kit (Qiagen were employed in the study. Gel agarose electrophoresis for primary verification of DNA quality was performed. The isolates were subsequently assessed for quantity and quality using by spectrophotometer Nanodrop 2000 (Thermo Scientific. To verify of template usability and quality of isolated DNA, the polymerase chain reaction (PCR was used.Differences between isolated DNA from tinned products and meat, ham, sausage, granulated dog feed and chicken flour were found. In tinned food and feed, the DNA was more degraded, DNA content and DNA purity was lower and also PCR amplification was the most difficult. Overall DNA yield and quality have important influence on PCR products amplification. The best results were obtained with NucleoSpin Food and JetQuick Tissue DNA Spin Kit. DNA extracted by these methods proved highest yields, purity and template quality in all foods and feeds and the results of PCR analysis are excellent reproducible. Analyses showed that results depended on different food or feed using and dif­fe­rent isolation system.The results of this work will be utilized to choose the suitable isolating kit for educational course, which is designed for students and

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

    Science.gov (United States)

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

    2015-06-01

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

  13. Identifying patients suitable for palliative care - a descriptive analysis of enquiries using a Case Management Process Model approach

    Directory of Open Access Journals (Sweden)

    Kuhn Ulrike

    2012-11-01

    Full Text Available Abstract Background In Germany, case management in a palliative care unit was first implemented in 2005 at the Department of Palliative Medicine at the University Hospital Cologne. One of the purposes of this case management is to deal with enquiries from patients and their relatives as well as medical professionals. Using the Case Management Process Model of the Case Management Society of America as a reference, this study analysed (a how this case management was used by different enquiring groups and (b how patients were identified for case management and for palliative care services. The first thousand enquiries were analysed considering patient variables, properties of the enquiring persons and the content of the consultations. Results Most enquiries to the case management were made by telephone. The majority of requests regarded patients with oncological disease (84.3 %. The largest enquiring group was composed of patients and relatives (40.8 %, followed by internal professionals of the hospital (36.1 %. Most of the enquiring persons asked for a patient’s admission to the palliative care ward (46.4 %. The second most frequent request was for consultation and advice (30.9 %, followed by requests for the palliative home care service (13.3 %. Frequent reasons for actual admissions were the need for the treatment of pain, the presence of symptoms and the need for nursing care. More than half of the enquiries concerning admission to the palliative care ward were followed by an admission. Conclusions Case management has been made public among the relevant target groups. Case management as described by the Case Management Process Model helps to identify patients likely to benefit from case management and palliative care services. In addition, with the help of case management palliative patients may be allocated to particular health care services.

  14. Lipid ratio as a suitable tool to identify individuals with MetS risk: A case- control study.

    Science.gov (United States)

    Abbasian, Maryam; Delvarianzadeh, Mehri; Ebrahimi, Hossein; Khosravi, Farideh

    2017-11-01

    This study aimed to compare the serum lipids ratio in staff with and without metabolic syndrome (MetS) who were working in Shahroud University of Medical Sciences. This case-control study was conducted in 2015 on 499 personnel aged 30-60 years old. ATP III criteria were used to diagnose patients with MetS. The data were analyzed by using logistic regression and ROC curve. Mean lipid ratio was higher in individuals having the MetS in both sexes compared with those without. In addition, the mean levels of lipid ratios significantly increased with increasing number of MetS components in both sexes. Also it could be concluded that TG/HDL-C ratio is the best marker for the diagnosis of MetS in men and women. Moreover, the cut-off point for the TG/HDL-C was 2.86 in women and 4.03 in men. It was found that for any unit of increases in the TG/HDL-C, the risk of developing the MetS will increase by 2.12 times. TG/HDL-C ratio is found to be the best clinical marker for the diagnosis of MetS compare with other lipid ratios, therefore it is recommended to be used as a feasible tool to identify individuals with MetS risk. Copyright © 2016 Diabetes India. Published by Elsevier Ltd. All rights reserved.

  15. Conservation Below The Species Level: Suitable Evolutionarily Significant Units Among Mountain Vipers (The Montivipera Raddei Complex) in Iran.

    Science.gov (United States)

    Behrooz, Roozbeh; Kaboli, Mohammad; Arnal, Véronique; Nazarizadeh, Masoud; Asadi, Atefeh; Salmanian, Amin; Ahmadi, Mohsen; Montgelard, Claudine

    2018-02-01

    Northern and western mountains of Iran are among the most important biodiversity and endemism hot spots for reptiles in the Middle East. Among herpetofauna, the montivipers represent an emblematic and fragmented endemic group for which estimating their level of genetic differentiation and defining conservation priorities is urgently needed. Here, we present the most comprehensive phylogenetic study on the Montivipera raddei species group comprising all five known taxa, among which three are endemic to Iran. Based on two mitochondrial genes, phylogenetic and phylogeographic analyses revealed three major lineages each presenting very contrasting distribution area. The Iranian montivipers are highly structured in clades showing low genetic diversity and corresponding to high altitude summits. Molecular dating revealed the role of Quaternary paleo-climatic oscillations and altitudinal movements of montivipers in shaping genetic diversity and differentiation of these sky-island taxa. In addition, the best scenario of historical biogeography allowed identifying three possible refugial areas in Iran most likely arising by vicariance. Based on our mitochondrial results and pending additional data, we recognize three candidate species among the Montivipera raddei complex: M. raddei, M.latifii and M. kuhrangica that are coherent with their geographical distribution. We propose that the most appropriate Evolutionary Significant Units for conservation of the montivipers are represented by thirteen units among which six are recognized as high priority. Finally, we suggest some recommendations to the IUCN as well as to the Iranian conservation policies with respect to conservation prioritization. © The American Genetic Association 2018. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  16. DNA barcoding of shark meats identify species composition and CITES-listed species from the markets in Taiwan.

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    Shang-Yin Vanson Liu

    Full Text Available BACKGROUND: An increasing awareness of the vulnerability of sharks to exploitation by shark finning has contributed to a growing concern about an unsustainable shark fishery. Taiwan's fleet has the 4th largest shark catch in the world, accounting for almost 6% of the global figures. Revealing the diversity of sharks consumed by Taiwanese is important in designing conservation plans. However, fins make up less than 5% of the total body weight of a shark, and their bodies are sold as filets in the market, making it difficult or impossible to identify species using morphological traits. METHODS: In the present study, we adopted a DNA barcoding technique using a 391-bp fragment of the mitochondrial cytochrome oxidase I (COI gene to examine the diversity of shark filets and fins collected from markets and restaurants island-wide in Taiwan. RESULTS: Amongst the 548 tissue samples collected and sequenced, 20 major clusters were apparent by phylogenetic analyses, each of them containing individuals belonging to the same species (most with more than 95% bootstrap values, corresponding to 20 species of sharks. Additionally, Alopias pelagicus, Carcharhinus falciformis, Isurus oxyrinchus, and Prionace glauca consisted of 80% of the samples we collected, indicating that these species might be heavily consumed in Taiwan. Approximately 5% of the tissue samples used in this study were identified as species listed in CITES Appendix II, including two species of Sphyrna, C. longimanus and Carcharodon carcharias. CONCLUSION: DNA barcoding provides an alternative method for understanding shark species composition when species-specific data is unavailable. Considering the global population decline, stock assessments of Appendix II species and highly consumed species are needed to accomplish the ultimate goal of shark conservation.

  17. DNA barcoding of shark meats identify species composition and CITES-listed species from the markets in Taiwan.

    Science.gov (United States)

    Liu, Shang-Yin Vanson; Chan, Chia-Ling Carynn; Lin, Oceana; Hu, Chieh-Shen; Chen, Chaolun Allen

    2013-01-01

    An increasing awareness of the vulnerability of sharks to exploitation by shark finning has contributed to a growing concern about an unsustainable shark fishery. Taiwan's fleet has the 4th largest shark catch in the world, accounting for almost 6% of the global figures. Revealing the diversity of sharks consumed by Taiwanese is important in designing conservation plans. However, fins make up less than 5% of the total body weight of a shark, and their bodies are sold as filets in the market, making it difficult or impossible to identify species using morphological traits. In the present study, we adopted a DNA barcoding technique using a 391-bp fragment of the mitochondrial cytochrome oxidase I (COI) gene to examine the diversity of shark filets and fins collected from markets and restaurants island-wide in Taiwan. Amongst the 548 tissue samples collected and sequenced, 20 major clusters were apparent by phylogenetic analyses, each of them containing individuals belonging to the same species (most with more than 95% bootstrap values), corresponding to 20 species of sharks. Additionally, Alopias pelagicus, Carcharhinus falciformis, Isurus oxyrinchus, and Prionace glauca consisted of 80% of the samples we collected, indicating that these species might be heavily consumed in Taiwan. Approximately 5% of the tissue samples used in this study were identified as species listed in CITES Appendix II, including two species of Sphyrna, C. longimanus and Carcharodon carcharias. DNA barcoding provides an alternative method for understanding shark species composition when species-specific data is unavailable. Considering the global population decline, stock assessments of Appendix II species and highly consumed species are needed to accomplish the ultimate goal of shark conservation.

  18. Molecular marker to identify radiolarian species -toward establishment of paleo-environmental proxy-

    Science.gov (United States)

    Ishitani, Y.

    2017-12-01

    Marine fossilized unicellular plankton are known to have many genetically divergent species (biological species) in the single morphological species and these biological species show the species-specific environments much more precisely than that of morphological species. Among these plankton, Radiolaria are one of the best candidates for time- and environmental-indicators in the modern and past oceans, because radiolarians are the only group which represent entire water column from shallow to deep waters. However, the ecology and evolution of radiolarian were traditionally studied in paleontology and paleoceanography by morphological species. Even Radiolaria has a huge potential for novel proxy of wide and deep environments, there is no criterion to identify the biological species. The motivation for this study is setting the quantitative delimitation to establish the biological species of radiolarians based on molecular data, for leading the future ecological and paleo-environmental study. Identification of the biological species by ribosomal DNA sequences are mainly based on two ways: one is the evolutionary distance of the small subunit (SSU) rDNA, the internal transcribed spacer region of ribosomal DNA (ITS1 and 2), and the large subunit (LSU) rDNA; and the other is the secondary structure of ITS2. In the present study, all four possible genetic markers (SSU, ITS1, ITS2, and LSU rDNA) were amplified from 232 individuals of five radiolarian morphological species and applied to examine the evolutionary distance and secondary structure of rDNA. Comprehensive survey clearly shows that evolutionary distance of ITS1 rDNA and the secondary structure of ITS2 is good to identify the species. Notably, evolutionary distance of ITS1 rDNA is possible to set the common delimitation to identify the biological species, as 0.225 substitution per site. The results show that the ITS1 and ITS 2 rDNA could be the criterion for radiolarian species identification.

  19. Comparative analyses identified species-specific functional roles in oral microbial genomes

    Science.gov (United States)

    Chen, Tsute; Gajare, Prasad; Olsen, Ingar; Dewhirst, Floyd E.

    2017-01-01

    ABSTRACT The advent of next generation sequencing is producing more genomic sequences for various strains of many human oral microbial species and allows for insightful functional comparisons at both intra- and inter-species levels. This study performed in-silico functional comparisons for currently available genomic sequences of major species associated with periodontitis including Aggregatibacter actinomycetemcomitans (AA), Porphyromonas gingivalis (PG), Treponema denticola (TD), and Tannerella forsythia (TF), as well as several cariogenic and commensal streptococcal species. Complete or draft sequences were annotated with the RAST to infer structured functional subsystems for each genome. The subsystems profiles were clustered to groups of functions with similar patterns. Functional enrichment and depletion were evaluated based on hypergeometric distribution to identify subsystems that are unique or missing between two groups of genomes. Unique or missing metabolic pathways and biological functions were identified in different species. For example, components involved in flagellar motility were found only in the motile species TD, as expected, with few exceptions scattered in several streptococcal species, likely associated with chemotaxis. Transposable elements were only found in the two Bacteroidales species PG and TF, and half of the AA genomes. Genes involved in CRISPR were prevalent in most oral species. Furthermore, prophage related subsystems were also commonly found in most species except for PG and Streptococcus mutans, in which very few genomes contain prophage components. Comparisons between pathogenic (P) and nonpathogenic (NP) genomes also identified genes potentially important for virulence. Two such comparisons were performed between AA (P) and several A. aphrophilus (NP) strains, and between S. mutans + S. sobrinus (P) and other oral streptococcal species (NP). This comparative genomics approach can be readily used to identify functions unique to

  20. Using the Developmental Gene Bicoid to Identify Species of Forensically Important Blowflies (Diptera: Calliphoridae

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    Seong Hwan Park

    2013-01-01

    Full Text Available Identifying species of insects used to estimate postmortem interval (PMI is a major subject in forensic entomology. Because forensic insect specimens are morphologically uniform and are obtained at various developmental stages, DNA markers are greatly needed. To develop new autosomal DNA markers to identify species, partial genomic sequences of the bicoid (bcd genes, containing the homeobox and its flanking sequences, from 12 blowfly species (Aldrichina grahami, Calliphora vicina, Calliphora lata, Triceratopyga calliphoroides, Chrysomya megacephala, Chrysomya pinguis, Phormia regina, Lucilia ampullacea, Lucilia caesar, Lucilia illustris, Hemipyrellia ligurriens and Lucilia sericata; Calliphoridae: Diptera were determined and analyzed. This study first sequenced the ten blowfly species other than C. vicina and L. sericata. Based on the bcd sequences of these 12 blowfly species, a phylogenetic tree was constructed that discriminates the subfamilies of Calliphoridae (Luciliinae, Chrysomyinae, and Calliphorinae and most blowfly species. Even partial genomic sequences of about 500 bp can distinguish most blowfly species. The short intron 2 and coding sequences downstream of the bcd homeobox in exon 3 could be utilized to develop DNA markers for forensic applications. These gene sequences are important in the evolution of insect developmental biology and are potentially useful for identifying insect species in forensic science.

  1. Using the Developmental Gene Bicoid to Identify Species of Forensically Important Blowflies (Diptera: Calliphoridae)

    Science.gov (United States)

    Park, Seong Hwan; Park, Chung Hyun; Zhang, Yong; Piao, Huguo; Chung, Ukhee; Kim, Seong Yoon; Ko, Kwang Soo; Yi, Cheong-Ho; Jo, Tae-Ho; Hwang, Juck-Joon

    2013-01-01

    Identifying species of insects used to estimate postmortem interval (PMI) is a major subject in forensic entomology. Because forensic insect specimens are morphologically uniform and are obtained at various developmental stages, DNA markers are greatly needed. To develop new autosomal DNA markers to identify species, partial genomic sequences of the bicoid (bcd) genes, containing the homeobox and its flanking sequences, from 12 blowfly species (Aldrichina grahami, Calliphora vicina, Calliphora lata, Triceratopyga calliphoroides, Chrysomya megacephala, Chrysomya pinguis, Phormia regina, Lucilia ampullacea, Lucilia caesar, Lucilia illustris, Hemipyrellia ligurriens and Lucilia sericata; Calliphoridae: Diptera) were determined and analyzed. This study first sequenced the ten blowfly species other than C. vicina and L. sericata. Based on the bcd sequences of these 12 blowfly species, a phylogenetic tree was constructed that discriminates the subfamilies of Calliphoridae (Luciliinae, Chrysomyinae, and Calliphorinae) and most blowfly species. Even partial genomic sequences of about 500 bp can distinguish most blowfly species. The short intron 2 and coding sequences downstream of the bcd homeobox in exon 3 could be utilized to develop DNA markers for forensic applications. These gene sequences are important in the evolution of insect developmental biology and are potentially useful for identifying insect species in forensic science. PMID:23586044

  2. Using various lines of evidence to identify Chironomus species (Diptera: Chironomidae) in eastern Canadian lakes.

    Science.gov (United States)

    Proulx, Isabelle; Martin, Jon; Carew, Melissa; Hare, Landis

    2013-11-29

    Chironomus Meigen (Diptera, Chironomidae) larvae are usually the largest sediment-burrowing chironomids, and as such often constitute a major part of the freshwater infaunal biomass. However, use of this genus in ecological, environmental and paleoecological studies is hampered by the fact that Chironomus larvae are difficult to identify to species because the larvae of many species are morphologically similar. We used a combination of morphological, cytological and genetic techniques to distinguish Chironomus larvae collected from 31 water bodies located in eastern Canada, producing 17 distinguishable groupings. These groups of larvae were ultimately identified as belonging to 14 known species (C. anthracinus, C. bifurcatus, C. cucini, C. decorus-group sp. 2, C. dilutus, C. entis, C. frommeri, C. harpi, C. maturus, C. nr. atroviridis (sp. 2i), C. ochreatus, C. plumosus, C. staegeri and C. 'tigris') and three other species that remain unidentified (C. sp. NAI-III). No single approach served to delimit and identify larvae of all 17 Chironomus species that we collected. Although we expected that morphological criteria alone would be insufficient, our results suggest that DNA barcoding, using either the mitochondrial cox1 or the nuclear gb2β gene, was also inadequate for separating some Chironomus species. Thus we suggest that multiple approaches will often be needed to correctly identify Chironomus larvae to species.

  3. Ecological Flow Assessment to Improve the Spawning Habitat for the Four Major Species of Carp of the Yangtze River: A Study on Habitat Suitability Based on Ultrasonic Telemetry

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    Lixiong Yu

    2018-05-01

    Full Text Available Four major species of Chinese carp, namely black carp (Mylopharyngodon piceus, grass carp (Ctenopharyngodon idellus, silver carp (Hypophthalmichthys molitrix and bighead carp (Hypophthalmichthys nobilis, are important economic freshwater fish varieties in China. They primarily inhabit and breed in the Yangtze River. Unfortunately, the construction and operation of the Gezhouba Dam and the Three Gorges Dam have dramatically changed the hydrodynamic conditions in the middle reaches of the Yangtze River, leading to a sharp decline in the reproduction rates of these carp. The egg abundance of the four species of carp downstream from the Three Gorges Dam reached 8.35 billion in 1965, but abundance during 2005–2012 was only 0.25 billion. One of the main reasons was that the hydrodynamic conditions of the spawning ground could not meet the four species’ breeding requirements. However, due to the limitations of traditional detection tools, the spawning characteristics of these four species of carp were still unclear. In this study, the ultrasonic telemetry and a three–dimensional hydrodynamic model were utilized to build the habitat suitability index (HSI curves for the four species of carp. The habitat suitability model was then built based on HSI curves to assess spawning habitat quantity under different flow conditions. Finally, the habitat suitability model in the Yidu spawning ground was validated using 32 groups of sampling data in 2015 and 2017. The statistical results showed that the most suitable velocity ranged from 0.78 m/s to 0.93 m/s. The most suitable water depth ranged from 14.56 m to 16.35 m, and the most suitable Froude number ranged from 0.049 to 0.129. The habitat suitability model simulation results indicated that when the discharge was between 15,000 m3/s and 21,300 m3/s, the weighted usable area (WUA values in both the Yidu and Zhicheng spawning grounds would remain at a high level. The validation results showed that most

  4. EXTINCTION RISK OR LACK OF SAMPLING IN A THREATENED SPECIES: GENETIC STRUCTURE AND ENVIRONMENTAL SUITABILITY OF THE NEOTROPICAL FROG PRISTIMANTIS PENELOPUS (ANURA: CRAUGASTORIDAE)

    OpenAIRE

    RESTREPO, ADRIANA; VELASCO, JULIAN A.; DAZA, JUAN M.

    2017-01-01

    ABSTRACT IUCN Red Lists have been a valuable tool to prioritize conservation plans in endemic neotropical frogs. However, many areas in this region are poorly known in terms of their diversity and endemism. Based on examined museum specimens of the threatened species Pristimantis penelopus we revised its geographic distribution and determined the habitat suitability using niche modeling techniques. Using a mitochondrial fragment of COI gene, we determine the phylogenetic position and the exte...

  5. Identifying the main mosquito species in China based on DNA barcoding.

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    Gang Wang

    Full Text Available Mosquitoes are insects of the Diptera, Nematocera, and Culicidae families, some species of which are important disease vectors. Identifying mosquito species based on morphological characteristics is difficult, particularly the identification of specimens collected in the field as part of disease surveillance programs. Because of this difficulty, we constructed DNA barcodes of the cytochrome c oxidase subunit 1, the COI gene, for the more common mosquito species in China, including the major disease vectors. A total of 404 mosquito specimens were collected and assigned to 15 genera and 122 species and subspecies on the basis of morphological characteristics. Individuals of the same species grouped closely together in a Neighborhood-Joining tree based on COI sequence similarity, regardless of collection site. COI gene sequence divergence was approximately 30 times higher for species in the same genus than for members of the same species. Divergence in over 98% of congeneric species ranged from 2.3% to 21.8%, whereas divergence in conspecific individuals ranged from 0% to 1.67%. Cryptic species may be common and a few pseudogenes were detected.

  6. Development of Multiplexed Marker Sets to Identify the Most Relevant Poplar Species for Breeding

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    Hilke Schroeder

    2017-12-01

    Full Text Available Within the genus Populus, about 30 species are classified into six sections, of which some are cross-compatible. Besides naturally occurring hybrids, huge breeding programs have led to a high number of artificially produced hybrids, for which the determination of genetically involved species by morphological characteristics is often difficult. This necessitates the use of molecular markers for the identification of both maternal as well as paternal species, and in the case of complex hybrids, the genealogy. For this reason, we developed new chloroplast and nuclear markers for the differentiation of up to 19 poplar species, with one to 32 individuals per species regularly used in breeding programs based on already known barcoding, other chloroplast regions, and nuclear genes of interest. We developed methods to identify species by either species-specific nucleotide variations or, when no initial information for the species was given, by using a set of markers either in a procedure of exclusion or in a multiplexed marker set. The developed markers can all be used with low-cost equipment, and some can additionally be applied using a genetic analyzer. We combined these markers in multiplexes for a very fast and easy-to-use application for the identification of poplar species and their hybrids.

  7. Takifugu obscurus is a euryhaline fugu species very close to Takifugu rubripes and suitable for studying osmoregulation

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    Sakai Harumi

    2005-12-01

    Full Text Available Abstract Background The genome sequence of the pufferfish Takifugu rubripes is an enormously useful tool in the molecular physiology of fish. Euryhaline fish that can survive both in freshwater (FW and seawater (SW are also very useful for studying fish physiology, especially osmoregulation. Recently we learned that there is a pufferfish, Takifugu obscurus, common name "mefugu" that migrates into FW to spawn. If T. obscurus is indeed a euryhaline fish and shares a high sequence homology with T. rubripes, it will become a superior animal model for studying the mechanism of osmoregulation. We have therefore determined its euryhalinity and phylogenetic relationship to the members of the Takifugu family. Results The following six Takifugu species were used for the analyses: T. obscurus, T. rubripes, T. niphobles, T. pardalis, T. poecilonotus, and T. porphyreus. When transferred to FW, only T. obscurus could survive while the others could not survive more than ten days in FW. During this course of FW adaptation, serum Na+ concentration of T. obscurus decreased only slightly, but a rapid and large decrease occurred even in the case of T. niphobles, a peripheral fresh water species that is often seen in brackish river mouths. Phylogenetic analysis using nucleotide sequences of the mitochondrial 16S ribosomal RNA gene of each species indicated that the six Takifugu species are very closely related with each other. Conclusion T. obscurus is capable of adapting to both FW and SW. Its genomic sequence shares a very high homology with those of the other Takifugu species such that the existing Takifugu genomic information resources can be utilized. These properties make "mefugu", which has drawn little attention from animal physiologists until this study, a useful model animal for studying the molecular mechanism of maintaining body fluid homeostasis.

  8. New chloroplast microsatellite markers suitable for assessing genetic diversity of Lolium perenne and other related grass species.

    Science.gov (United States)

    Diekmann, Kerstin; Hodkinson, Trevor R; Barth, Susanne

    2012-11-01

    Lolium perenne (perennial ryegrass) is the most important forage grass species of temperate regions. We have previously released the chloroplast genome sequence of L. perenne 'Cashel'. Here nine chloroplast microsatellite markers are published, which were designed based on knowledge about genetically variable regions within the L. perenne chloroplast genome. These markers were successfully used for characterizing the genetic diversity in Lolium and different grass species. Chloroplast genomes of 14 Poaceae taxa were screened for mononucleotide microsatellite repeat regions and primers designed for their amplification from nine loci. The potential of these markers to assess genetic diversity was evaluated on a set of 16 Irish and 15 European L. perenne ecotypes, nine L. perenne cultivars, other Lolium taxa and other grass species. All analysed Poaceae chloroplast genomes contained more than 200 mononucleotide repeats (chloroplast simple sequence repeats, cpSSRs) of at least 7 bp in length, concentrated mainly in the large single copy region of the genome. Nucleotide composition varied considerably among subfamilies (with Pooideae biased towards poly A repeats). The nine new markers distinguish L. perenne from all non-Lolium taxa. TeaCpSSR28 was able to distinguish between all Lolium species and Lolium multiflorum due to an elongation of an A(8) mononucleotide repeat in L. multiflorum. TeaCpSSR31 detected a considerable degree of microsatellite length variation and single nucleotide polymorphism. TeaCpSSR27 revealed variation within some L. perenne accessions due to a 44-bp indel and was hence readily detected by simple agarose gel electrophoresis. Smaller insertion/deletion events or single nucleotide polymorphisms detected by these new markers could be visualized by polyacrylamide gel electrophoresis or DNA sequencing, respectively. The new markers are a valuable tool for plant breeding companies, seed testing agencies and the wider scientific community due to

  9. Use of a mitochondrial COI sequence to identify species of the subtribe Aphidina (Hemiptera, Aphididae

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    Jianfeng WANG

    2011-08-01

    Full Text Available Aphids of the subtribe Aphidina are found mainly in the North Temperate Zone. The relative lack of diagnostic morphological characteristics has obscured the identification of species in this group. However, DNA-based taxonomic methods can clarify species relationships within this group. Sequence variation in a partial segment of the mitochondrial COI gene was highly effective for resolving species relationships within Aphidina. Forty-five species were correctly identified in a neighbor-joining tree. Mean intraspecific sequence divergence was 0.17%, with a range of 0.00% to 1.54%. Mean interspecific divergence within previously recognized genera or morphologically similar species groups was 4.54%, with variation mainly in the range of 3.50% to 8.00%. Possible reasons for anomalous levels of mean nucleotide divergence within or between some taxa are discussed.

  10. Using citizen science data to identify the sensitivity of species to human land use.

    Science.gov (United States)

    Todd, Brian D; Rose, Jonathan P; Price, Steven J; Dorcas, Michael E

    2016-12-01

    Conservation practitioners must contend with an increasing array of threats that affect biodiversity. Citizen scientists can provide timely and expansive information for addressing these threats across large scales, but their data may contain sampling biases. We used randomization procedures to account for possible sampling biases in opportunistically reported citizen science data to identify species' sensitivities to human land use. We analyzed 21,044 records of 143 native reptile and amphibian species reported to the Carolina Herp Atlas from North Carolina and South Carolina between 1 January 1990 and 12 July 2014. Sensitive species significantly associated with natural landscapes were 3.4 times more likely to be legally protected or treated as of conservation concern by state resource agencies than less sensitive species significantly associated with human-dominated landscapes. Many of the species significantly associated with natural landscapes occurred primarily in habitats that had been nearly eradicated or otherwise altered in the Carolinas, including isolated wetlands, longleaf pine savannas, and Appalachian forests. Rare species with few reports were more likely to be associated with natural landscapes and 3.2 times more likely to be legally protected or treated as of conservation concern than species with at least 20 reported occurrences. Our results suggest that opportunistically reported citizen science data can be used to identify sensitive species and that species currently restricted primarily to natural landscapes are likely at greatest risk of decline from future losses of natural habitat. Our approach demonstrates the usefulness of citizen science data in prioritizing conservation and in helping practitioners address species declines and extinctions at large extents. © 2016 Society for Conservation Biology.

  11. A novel mini-DNA barcoding assay to identify processed fins from internationally protected shark species.

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    Fields, Andrew T; Abercrombie, Debra L; Eng, Rowena; Feldheim, Kevin; Chapman, Demian D

    2015-01-01

    There is a growing need to identify shark products in trade, in part due to the recent listing of five commercially important species on the Appendices of the Convention on International Trade in Endangered Species (CITES; porbeagle, Lamna nasus, oceanic whitetip, Carcharhinus longimanus scalloped hammerhead, Sphyrna lewini, smooth hammerhead, S. zygaena and great hammerhead S. mokarran) in addition to three species listed in the early part of this century (whale, Rhincodon typus, basking, Cetorhinus maximus, and white, Carcharodon carcharias). Shark fins are traded internationally to supply the Asian dried seafood market, in which they are used to make the luxury dish shark fin soup. Shark fins usually enter international trade with their skin still intact and can be identified using morphological characters or standard DNA-barcoding approaches. Once they reach Asia and are traded in this region the skin is removed and they are treated with chemicals that eliminate many key diagnostic characters and degrade their DNA ("processed fins"). Here, we present a validated mini-barcode assay based on partial sequences of the cytochrome oxidase I gene that can reliably identify the processed fins of seven of the eight CITES listed shark species. We also demonstrate that the assay can even frequently identify the species or genus of origin of shark fin soup (31 out of 50 samples).

  12. A novel mini-DNA barcoding assay to identify processed fins from internationally protected shark species.

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    Andrew T Fields

    Full Text Available There is a growing need to identify shark products in trade, in part due to the recent listing of five commercially important species on the Appendices of the Convention on International Trade in Endangered Species (CITES; porbeagle, Lamna nasus, oceanic whitetip, Carcharhinus longimanus scalloped hammerhead, Sphyrna lewini, smooth hammerhead, S. zygaena and great hammerhead S. mokarran in addition to three species listed in the early part of this century (whale, Rhincodon typus, basking, Cetorhinus maximus, and white, Carcharodon carcharias. Shark fins are traded internationally to supply the Asian dried seafood market, in which they are used to make the luxury dish shark fin soup. Shark fins usually enter international trade with their skin still intact and can be identified using morphological characters or standard DNA-barcoding approaches. Once they reach Asia and are traded in this region the skin is removed and they are treated with chemicals that eliminate many key diagnostic characters and degrade their DNA ("processed fins". Here, we present a validated mini-barcode assay based on partial sequences of the cytochrome oxidase I gene that can reliably identify the processed fins of seven of the eight CITES listed shark species. We also demonstrate that the assay can even frequently identify the species or genus of origin of shark fin soup (31 out of 50 samples.

  13. Identifying knowledge gaps for gene drive research to control invasive animal species: The next CRISPR step

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    Dorian Moro

    2018-01-01

    Full Text Available Invasive animals have been linked to the extinctions of native wildlife, and to significant agricultural financial losses or impacts. Current approaches to control invasive species require ongoing resources and management over large geographic scales, and often result in the short-term suppression of populations. New and innovative approaches are warranted. Recently, the RNA guided gene drive system based on CRISPR/Cas9 is being proposed as a potential gene editing tool that could be used by wildlife managers as a non-lethal addition or alternative to help reduce pest animal populations. While regulatory control and social acceptance are crucial issues that must be addressed, there is an opportunity now to identify the knowledge and research gaps that exist for some important invasive species. Here we systematically determine the knowledge gaps for pest species for which gene drives could potentially be applied. We apply a conceptual ecological risk framework within the gene drive context within an Australian environment to identify key requirements for undertaking work on seven exemplar invasive species in Australia. This framework allows an evaluation of the potential research on an invasive species of interest and within a gene drive and risk context. We consider the currently available biological, genetic and ecological information for the house mouse, European red fox, feral cat, European rabbit, cane toad, black rat and European starling to evaluate knowledge gaps and identify candidate species for future research. We discuss these findings in the context of future thematic areas of research worth pursuing in preparation for a more formal assessment of the use of gene drives as a novel strategy for the control of these and other invasive species. Keywords: Invasive species, Gene drive, CRISPR, Pest management, Islands

  14. An exploration on greenhouse gas and ammonia production by insect species suitable for animal or human consumption.

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    Dennis G A B Oonincx

    Full Text Available BACKGROUND: Greenhouse gas (GHG production, as a cause of climate change, is considered as one of the biggest problems society is currently facing. The livestock sector is one of the large contributors of anthropogenic GHG emissions. Also, large amounts of ammonia (NH(3, leading to soil nitrification and acidification, are produced by livestock. Therefore other sources of animal protein, like edible insects, are currently being considered. METHODOLOGY/PRINCIPAL FINDINGS: An experiment was conducted to quantify production of carbon dioxide (CO₂ and average daily gain (ADG as a measure of feed conversion efficiency, and to quantify the production of the greenhouse gases methane (CH₄ and nitrous oxide (N₂O as well as NH₃ by five insect species of which the first three are considered edible: Tenebrio molitor, Acheta domesticus, Locusta migratoria, Pachnoda marginata, and Blaptica dubia. Large differences were found among the species regarding their production of CO₂ and GHGs. The insects in this study had a higher relative growth rate and emitted comparable or lower amounts of GHG than described in literature for pigs and much lower amounts of GHG than cattle. The same was true for CO₂ production per kg of metabolic weight and per kg of mass gain. Furthermore, also the production of NH₃ by insects was lower than for conventional livestock. CONCLUSIONS/SIGNIFICANCE: This study therefore indicates that insects could serve as a more environmentally friendly alternative for the production of animal protein with respect to GHG and NH₃ emissions. The results of this study can be used as basic information to compare the production of insects with conventional livestock by means of a life cycle analysis.

  15. An exploration on greenhouse gas and ammonia production by insect species suitable for animal or human consumption.

    Science.gov (United States)

    Oonincx, Dennis G A B; van Itterbeeck, Joost; Heetkamp, Marcel J W; van den Brand, Henry; van Loon, Joop J A; van Huis, Arnold

    2010-12-29

    Greenhouse gas (GHG) production, as a cause of climate change, is considered as one of the biggest problems society is currently facing. The livestock sector is one of the large contributors of anthropogenic GHG emissions. Also, large amounts of ammonia (NH(3)), leading to soil nitrification and acidification, are produced by livestock. Therefore other sources of animal protein, like edible insects, are currently being considered. An experiment was conducted to quantify production of carbon dioxide (CO₂) and average daily gain (ADG) as a measure of feed conversion efficiency, and to quantify the production of the greenhouse gases methane (CH₄) and nitrous oxide (N₂O) as well as NH₃ by five insect species of which the first three are considered edible: Tenebrio molitor, Acheta domesticus, Locusta migratoria, Pachnoda marginata, and Blaptica dubia. Large differences were found among the species regarding their production of CO₂ and GHGs. The insects in this study had a higher relative growth rate and emitted comparable or lower amounts of GHG than described in literature for pigs and much lower amounts of GHG than cattle. The same was true for CO₂ production per kg of metabolic weight and per kg of mass gain. Furthermore, also the production of NH₃ by insects was lower than for conventional livestock. This study therefore indicates that insects could serve as a more environmentally friendly alternative for the production of animal protein with respect to GHG and NH₃ emissions. The results of this study can be used as basic information to compare the production of insects with conventional livestock by means of a life cycle analysis.

  16. Land Suitability Evaluation for Blueberry Crop by Determining the Qualitative Properties of the Identified Soil Type Related with the Antioxidant Capacity of Fruits

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    Amalia Ioana BOT

    2017-12-01

    Full Text Available Organic and inorganic forms of nitrogen and carbon were measured in order to determine soil fertility. The amount of total nitrogen ranged between 0.849 g/kg and 1.755 g/kg in the samples gathered from soil in modified state and between 0.961 k/kg and 2.427 g/kg in the samples collected from the soil in natural state. Based on these results it could be concluded that in comparing with the previous year, plants used the soil nutrients for their development. The activities of different enzymes were measured as well. Nitrate reductase activity was also higher in samples collected from soil in modified state (from bilon than in the samples collected near plantations (control samples and the values ranged between 0.055 ± 0.012 μmol⋅h-1⋅g-1 and 1.018 ± 0.117 μmol⋅h-1⋅g-1 in samples from soil in natural state and between 0.013 ± 0.002 μmol⋅h-1⋅g-1 and 0.447 ± 0.083 μmol⋅h-1⋅g-1 in bilons. Using GIS techniques of spatial analysis to determine the exact type of soil from each studied blueberry plantation from the Northwest Region of Development and also based on the soil bio-chemical analyses, it was possible to achieve a qualitative characterization of the territory, taking into account the requirements of blueberries for cultivation and to achieve a land suitability for blueberry crop. Combining laboratory approach, consisting from soil bio-chemical and physico-chemical analyses and chemical analyses of blueberry fruits, with the techniques used in order to determine the soil type and land suitability, the study conducted in the Northwest Region of Development identified the best conditions for blueberry crop, based on the qualitative characterization of land.

  17. Applying high-resolution melting (HRM) technology to identify five commonly used Artemisia species.

    Science.gov (United States)

    Song, Ming; Li, Jingjian; Xiong, Chao; Liu, Hexia; Liang, Junsong

    2016-10-04

    Many members of the genus Artemisia are important for medicinal purposes with multiple pharmacological properties. Often, these herbal plants sold on the markets are in processed forms so it is difficult to authenticate. Routine testing and identification of these herbal materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. In this study, five commonly used Artemisia species included Artemisia argyi, Artemisia annua, Artemisia lavandulaefolia, Artemisia indica, and Artemisia atrovirens were analyzed using high resolution melting (HRM) analysis based on the internal transcribed spacer 2 (ITS2) sequences. The melting profiles of the ITS2 amplicons of the five closely related herbal species are clearly separated so that they can be differentiated by HRM method. The method was further applied to authenticate commercial products in powdered. HRM curves of all the commercial samples tested are similar to the botanical species as labeled. These congeneric medicinal products were also clearly separated using the neighbor-joining (NJ) tree. Therefore, HRM method could provide an efficient and reliable authentication system to distinguish these commonly used Artemisia herbal products on the markets and offer a technical reference for medicines quality control in the drug supply chain.

  18. Potential use of ionic species for identifying source land-uses of stormwater runoff.

    Science.gov (United States)

    Lee, Dong Hoon; Kim, Jin Hwi; Mendoza, Joseph A; Lee, Chang-Hee; Kang, Joo-Hyon

    2017-02-01

    Identifying critical land-uses or source areas is important to prioritize resources for cost-effective stormwater management. This study investigated the use of information on ionic composition as a fingerprint to identify the source land-use of stormwater runoff. We used 12 ionic species in stormwater runoff monitored for a total of 20 storm events at five sites with different land-use compositions during the 2012-2014 wet seasons. A stepwise forward discriminant function analysis (DFA) with the jack-knifed cross validation approach was used to select ionic species that better discriminate the land-use of its source. Of the 12 ionic species, 9 species (K + , Mg 2+ , Na + , NH 4 + , Br - , Cl - , F - , NO 2 - , and SO 4 2- ) were selected for better performance of the DFA. The DFA successfully differentiated stormwater samples from urban, rural, and construction sites using concentrations of the ionic species (70%, 95%, and 91% of correct classification, respectively). Over 80% of the new data cases were correctly classified by the trained DFA model. When applied to data cases from a mixed land-use catchment and downstream, the DFA model showed the greater impact of urban areas and rural areas respectively in the earlier and later parts of a storm event.

  19. PCR-RFLP diagnostic method for identifying Globodera species in Slovenia

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    Sasa ŠIRCA

    2011-01-01

    Full Text Available Species identification within the genus Globodera is based on the morphological and morphometrical characters of the cysts and second stage juveniles, and these are included in the majority of identification keys. Morphometrical methods are fast and can be applied to most of samples but they demand a trained and experienced specialist. Furthermore, some morphometrical characters may overlap between populations and beetwen species, leading to inaccurate identification. To confirm and complement the morphometrical identification of Globodera species molecular methods have been developed. Sequences of the internal transcribed spacer regions ITS1 and ITS2 of the rDNA gene cluster proved to be useful for identifying nematode species identification. A PCR-RFLP molecular method was used to identify Globodera rostochiensis, G. pallida, G. tabacum and G. achilleae. Globodera rostochiensis, G. pallida, G. tabacum and G. achilleae can be distinguished with PCR-RFLP analysis of the rDNA ITS fragment using five restriction enzymes. The RFLP patterns of G. rostochiensis, G. tabacum and G. achilleae were species-specific, while those of G. pallida varied. South American populations of G. pallida differed from other populations as their RFLP patterns were demonstrated to be distinct by in silico restriction of the ITS sequences deposited at NCBI.

  20. Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease.

    Science.gov (United States)

    Gomez-Valero, Laura; Rusniok, Christophe; Rolando, Monica; Neou, Mario; Dervins-Ravault, Delphine; Demirtas, Jasmin; Rouy, Zoe; Moore, Robert J; Chen, Honglei; Petty, Nicola K; Jarraud, Sophie; Etienne, Jerome; Steinert, Michael; Heuner, Klaus; Gribaldo, Simonetta; Médigue, Claudine; Glöckner, Gernot; Hartland, Elizabeth L; Buchrieser, Carmen

    2014-01-01

    The genus Legionella comprises over 60 species. However, L. pneumophila and L. longbeachae alone cause over 95% of Legionnaires’ disease. To identify the genetic bases underlying the different capacities to cause disease we sequenced and compared the genomes of L. micdadei, L. hackeliae and L. fallonii (LLAP10), which are all rarely isolated from humans. We show that these Legionella species possess different virulence capacities in amoeba and macrophages, correlating with their occurrence in humans. Our comparative analysis of 11 Legionella genomes belonging to five species reveals highly heterogeneous genome content with over 60% representing species-specific genes; these comprise a complete prophage in L. micdadei, the first ever identified in a Legionella genome. Mobile elements are abundant in Legionella genomes; many encode type IV secretion systems for conjugative transfer, pointing to their importance for adaptation of the genus. The Dot/Icm secretion system is conserved, although the core set of substrates is small, as only 24 out of over 300 described Dot/Icm effector genes are present in all Legionella species. We also identified new eukaryotic motifs including thaumatin, synaptobrevin or clathrin/coatomer adaptine like domains. Legionella genomes are highly dynamic due to a large mobilome mainly comprising type IV secretion systems, while a minority of core substrates is shared among the diverse species. Eukaryotic like proteins and motifs remain a hallmark of the genus Legionella. Key factors such as proteins involved in oxygen binding, iron storage, host membrane transport and certain Dot/Icm substrates are specific features of disease-related strains.

  1. PCR-RFLP Method to Identify Salmonid Species of Economic Importance

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    Andreea Dudu

    2011-05-01

    Full Text Available The identification of different fish species by molecular methods has become necessary to avoid both the incorrect labelling of individuals involved in repopulation programmes and the commercial frauds on the fish market. Different fish species of great economical importance, like the salmonids, which are very much requested for their meat, can be identified using molecular techniques such as PCR-RFLP. The method is based on the amplification of a target region from the genome by PCR reaction followed by endonucleases digestion to detect the polymorphism of restriction fragments. In our study we analysed the following salmonid species from Romania: Salmo trutta fario, Salmo labrax, Salvelinus fontinalis, Onchorhynchus mykiss, Thymallus thymallus and Hucho hucho. In order to discriminate between the analysed species we amplified a fragment of mitochondrial genome comprising tRNAGlu/ cytochrome b/ tRNAThr/ tRNAPro/ D-loop/ tRNAPhe, followed by digestion with a specific restriction enzyme. The direct digestion of unpurified PCR products generated species-specific restriction patterns and proved to be a simple, reliable, inexpensive and fast method. Thus, it may be successfully utilized in specialized laboratories for the correct identification of the fish species for multiple purposes, including the traceability of fish food products.

  2. A molecular method to detect and identify the native species of southwestern Atlantic Crassostrea (Mollusca: Ostreidae

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    Sandra Ludwig

    2011-08-01

    Full Text Available Among oysters, species of Crassostrea (Sacco, 1897 are the most attractive to aquaculture. In Brazil, the genus is represented by C. rhizophorae (Guilding, 1828 and C. brasiliana (Lamarck, 1819. Because the maturation and breeding technology is not well developed for these species, aquaculturists need a reliable method to decide the correct time to place spat collectors in the field, and to identify both species, which are morphologically similar. In this study a specific Multiplex PCR protocol was developed, using one pair of universal primers from 18S rDNA as a positive control and a pair of specific primers for each target species. The sensitivity and specificity of the protocol was evaluated. It detected C. rhizophorae DNA in low concentrations, and C. brasiliana DNA in even lower concentrations. Further, the Multiplex PCR proved efficient in detecting DNA in concentrations equivalent to that of a single larva of each species, either separated or combined, when mixed with total DNA extract of a plankton sample representing 1000 L of filtered water. Field tests confirmed the applicability of the protocol, which holds the promise to become an important tool for aquaculture or conservation programs, allowing for the continuous monitoring of the life cycle of C. brasiliana and C. rhizophorae, by detecting the right periods of larval release and settlement.

  3. Analysis of sequence diversity through internal transcribed spacers and simple sequence repeats to identify Dendrobium species.

    Science.gov (United States)

    Liu, Y T; Chen, R K; Lin, S J; Chen, Y C; Chin, S W; Chen, F C; Lee, C Y

    2014-04-08

    The Orchidaceae is one of the largest and most diverse families of flowering plants. The Dendrobium genus has high economic potential as ornamental plants and for medicinal purposes. In addition, the species of this genus are able to produce large crops. However, many Dendrobium varieties are very similar in outward appearance, making it difficult to distinguish one species from another. This study demonstrated that the 12 Dendrobium species used in this study may be divided into 2 groups by internal transcribed spacer (ITS) sequence analysis. Red and yellow flowers may also be used to separate these species into 2 main groups. In particular, the deciduous characteristic is associated with the ITS genetic diversity of the A group. Of 53 designed simple sequence repeat (SSR) primer pairs, 7 pairs were polymorphic for polymerase chain reaction products that were amplified from a specific band. The results of this study demonstrate that these 7 SSR primer pairs may potentially be used to identify Dendrobium species and their progeny in future studies.

  4. EXTINCTION RISK OR LACK OF SAMPLING IN A THREATENED SPECIES: GENETIC STRUCTURE AND ENVIRONMENTAL SUITABILITY OF THE NEOTROPICAL FROG PRISTIMANTIS PENELOPUS (ANURA: CRAUGASTORIDAE

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    ADRIANA RESTREPO

    Full Text Available ABSTRACT IUCN Red Lists have been a valuable tool to prioritize conservation plans in endemic neotropical frogs. However, many areas in this region are poorly known in terms of their diversity and endemism. Based on examined museum specimens of the threatened species Pristimantis penelopus we revised its geographic distribution and determined the habitat suitability using niche modeling techniques. Using a mitochondrial fragment of COI gene, we determine the phylogenetic position and the extent of the genetic variation across its distribution in Colombia. We present the first records of P. penelopus for the Cordillera Oriental, the western versant of Cordillera Occidental and the northern portion of the Cauca river basin. Based on the molecular phylogenetic analysis, Pristimantis penelopus belongs to the P. ridens series sensu (Padial et al., 2014. The mean of intraspecific genetic variation is 2.1% and the variation among population ranges between 2.3 and 3.5%. The genetic distance between the western populations and the Magdalena Valley populations suggests a potential phylogeographic break in northwestern Antioquia. We expand the realized distribution by 258 kilometers north, 200 km east and 223 km northwest. Based on our results and according to the IUCN criteria we propose a new category for the species and highlight the need to increase the surveys in poorly known regions to better understand the geographic distribution and conservation status of listed species.

  5. Microsatellite Primers Identified by 454 Sequencing in the Floodplain Tree Species Eucalyptus victrix (Myrtaceae

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    Paul G. Nevill

    2013-05-01

    Full Text Available Premise of the study: Microsatellite primers were developed for Eucalyptus victrix (Myrtaceae to evaluate the population and spatial genetic structure of this widespread northwestern Australian riparian tree species, which may be impacted by hydrological changes associated with mining activity. Methods and Results: 454 GS-FLX shotgun sequencing was used to obtain 1895 sequences containing putative microsatellite motifs. Ten polymorphic microsatellite loci were identified and screened for variation in individuals from two populations in the Pilbara region. Observed heterozygosities ranged from 0.44 to 0.91 (mean: 0.66 and the number of alleles per locus ranged from five to 25 (average: 11. Conclusions: These microsatellite loci will be useful in future studies of population and spatial genetic structure in E. victrix, and inform the development of seed sourcing strategies for the species.

  6. A suite of molecular markers for identifying species, detecting introgression and describing population structure in spadefoot toads (Spea spp.).

    Science.gov (United States)

    Pfennig, Karin S; Allenby, Ashley; Martin, Ryan A; Monroy, Anaïs; Jones, Corbin D

    2012-09-01

    Two congeneric species of spadefoot toad, Spea multiplicata and Spea bombifrons, have been the focus of hybridization studies since the 1970s. Because complex hybrids are not readily distinguished phenotypically, genetic markers are needed to identify introgressed individuals. We therefore developed a set of molecular markers (amplified fragment length polymorphism, polymerase chain reaction-restriction fragment length polymorphism and single nucleotide polymorphism) for identifying pure-species, F1 hybrids and more complex introgressed types. To do so, we tested a series of markers across both species and known hybrids using populations in both allopatry and sympatry. We retained those markers that differentiated the two pure-species and also consistently identified known species hybrids. These markers are well suited for identifying hybrids between these species. Moreover, those markers that show variation within each species can be used in conjunction with existing molecular markers in studies of population structure and gene flow. © 2012 Blackwell Publishing Ltd.

  7. A cross-species genetic analysis identifies candidate genes for mouse anxiety and human bipolar disorder

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    David G Ashbrook

    2015-07-01

    Full Text Available Bipolar disorder (BD is a significant neuropsychiatric disorder with a lifetime prevalence of ~1%. To identify genetic variants underlying BD genome-wide association studies (GWAS have been carried out. While many variants of small effect associated with BD have been identified few have yet been confirmed, partly because of the low power of GWAS due to multiple comparisons being made. Complementary mapping studies using murine models have identified genetic variants for behavioral traits linked to BD, often with high power, but these identified regions often contain too many genes for clear identification of candidate genes. In the current study we have aligned human BD GWAS results and mouse linkage studies to help define and evaluate candidate genes linked to BD, seeking to use the power of the mouse mapping with the precision of GWAS. We use quantitative trait mapping for open field test and elevated zero maze data in the largest mammalian model system, the BXD recombinant inbred mouse population, to identify genomic regions associated with these BD-like phenotypes. We then investigate these regions in whole genome data from the Psychiatric Genomics Consortium’s bipolar disorder GWAS to identify candidate genes associated with BD. Finally we establish the biological relevance and pathways of these genes in a comprehensive systems genetics analysis.We identify four genes associated with both mouse anxiety and human BD. While TNR is a novel candidate for BD, we can confirm previously suggested associations with CMYA5, MCTP1 and RXRG. A cross-species, systems genetics analysis shows that MCTP1, RXRG and TNR coexpress with genes linked to psychiatric disorders and identify the striatum as a potential site of action. CMYA5, MCTP1, RXRG and TNR are associated with mouse anxiety and human BD. We hypothesize that MCTP1, RXRG and TNR influence intercellular signaling in the striatum.

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

    Science.gov (United States)

    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.

  9. Identifying Chloris Species from Cuban Citrus Orchards and Determining Their Glyphosate-Resistance Status

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    Enzo R. Bracamonte

    2017-11-01

    Full Text Available The Chloris genus is a C4 photosynthetic species mainly distributed in tropical and subtropical regions. Populations of three Chloris species occurring in citrus orchards from central Cuba, under long history glyphosate-based weed management, were studied for glyphosate-resistant status by characterizing their herbicide resistance/tolerance mechanisms. Morphological and molecular analyses allowed these species to be identified as C. ciliata Sw., Chloris elata Desv., and Chloris barbata Sw. Based on the glyphosate rate that causes 50% mortality of the treated plants, glyphosate resistance (R was confirmed only in C. elata, The R population was 6.1-fold more resistant compared to the susceptible (S population. In addition, R plants of C. elata accumulated 4.6-fold less shikimate after glyphosate application than S plants. Meanwhile, populations of C. barbata and C. ciliata with or without glyphosate application histories showed similar LD50 values and shikimic acid accumulation rates, demonstrating that resistance to glyphosate have not evolved in these species. Plants of R and S populations of C. elata differed in 14C-glyphosate absorption and translocation. The R population exhibited 27.3-fold greater 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS activity than the S population due to a target site mutation corresponding to a Pro-106-Ser substitution found in the EPSPS gene. These reports show the innate tolerance to glyphosate of C. barbata and C. ciliata, and confirm the resistance of C. elata to this herbicide, showing that both non-target site and target-site mechanisms are involved in its resistance to glyphosate. This is the first case of herbicide resistance in Cuba.

  10. Identifying Feasible Locations for Wetland Creation or Restoration in Catchments by Suitability Modelling Using Light Detection and Ranging (LiDAR Digital Elevation Model (DEM

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    Evelyn Uuemaa

    2018-04-01

    Full Text Available Wetlands play a key role in controlling flooding and non-point-source (diffuse pollution. They are therefore an important tool for mitigating diffuse water pollution from farms. However, to use this tool, it is necessary to obtain detailed assessments and identification of potential wetland restoration or creation sites. This is complicated by the diversity of landscapes, environmental conditions, and land ownership. Site suitability for wetland restoration or creation depends on many factors: the underlying geology, soils, topography, hydrology, drainage, and land ownership. Local hydrology and soils are among the most important factors. However, the inventory and characterization of a site’s soils and hydrology often requires extensive, expensive, and time-consuming ground surveys, and it is therefore limited to small areas. Another possibility would be to consider topography, which strongly determines water movement patterns. Light detection and ranging (LiDAR data provides detailed topographic information and can be acquired by remote sensing. Our study showed that terrain analysis using high-resolution topographical data can produce suitability maps for wetlands that can be easily used by decision makers and planners in watershed management. The rapid methodology reveals potential wetland creation or restoration sites at a reasonable cost; with the resulting spatially explicit suitability map, managers can plan for wetland creation or restoration without having to wait for field-data collection.

  11. Comparative and bioinformatics analyses of pathogenic bacterial secretomes identified by mass spectrometry in Burkholderia species.

    Science.gov (United States)

    Nguyen, Thao Thi; Chon, Tae-Soo; Kim, Jaehan; Seo, Young-Su; Heo, Muyoung

    2017-07-01

    Secreted proteins (secretomes) play crucial roles during bacterial pathogenesis in both plant and human hosts. The identification and characterization of secretomes in the two plant pathogens Burkholderia glumae BGR1 and B. gladioli BSR3, which cause diseases in rice such as seedling blight, panicle blight, and grain rot, are important steps to not only understand the disease-causing mechanisms but also find remedies for the diseases. Here, we identified two datasets of secretomes in B. glumae BGR1 and B. gladioli BSR3, which consist of 118 and 111 proteins, respectively, using mass spectrometry approach and literature curation. Next, we characterized the functional properties, potential secretion pathways and sequence information properties of secretomes of two plant pathogens in a comparative analysis by various computational approaches. The ratio of potential non-classically secreted proteins (NCSPs) to classically secreted proteins (CSPs) in B. glumae BGR1 was greater than that in B. gladioli BSR3. For CSPs, the putative hydrophobic regions (PHRs) which are essential for secretion process of CSPs were screened in detail at their N-terminal sequences using hidden Markov model (HMM)-based method. Total 31 pairs of homologous proteins in two bacterial secretomes were indicated based on the global alignment (identity ≥ 70%). Our results may facilitate the understanding of the species-specific features of secretomes in two plant pathogenic Burkholderia species.

  12. Cross-species epigenetics identifies a critical role for VAV1 in SHH subgroup medulloblastoma maintenance.

    Science.gov (United States)

    Lindsey, J C; Kawauchi, D; Schwalbe, E C; Solecki, D J; Selby, M P; McKinnon, P J; Olson, J M; Hayden, J T; Grundy, R G; Ellison, D W; Williamson, D; Bailey, S; Roussel, M F; Clifford, S C

    2015-09-03

    The identification of key tumorigenic events in Sonic Hedgehog (SHH) subgroup medulloblastomas (MBSHH) will be essential for the development of individualized therapies and improved outcomes. However, beyond confirmation of characteristic SHH pathway mutations, recent genome-wide sequencing studies have not revealed commonly mutated genes with widespread relevance as potential therapeutic targets. We therefore examined any role for epigenetic DNA methylation events in MBSHH using a cross-species approach to candidate identification, prioritization and validation. MBSHH-associated DNA methylation events were first identified in 216 subgrouped human medulloblastomas (50 MBSHH, 28 Wnt/Wingless, 44 Group 3 and 94 Group 4) and their conservation then assessed in tumors arising from four independent murine models of Shh medulloblastoma, alongside any role in tumorigenesis using functional assessments in mouse and human models. This strategy identified widespread regional CpG hypo-methylation of VAV1, leading to its elevated expression, as a conserved aberrant epigenetic event, which characterizes the majority of MBSHH tumors in both species, and is associated with a poor outcome in MBSHH patients. Moreover, direct modulation of VAV1 in mouse and human models revealed a critical role in tumor maintenance, and its abrogation markedly reduced medulloblastoma growth. Further, Vav1 activity regulated granule neuron precursor germinal zone exit and migration initiation in an ex vivo model of early postnatal cerebellar development. These findings establish VAV1 as a critical epigenetically regulated oncogene with a key role in MBSHH maintenance, and highlight its potential as a validated therapeutic target and prognostic biomarker for the improved therapy of medulloblastoma.

  13. Imaging mass spectrometry identifies prognostic ganglioside species in rodent intracranial transplants of glioma and medulloblastoma.

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    Leonardo Ermini

    Full Text Available Matrix-assisted laser desorption ionization (MALDI imaging mass spectrometry (MALDI-MSI allows us to investigate the distribution of lipid molecules within tissues. We used MALDI-MSI to identify prognostic gangliosides in tissue sections of rat intracranial allografts of rat glioma and mouse intracranial xenografts of human medulloblastoma. In the healthy adult rodent brain, GM1 and GD1 were the main types of glycolipids. Both gangliosides were absent in both intracranial transplants. The ganglioside GM3 was not present in the healthy adult brain but was highly expressed in rat glioma allografts. In combination with tandem mass spectrometry GM3 (d18:1/C24:0 was identified as the most abundant ganglioside species in the glioma allotransplant. By contrast, mouse xenografts of human medulloblastoma were characterized by prominent expression of the ganglioside GM2 (d18:0/C18:0. Together, these data demonstrate that tissue-based MALDI-MSI of gangliosides is able to discriminate between different brain tumors and may be a useful clinical tool for their classification and grading.

  14. Competitive interactions between co-occurring invaders: identifying asymmetries between two invasive crayfish species

    NARCIS (Netherlands)

    Hudina, S.; Galic, N.G.; Roessink, I.; Hock, K.

    2011-01-01

    Ecosystems today increasingly suffer invasions by multiple invasive species. Complex interactions between invasive species can have different fitness implications for each invader, which can in turn determine the future progression of their invasions and result in differential impacts on native

  15. Using single strand conformational polymorphisms (SSCP) to identify Phytophthora species in Oregon forests affected by sudden oak death

    Science.gov (United States)

    E. Hansen; C. Hesse; P. Reeser; W. Sutton; L. Winton

    2006-01-01

    Phytophthora species are abundant in streams, widespread in soils and occasionally found in diseased plants in the tanoak forests of southwestern Oregon. It is time-consuming and expensive to identify hundreds of isolates to species using morphology or internal transribed spacer (ITS) sequencing. We modified a published Phytophthora...

  16. A framework for identifying plant species to be used as 'ecological engineers' for fixing soil on unstable slopes.

    Science.gov (United States)

    Ghestem, Murielle; Cao, Kunfang; Ma, Wenzhang; Rowe, Nick; Leclerc, Raphaëlle; Gadenne, Clément; Stokes, Alexia

    2014-01-01

    Major reforestation programs have been initiated on hillsides prone to erosion and landslides in China, but no framework exists to guide managers in the choice of plant species. We developed such a framework based on the suitability of given plant traits for fixing soil on steep slopes in western Yunnan, China. We examined the utility of 55 native and exotic species with regard to the services they provided. We then chose nine species differing in life form. Plant root system architecture, root mechanical and physiological traits were then measured at two adjacent field sites. One site was highly unstable, with severe soil slippage and erosion. The second site had been replanted 8 years previously and appeared to be physically stable. How root traits differed between sites, season, depth in soil and distance from the plant stem were determined. Root system morphology was analysed by considering architectural traits (root angle, depth, diameter and volume) both up- and downslope. Significant differences between all factors were found, depending on species. We estimated the most useful architectural and mechanical traits for physically fixing soil in place. We then combined these results with those concerning root physiological traits, which were used as a proxy for root metabolic activity. Scores were assigned to each species based on traits. No one species possessed a suite of highly desirable traits, therefore mixtures of species should be used on vulnerable slopes. We also propose a conceptual model describing how to position plants on an unstable site, based on root system traits.

  17. A framework for identifying plant species to be used as 'ecological engineers' for fixing soil on unstable slopes.

    Directory of Open Access Journals (Sweden)

    Murielle Ghestem

    Full Text Available Major reforestation programs have been initiated on hillsides prone to erosion and landslides in China, but no framework exists to guide managers in the choice of plant species. We developed such a framework based on the suitability of given plant traits for fixing soil on steep slopes in western Yunnan, China. We examined the utility of 55 native and exotic species with regard to the services they provided. We then chose nine species differing in life form. Plant root system architecture, root mechanical and physiological traits were then measured at two adjacent field sites. One site was highly unstable, with severe soil slippage and erosion. The second site had been replanted 8 years previously and appeared to be physically stable. How root traits differed between sites, season, depth in soil and distance from the plant stem were determined. Root system morphology was analysed by considering architectural traits (root angle, depth, diameter and volume both up- and downslope. Significant differences between all factors were found, depending on species. We estimated the most useful architectural and mechanical traits for physically fixing soil in place. We then combined these results with those concerning root physiological traits, which were used as a proxy for root metabolic activity. Scores were assigned to each species based on traits. No one species possessed a suite of highly desirable traits, therefore mixtures of species should be used on vulnerable slopes. We also propose a conceptual model describing how to position plants on an unstable site, based on root system traits.

  18. Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes.

    Directory of Open Access Journals (Sweden)

    Martin Poot

    2011-05-01

    Full Text Available Understanding complex networks that modulate development in humans is hampered by genetic and phenotypic heterogeneity within and between populations. Here we present a method that exploits natural variation in highly diverse mouse genetic reference panels in which genetic and environmental factors can be tightly controlled. The aim of our study is to test a cross-species genetic mapping strategy, which compares data of gene mapping in human patients with functional data obtained by QTL mapping in recombinant inbred mouse strains in order to prioritize human disease candidate genes.We exploit evolutionary conservation of developmental phenotypes to discover gene variants that influence brain development in humans. We studied corpus callosum volume in a recombinant inbred mouse panel (C57BL/6J×DBA/2J, BXD strains using high-field strength MRI technology. We aligned mouse mapping results for this neuro-anatomical phenotype with genetic data from patients with abnormal corpus callosum (ACC development.From the 61 syndromes which involve an ACC, 51 human candidate genes have been identified. Through interval mapping, we identified a single significant QTL on mouse chromosome 7 for corpus callosum volume with a QTL peak located between 25.5 and 26.7 Mb. Comparing the genes in this mouse QTL region with those associated with human syndromes (involving ACC and those covered by copy number variations (CNV yielded a single overlap, namely HNRPU in humans and Hnrpul1 in mice. Further analysis of corpus callosum volume in BXD strains revealed that the corpus callosum was significantly larger in BXD mice with a B genotype at the Hnrpul1 locus than in BXD mice with a D genotype at Hnrpul1 (F = 22.48, p<9.87*10(-5.This approach that exploits highly diverse mouse strains provides an efficient and effective translational bridge to study the etiology of human developmental disorders, such as autism and schizophrenia.

  19. Cross-species microarray hybridization to identify developmentally regulated genes in the filamentous fungus Sordaria macrospora.

    Science.gov (United States)

    Nowrousian, Minou; Ringelberg, Carol; Dunlap, Jay C; Loros, Jennifer J; Kück, Ulrich

    2005-04-01

    The filamentous fungus Sordaria macrospora forms complex three-dimensional fruiting bodies that protect the developing ascospores and ensure their proper discharge. Several regulatory genes essential for fruiting body development were previously isolated by complementation of the sterile mutants pro1, pro11 and pro22. To establish the genetic relationships between these genes and to identify downstream targets, we have conducted cross-species microarray hybridizations using cDNA arrays derived from the closely related fungus Neurospora crassa and RNA probes prepared from wild-type S. macrospora and the three developmental mutants. Of the 1,420 genes which gave a signal with the probes from all the strains used, 172 (12%) were regulated differently in at least one of the three mutants compared to the wild type, and 17 (1.2%) were regulated differently in all three mutant strains. Microarray data were verified by Northern analysis or quantitative real time PCR. Among the genes that are up- or down-regulated in the mutant strains are genes encoding the pheromone precursors, enzymes involved in melanin biosynthesis and a lectin-like protein. Analysis of gene expression in double mutants revealed a complex network of interaction between the pro gene products.

  20. An expert botanical feature extraction technique based on phenetic features for identifying plant species.

    Directory of Open Access Journals (Sweden)

    Hoshang Kolivand

    Full Text Available In this paper, we present a new method to recognise the leaf type and identify plant species using phenetic parts of the leaf; lobes, apex and base detection. Most of the research in this area focuses on the popular features such as the shape, colour, vein, and texture, which consumes large amounts of computational processing and are not efficient, especially in the Acer database with a high complexity structure of the leaves. This paper is focused on phenetic parts of the leaf which increases accuracy. Detecting the local maxima and local minima are done based on Centroid Contour Distance for Every Boundary Point, using north and south region to recognise the apex and base. Digital morphology is used to measure the leaf shape and the leaf margin. Centroid Contour Gradient is presented to extract the curvature of leaf apex and base. We analyse 32 leaf images of tropical plants and evaluated with two different datasets, Flavia, and Acer. The best accuracy obtained is 94.76% and 82.6% respectively. Experimental results show the effectiveness of the proposed technique without considering the commonly used features with high computational cost.

  1. An expert botanical feature extraction technique based on phenetic features for identifying plant species

    Science.gov (United States)

    Fern, Bong Mei; Rahim, Mohd Shafry Mohd; Sulong, Ghazali; Baker, Thar; Tully, David

    2018-01-01

    In this paper, we present a new method to recognise the leaf type and identify plant species using phenetic parts of the leaf; lobes, apex and base detection. Most of the research in this area focuses on the popular features such as the shape, colour, vein, and texture, which consumes large amounts of computational processing and are not efficient, especially in the Acer database with a high complexity structure of the leaves. This paper is focused on phenetic parts of the leaf which increases accuracy. Detecting the local maxima and local minima are done based on Centroid Contour Distance for Every Boundary Point, using north and south region to recognise the apex and base. Digital morphology is used to measure the leaf shape and the leaf margin. Centroid Contour Gradient is presented to extract the curvature of leaf apex and base. We analyse 32 leaf images of tropical plants and evaluated with two different datasets, Flavia, and Acer. The best accuracy obtained is 94.76% and 82.6% respectively. Experimental results show the effectiveness of the proposed technique without considering the commonly used features with high computational cost. PMID:29420568

  2. Identifying and characterizing the most significant β-glucosidase of the novel species Aspergillus saccharolyticus

    Energy Technology Data Exchange (ETDEWEB)

    Sorensen, Anette; Ahring, Birgitte K.; Lubeck, Mette; Ubhayasekera, Wimal; Bruno, Kenneth S.; Culley, David E.; Lubeck, Peter S.

    2012-08-20

    A newly discovered fungal species, Aspergillus saccharolyticus, was found to produce a culture broth rich in beta-glucosidase activity. In this present work, the main beta-glucosidase of A. saccharolyticus responsible for the efficient hydrolytic activity was identified, isolated, and characterized. Ion exchange chromatography was used to fractionate the culture broth, yielding fractions with high beta-glucosidase activity and only one visible band on an SDS-PAGE gel. Mass spectrometry analysis of this band gave peptide matches to beta-glucosidases from aspergilli. Through a PCR approach using degenerate primers and genome walking, a 2919 base pair sequence encoding the 860 amino acid BGL1 polypeptide was determined. BGL1 of A. saccharolyticus has 91% and 82% identity with BGL1 from Aspergillus aculeatus and BGL1 from Aspergillus niger, respectively, both belonging to Glycoside hydrolase family 3. Homology modeling studies suggested beta-glucosidase activity with preserved retaining mechanism and a wider catalytic pocket compared to other beta-glucosidases. The bgl1 gene was heterologously expressed in Trichoderma reesei QM6a, purified, and characterized by enzyme kinetics studies. The enzyme can hydrolyze cellobiose, pNPG, and cellodextrins. The enzyme showed good thermostability, was stable at 50°C, and at 60°C it had a half-life of approximately 6 hours.

  3. Does taxonomic diversity in indicator groups influence their effectiveness in identifying priority areas for species conservation?

    DEFF Research Database (Denmark)

    Bladt, Jesper Stentoft; Larsen, Frank Wugt; Rahbek, Carsten

    2008-01-01

    The identification of priority areas for biodiversity conservation is a cornerstone of systematic conservation planning. However, biodiversity, or even the distribution of all species, cannot be directly quantified, due to the inherent complexity of natural systems. Species indicator groups may...... serve as important tools for the identification of priority areas for conservation. Yet, it is unclear which factors make certain indicator groups perform better than others. In this study, using data on the Danish distribution of 847 species of plants, vertebrates and insects, we assessed whether...... the taxonomic diversity in species indicator groups influence their effectiveness in the identification of priority areas for species conservation. We tested whether indicator groups comprising a higher taxonomic diversity (i.e. indicator groups consisting of species from many different taxonomic groups...

  4. Status of neotropical migrant landbirds in the Midwest: identifying species of management concern

    Science.gov (United States)

    Frank R. Thompson; Stephen J. Lewis; Janet D. Green; David N. Ewert

    1993-01-01

    We ranked species of neotropical migrant landbirds by decreasing management concern for their viability in the Midwest. This was part of a coordinated effort by regional working groups of the Partners In Flight Program, an interagency program for the conservation of neotropical migratory birds (NTMBs). Species were ranked by seven criteria, developed by working group...

  5. Data-Wave-Based Features Extraction and Its Application in Symbol Identifier Recognition and Positioning Suitable for Multi-Robot Systems

    Directory of Open Access Journals (Sweden)

    Xilong Liu

    2012-12-01

    Full Text Available In this paper, feature extraction based on data-wave is proposed. The concept of data-wave is introduced to describe the rising and falling trends of the data over the long-term which are detected based on ripple and wave filters. Supported by data-wave, a novel symbol identifier with significant structure features is designed and these features are extracted by constructing pixel chains. On this basis, the corresponding recognition and positioning approach is presented. The effectiveness of the proposed approach is verified by experiments.

  6. A multistage decision support framework to guide tree species management under climate change via habitat suitability and colonization models, and a knowledge-based scoring system

    Science.gov (United States)

    Anantha M. Prasad; Louis R. Iverson; Stephen N. Matthews; Matthew P. Peters

    2016-01-01

    Context. No single model can capture the complex species range dynamics under changing climates--hence the need for a combination approach that addresses management concerns. Objective. A multistage approach is illustrated to manage forested landscapes under climate change. We combine a tree species habitat model--DISTRIB II, a species colonization model--SHIFT, and...

  7. Identifying keystone species in the human gut microbiome from metagenomic timeseries using sparse linear regression.

    Directory of Open Access Journals (Sweden)

    Charles K Fisher

    Full Text Available Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is now possible to follow the relative abundance of microbes in a community over time. These microbial communities exhibit rich ecological dynamics and an important goal of microbial ecology is to infer the ecological interactions between species directly from sequence data. Any algorithm for inferring ecological interactions must overcome three major obstacles: 1 a correlation between the abundances of two species does not imply that those species are interacting, 2 the sum constraint on the relative abundances obtained from metagenomic studies makes it difficult to infer the parameters in timeseries models, and 3 errors due to experimental uncertainty, or mis-assignment of sequencing reads into operational taxonomic units, bias inferences of species interactions due to a statistical problem called "errors-in-variables". Here we introduce an approach, Learning Interactions from MIcrobial Time Series (LIMITS, that overcomes these obstacles. LIMITS uses sparse linear regression with boostrap aggregation to infer a discrete-time Lotka-Volterra model for microbial dynamics. We tested LIMITS on synthetic data and showed that it could reliably infer the topology of the inter-species ecological interactions. We then used LIMITS to characterize the species interactions in the gut microbiomes of two individuals and found that the interaction networks varied significantly between individuals. Furthermore, we found that the interaction networks of the two individuals are dominated by distinct "keystone species", Bacteroides fragilis and Bacteroided stercosis, that have a disproportionate influence on the structure of the gut microbiome even though they are only found in moderate abundance. Based on our results, we hypothesize that the abundances of certain keystone species may be responsible for individuality in

  8. gyrB analysis as a tool for identifying Nocardia species and exploring their phylogeny.

    Science.gov (United States)

    Carrasco, Gema; Valdezate, Sylvia; Garrido, Noelia; Medina-Pascual, María J; Villalón, Pilar; Sáez-Nieto, Juan A

    2015-03-01

    gyrB is used to improve the identification of the Nocardia species N. brasiliensis, N. higoensis, N. ignorata, N. otitidiscaviarum, N. paucivorans, N. pneumoniae, N. puris, N. takedensis, N. veterana, and N. vinacea, but it does not improve the identification of another 12 Nocardia studied species. gyrB provides typing and phylogenetic markers for N. carnea, N. transvalensis, N. brasiliensis, and N. otitidiscaviarum. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

  9. Identifying the World's Most Climate Change Vulnerable Species: A Systematic Trait-Based Assessment of all Birds, Amphibians and Corals

    Science.gov (United States)

    Foden, Wendy B.; Butchart, Stuart H. M.; Stuart, Simon N.; Vié, Jean-Christophe; Akçakaya, H. Resit; Angulo, Ariadne; DeVantier, Lyndon M.; Gutsche, Alexander; Turak, Emre; Cao, Long; Donner, Simon D.; Katariya, Vineet; Bernard, Rodolphe; Holland, Robert A.; Hughes, Adrian F.; O’Hanlon, Susannah E.; Garnett, Stephen T.; Şekercioğlu, Çagan H.; Mace, Georgina M.

    2013-01-01

    Climate change will have far-reaching impacts on biodiversity, including increasing extinction rates. Current approaches to quantifying such impacts focus on measuring exposure to climatic change and largely ignore the biological differences between species that may significantly increase or reduce their vulnerability. To address this, we present a framework for assessing three dimensions of climate change vulnerability, namely sensitivity, exposure and adaptive capacity; this draws on species’ biological traits and their modeled exposure to projected climatic changes. In the largest such assessment to date, we applied this approach to each of the world’s birds, amphibians and corals (16,857 species). The resulting assessments identify the species with greatest relative vulnerability to climate change and the geographic areas in which they are concentrated, including the Amazon basin for amphibians and birds, and the central Indo-west Pacific (Coral Triangle) for corals. We found that high concentration areas for species with traits conferring highest sensitivity and lowest adaptive capacity differ from those of highly exposed species, and we identify areas where exposure-based assessments alone may over or under-estimate climate change impacts. We found that 608–851 bird (6–9%), 670–933 amphibian (11–15%), and 47–73 coral species (6–9%) are both highly climate change vulnerable and already threatened with extinction on the IUCN Red List. The remaining highly climate change vulnerable species represent new priorities for conservation. Fewer species are highly climate change vulnerable under lower IPCC SRES emissions scenarios, indicating that reducing greenhouse emissions will reduce climate change driven extinctions. Our study answers the growing call for a more biologically and ecologically inclusive approach to assessing climate change vulnerability. By facilitating independent assessment of the three dimensions of climate change vulnerability

  10. Suitability of dried herbarium specimens for NMR metabolomics of mushrooms. A comparison of four species of the genera Kuehneromyces and Hypholoma (Strophariaceae).

    Science.gov (United States)

    Jafari, Tahereh; Alanne, Aino-Liisa; Issakainen, Jouni; Pihlaja, Kati; Sinkkonen, Jari

    Herbarium specimens are a treasure trove for biochemical studies. However, this implies understanding of the chemical changes during the drying and storage of the specimen. We compared herbarium specimens at different ages and fresh samples of four mushroom species (Kuehneromyces mutabilis, Hypholoma capnoides, Kuehneromyces lignicola, Hypholoma fasciculare) of two genera in the family Strophariaceae by using proton nuclear magnetic resonance ( 1 H NMR) spectroscopy combined with principal component analysis (PCA). 25 metabolites were identified. No significant alterations were found between herbarium samples at different ages, suggesting that they are stable enough for comparative studies. The most dominant differences between fresh and herbarium samples was that sugars such as α-α-trehalose, and fumaric and malic acids were more abundant in fresh fungi. Total contents of fatty and amino acids, uracil and γ-aminobutyric acid (GABA) were higher in herbarium specimens. In addition, pyroglutamic acid was observed only in Kuehneromyces mutabilis and fasciculic acid E in Hypholomafasciculare. Hence, based on results of the studied taxa, we conclude that NMR metabolomics can be used for both fresh and dried mushrooms when such alterations are properly addressed. Copyright © 2017 British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  11. Use of DNA sequences to identify forensically important fly species and their distribution in the coastal region of Central California.

    Science.gov (United States)

    Nakano, Angie; Honda, Jeff

    2015-08-01

    Forensic entomology has gained prominence in recent years, as improvements in DNA technology and molecular methods have allowed insect and other arthropod evidence to become increasingly useful in criminal and civil investigations. However, comprehensive faunal inventories are still needed, including cataloging local DNA sequences for forensically significant Diptera. This multi-year fly-trapping study was built upon and expanded a previous survey of these flies in Santa Clara County, including the addition of genetic barcoding data from collected species of flies. Flies from the families Calliphoridae, Sarcophagidae, and Muscidae were trapped in meat-baited traps set in a variety of locations throughout the county. Flies were identified using morphological features and confirmed by molecular analysis. A total of 16 calliphorid species, 11 sarcophagid species, and four muscid species were collected and differentiated. This study found more species of flies than previous area surveys and established new county records for two calliphorid species: Cynomya cadaverina and Chrysomya rufifacies. Differences were found in fly fauna in different areas of the county, indicating the importance of microclimates in the distribution of these flies. Molecular analysis supported the use of DNA barcoding as an effective method of identifying cryptic fly species. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  12. Use of DNA barcodes to identify invasive armyworm Spodoptera species in Florida

    Science.gov (United States)

    A critical component for sustaining adequate food production is the protection of local agriculture from invasive pest insects. Essential to this goal is the ability to accurately distinguish foreign from closely related domestic species, a process that has traditionally required identification of d...

  13. Using aflp to identify genetic relationships in cassia species from Thailand

    International Nuclear Information System (INIS)

    Sihanat, A.; Rungsihirunrat, K.; Chareonsap, P. P.; Ruangrungsi, N.

    2017-01-01

    Several species of Cassia are used in Thai folk medicine as a laxative and a treatment for skin infections. However, the taxonomy of the GenusCassia is quite complex and intriguing. Thus, the correct identification of the species of this genus is necessary for efficacy and safety. The phylogenetic relationships among the 16 species of Cassiagenus existing in Thailand were evaluated using Amplified Fragment Length Polymorphism (AFLP) technique. Combinations of 70 primers were screened and eleven primer combinations produced a total of 849 distinct and reproducible bands ranging from 60 to 100 bands with an average of 77.18 bands per primer combination. The genetic distances were calculated based on the AFLP bands that had been amplified using the eleven primer combinations. The similarity indices (SI) ranged from 0.25 to 0.78. The dendrogram was created using the Unweighted Pair Group Method of the Arithmetic Average (UPGMA) and the genotypes were divided into two major groups. The results indicate that the phylogenetic relationships are associated with the morphological characterization. In conclusion, an AFLP marker could be an efficient and reliable tool for the identification of a Cassia species. (author)

  14. A new approach to horizon-scanning: identifying potentially invasive alien species and their introduction pathways

    NARCIS (Netherlands)

    Matthews, Jonathan; Beringen, Ruud; Creemers, Raymond; Hollander, Hans; van Kessel, Nils; van Kleef, Hein; de Koppel, Sander van; Lemaire, Adrienne J. J.; Ode, Baudewijn; Verbrugge, Laura N. H.; Hendriks, A. Jan; Schipper, Aafke M.; van der Velde, Gerard; Leuven, Rob S. E. W.

    Invasive alien species (IAS) are considered an important threat to global biodiversity due to major ecological impacts. In 2014, the European Union (EU) introduced a regulation (EU) No 1143/2014 on the prevention and management of the introduction and spread of IAS. The first risk prioritized list

  15. Using combined morphological, allometric and molecular approaches to identify species of the genus Raillietiella (Pentastomida.

    Directory of Open Access Journals (Sweden)

    Crystal Kelehear

    Full Text Available Taxonomic studies of parasites can be severely compromised if the host species affects parasite morphology; an uncritical analysis might recognize multiple taxa simply because of phenotypically plastic responses of parasite morphology to host physiology. Pentastomids of the genus Raillietiella are endoparasitic crustaceans primarily infecting the respiratory system of carnivorous reptiles, but also recorded from bufonid anurans. The delineation of pentastomids at the generic level is clear, but the taxonomic status of many species is not. We collected raillietiellids from lungs of the invasive cane toad (Rhinella marina, the invasive Asian house gecko (Hemidactylus frenatus, and a native tree frog (Litoria caerulea in tropical Australia, and employed a combination of genetic analyses, and traditional and novel morphological methods to clarify their identity. Conventional analyses of parasite morphology (which focus on raw values of morphological traits revealed two discrete clusters in terms of pentastome hook size, implying two different species of pentastomes: one from toads and a tree frog (Raillietiella indica and another from lizards (Raillietiella frenatus. However, these clusters disappeared in allometric analyses that took pentastome body size into account, suggesting that only a single pentastome taxon may be involved. Our molecular data revealed no genetic differences between parasites in toads versus lizards, confirming that there was only one species: R. frenatus. This pentastome (previously known only from lizards clearly is also capable of maturing in anurans. Our analyses show that the morphological features used in pentastomid taxonomy change as the parasite transitions through developmental stages in the definitive host. To facilitate valid descriptions of new species of pentastomes, future taxonomic work should include both morphological measurements (incorporating quantitative measures of body size and hook bluntness and

  16. A novel computational method identifies intra- and inter-species recombination events in Staphylococcus aureus and Streptococcus pneumoniae.

    Directory of Open Access Journals (Sweden)

    Lisa Sanguinetti

    Full Text Available Advances in high-throughput DNA sequencing technologies have determined an explosion in the number of sequenced bacterial genomes. Comparative sequence analysis frequently reveals evidences of homologous recombination occurring with different mechanisms and rates in different species, but the large-scale use of computational methods to identify recombination events is hampered by their high computational costs. Here, we propose a new method to identify recombination events in large datasets of whole genome sequences. Using a filtering procedure of the gene conservation profiles of a test genome against a panel of strains, this algorithm identifies sets of contiguous genes acquired by homologous recombination. The locations of the recombination breakpoints are determined using a statistical test that is able to account for the differences in the natural rate of evolution between different genes. The algorithm was tested on a dataset of 75 genomes of Staphylococcus aureus and 50 genomes comprising different streptococcal species, and was able to detect intra-species recombination events in S. aureus and in Streptococcus pneumoniae. Furthermore, we found evidences of an inter-species exchange of genetic material between S. pneumoniae and Streptococcus mitis, a closely related commensal species that colonizes the same ecological niche. The method has been implemented in an R package, Reco, which is freely available from supplementary material, and provides a rapid screening tool to investigate recombination on a genome-wide scale from sequence data.

  17. Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L. Moench and related model species.

    Directory of Open Access Journals (Sweden)

    Adugna Abdi Woldesemayat

    Full Text Available Crop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major cause of concern in this regard. Identification of genes with multiple responses across environmental stresses is the genetic foundation that leads to crop adaptation to environmental perturbations.In this paper, we introduce an integrated approach to assess candidate genes for multiple stress responses across-species. The approach combines ontology based semantic data integration with expression profiling, comparative genomics, phylogenomics, functional gene enrichment and gene enrichment network analysis to identify genes associated with plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO, Trait Ontology (TO, Plant Ontology (PO, Growth Ontology (GRO and Environment Ontology (EO were used to semantically integrate drought related information.Target genes linked to Quantitative Trait Loci (QTLs controlling yield and stress tolerance in sorghum (Sorghum bicolor (L. Moench and closely related species were identified. Based on the enriched GO terms of the biological processes, 1116 sorghum genes with potential responses to 5 different stresses, such as drought (18%, salt (32%, cold (20%, heat (8% and oxidative stress (25% were identified to be over-expressed. Out of 169 sorghum drought responsive QTLs associated genes that were identified based on expression datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168 additional genes that have been evaluated for orthologous pairs, 90% were conserved across species for drought tolerance. Over 50% of identified maize and rice genes were responsive to drought and salt stresses and were co-located within multifunctional QTLs. Among the total identified multi-stress responsive genes, 272 targets were shown to be co-localized within QTLs

  18. Identifying game elements suitable for MOOCs

    NARCIS (Netherlands)

    Antonaci, Alessandra; Klemke, Roland; Stracke, Christian M.; Specht, Marcus

    2017-01-01

    Massive Online Open Courses (MOOCs) have increasingly become objects of research interest and studies in recent years. While MOOCs could be a means to address massive audiences, they suffer from high drop-out rates and low user engagement. Gamification is known as the application of game

  19. Serum profiling of healthy aging identifies phospho- and sphingolipid species as markers of human longevity.

    Science.gov (United States)

    Montoliu, Ivan; Scherer, Max; Beguelin, Fiona; DaSilva, Laeticia; Mari, Daniela; Salvioli, Stefano; Martin, Francois-Pierre J; Capri, Miriam; Bucci, Laura; Ostan, Rita; Garagnani, Paolo; Monti, Daniela; Biagi, Elena; Brigidi, Patrizia; Kussmann, Martin; Rezzi, Serge; Franceschi, Claudio; Collino, Sebastiano

    2014-01-01

    As centenarians well represent the model of healthy aging, there are many important implications in revealing the underlying molecular mechanisms behind such successful aging. By combining NMR metabonomics and shot-gun lipidomics in serum we analyzed metabolome and lipidome composition of a group of centenarians with respect to elderly individuals. Specifically, NMR metabonomics profiling of serum revealed that centenarians are characterized by a metabolic phenotype distinct from that of elderly subjects, in particular regarding amino acids and lipid species. Shot- gun lipidomics approach displays unique changes in lipids biosynthesis in centenarians, with 41 differently abundant lipid species with respect to elderly subjects. These findings reveal phospho/sphingolipids as putative markers and biological modulators of healthy aging, in humans. Considering the particular actions of these metabolites, these data are suggestive of a better counteractive antioxidant capacity and a well-developed membrane lipid remodelling process in the healthy aging phenotype.

  20. Infrared spectroscopy of pollen identifies plant species and genus as well as environmental conditions.

    Directory of Open Access Journals (Sweden)

    Boris Zimmermann

    Full Text Available BACKGROUND: It is imperative to have reliable and timely methodologies for analysis and monitoring of seed plants in order to determine climate-related plant processes. Moreover, impact of environment on plant fitness is predominantly based on studies of female functions, while the contribution of male gametophytes is mostly ignored due to missing data on pollen quality. We explored the use of infrared spectroscopy of pollen for an inexpensive and rapid characterization of plants. METHODOLOGY: The study was based on measurement of pollen samples by two Fourier transform infrared techniques: single reflectance attenuated total reflectance and transmission measurement of sample pellets. The experimental set, with a total of 813 samples, included five pollination seasons and 300 different plant species belonging to all principal spermatophyte clades (conifers, monocotyledons, eudicots, and magnoliids. RESULTS: The spectroscopic-based methodology enables detection of phylogenetic variations, including the separation of confamiliar and congeneric species. Furthermore, the methodology enables measurement of phenotypic plasticity by the detection of inter-annual variations within the populations. The spectral differences related to environment and taxonomy are interpreted biochemically, specifically variations of pollen lipids, proteins, carbohydrates, and sporopollenins. The study shows large variations of absolute content of nutrients for congenital species pollinating in the same environmental conditions. Moreover, clear correlation between carbohydrate-to-protein ratio and pollination strategy has been detected. Infrared spectral database with respect to biochemical variation among the range of species, climate and biogeography will significantly improve comprehension of plant-environment interactions, including impact of global climate change on plant communities.

  1. The morphology of saccular otoliths as a tool to identify different mugilid species from the Northeastern Atlantic and Mediterranean Sea

    Science.gov (United States)

    Callicó Fortunato, Roberta; Benedito Durà, Vicent; Volpedo, Alejandra

    2014-06-01

    In the Northeastern Atlantic and Mediterranean Sea there are 8 species of the Mugilidae family: Mugil cephalus, Liza aurata, Liza ramada, Oedalechilus labeo, Chelon labrosus, Liza saliens, Liza carinata and Liza haematocheila. The identification of mugilids is very important for local fisheries management and regulations, but it is difficult using gross morphological characters. This work aims to contribute to the identification of mullets present in the Northeastern Atlantic Ocean and Mediterranean Sea using saccular otolith features of each species. Specimens of C. labrosus, L. aurata, L. ramada, L. saliens and M. cephalus were obtained from Delta del Ebro (40°38'N-0°44'E) in artisanal catches. For L. carinata and O. labeo photographs extracted from AFORO online database were used. L. haematocheila was not studied for lack of otolith samples. A general pattern of the saccular otoliths for this family was identified: the shape of the otoliths are rectangular to oblong with irregular margins; they present a heterosulcoid, ostial sulcus acusticus, with an open funnel-like ostium to the anterior margin and a closed, tubular cauda, ending towards the posterior ventral corner, always larger than the ostium. In the present study, the mugilid species could be recognized using their saccular otolith morphology. Here we give the first key to identify Northeastern Atlantic and Mediterranean mullets. The distinctive features between the species were the position and centrality of the sulcus, the curvature of the cauda, the presence of areal depositions and plateaus, and the type of anterior and posterior regions. These features could be used not only to reinforce the identification keys through morphological and meristic characters of the species, but also to identify the species consumed by piscivores, being the otoliths the only identifiable remains of the individuals.

  2. The internal transcribed spacer (ITS region and trnH-psbA [corrected] are suitable candidate loci for DNA barcoding of tropical tree species of India.

    Directory of Open Access Journals (Sweden)

    Abhinandan Mani Tripathi

    Full Text Available DNA barcoding as a tool for species identification has been successful in animals and other organisms, including certain groups of plants. The exploration of this new tool for species identification, particularly in tree species, is very scanty from biodiversity-rich countries like India. rbcL and matK are standard barcode loci while ITS, and trnH-psbA are considered as supplementary loci for plants.Plant barcode loci, namely, rbcL, matK, ITS, trnH-psbA, and the recently proposed ITS2, were tested for their efficacy as barcode loci using 300 accessions of tropical tree species. We tested these loci for PCR, sequencing success, and species discrimination ability using three methods. rbcL was the best locus as far as PCR and sequencing success rate were concerned, but not for the species discrimination ability of tropical tree species. ITS and trnH-psbA were the second best loci in PCR and sequencing success, respectively. The species discrimination ability of ITS ranged from 24.4 percent to 74.3 percent and that of trnH-psbA was 25.6 percent to 67.7 percent, depending upon the data set and the method used. matK provided the least PCR success, followed by ITS2 (59. 0%. Species resolution by ITS2 and rbcL ranged from 9.0 percent to 48.7 percent and 13.2 percent to 43.6 percent, respectively. Further, we observed that the NCBI nucleotide database is poorly represented by the sequences of barcode loci studied here for tree species.Although a conservative approach of a success rate of 60-70 percent by both ITS and trnH-psbA may not be considered as highly successful but would certainly help in large-scale biodiversity inventorization, particularly for tropical tree species, considering the standard success rate of plant DNA barcode program reported so far. The recommended matK and rbcL primers combination may not work in tropical tree species as barcode markers.

  3. Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples.

    Science.gov (United States)

    Arulandhu, Alfred J; Staats, Martijn; Hagelaar, Rico; Voorhuijzen, Marleen M; Prins, Theo W; Scholtens, Ingrid; Costessi, Adalberto; Duijsings, Danny; Rechenmann, François; Gaspar, Frédéric B; Barreto Crespo, Maria Teresa; Holst-Jensen, Arne; Birck, Matthew; Burns, Malcolm; Haynes, Edward; Hochegger, Rupert; Klingl, Alexander; Lundberg, Lisa; Natale, Chiara; Niekamp, Hauke; Perri, Elena; Barbante, Alessandra; Rosec, Jean-Philippe; Seyfarth, Ralf; Sovová, Tereza; Van Moorleghem, Christoff; van Ruth, Saskia; Peelen, Tamara; Kok, Esther

    2017-10-01

    DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance. © The Authors 2017. Published by Oxford University Press.

  4. When alcohol is the answer: Trapping, identifying and quantifying simple alkylating species in aqueous environments.

    Science.gov (United States)

    Penketh, Philip G; Shyam, Krishnamurthy; Baumann, Raymond P; Zhu, Rui; Ishiguro, Kimiko; Sartorelli, Alan C; Ratner, Elena S

    2016-09-01

    Alkylating agents are a significant class of environmental carcinogens as well as commonly used anticancer therapeutics. Traditional alkylating activity assays have utilized the colorimetric reagent 4-(4-nitrobenzyl)pyridine (4NBP). However, 4NBP based assays have a relatively low sensitivity towards harder, more oxophilic alkylating species and are not well suited for the identification of the trapped alkyl moiety due to adduct instability. Herein we describe a method using water as the trapping agent which permits the trapping of simple alkylating electrophiles with a comparatively wide range of softness/hardness and permits the identification of donated simple alkyl moieties. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Combined molecular and biochemical approach identifies Aspergillus japonicus and Aspergillus aculeatus as two species

    DEFF Research Database (Denmark)

    Parenicova, L.; Skouboe, P.; Frisvad, Jens Christian

    2001-01-01

    of the internal transcribed spacers (ITS1 and ITS2) and the 5.8S rRNA gene could not be used to distinguish between A. japonicus and A. aculeatus but did show that these two taxa are more closely related to each other than to other species of black aspergilli. Aspergillus niger pyruvate kinase (pkiA) and pectin...... variation when they were probed with the pelA gene. The secondary-metabolite profiles supported division of the isolates into the two species and differed from those of other black aspergilli. The strains classified as A. japonicus produced indole alkaloids and a polar metabolite, while the A. aculeatus...... lyase A (pelA) and Agaricus bisporus 28S rRNA genes, which were used as probes in the RFLP analysis, revealed clear polymorphism between these two taxa. The A. niger pkiA and pelA probes placed six strains in an A. japonicus group and 12 isolates in an A. aculeatus group, which exhibited intraspecific...

  6. Brain development in rodents and humans: Identifying benchmarks of maturation and vulnerability to injury across species

    Science.gov (United States)

    Semple, Bridgette D.; Blomgren, Klas; Gimlin, Kayleen; Ferriero, Donna M.; Noble-Haeusslein, Linda J.

    2013-01-01

    Hypoxic-ischemic and traumatic brain injuries are leading causes of long-term mortality and disability in infants and children. Although several preclinical models using rodents of different ages have been developed, species differences in the timing of key brain maturation events can render comparisons of vulnerability and regenerative capacities difficult to interpret. Traditional models of developmental brain injury have utilized rodents at postnatal day 7–10 as being roughly equivalent to a term human infant, based historically on the measurement of post-mortem brain weights during the 1970s. Here we will examine fundamental brain development processes that occur in both rodents and humans, to delineate a comparable time course of postnatal brain development across species. We consider the timing of neurogenesis, synaptogenesis, gliogenesis, oligodendrocyte maturation and age-dependent behaviors that coincide with developmentally regulated molecular and biochemical changes. In general, while the time scale is considerably different, the sequence of key events in brain maturation is largely consistent between humans and rodents. Further, there are distinct parallels in regional vulnerability as well as functional consequences in response to brain injuries. With a focus on developmental hypoxicischemic encephalopathy and traumatic brain injury, this review offers guidelines for researchers when considering the most appropriate rodent age for the developmental stage or process of interest to approximate human brain development. PMID:23583307

  7. Identification and partial characterization of Taastrup virus: a newly identified member species of the Mononegavirales

    DEFF Research Database (Denmark)

    Bock, J.O.; Lundsgaard, T.; Pedersen, P.A.

    2004-01-01

    with the glycoproteins of Filoviridae and Pneumovirinae, and a nucleoprotein (N) with homology to the nucleoprotein of viral hemorrhagic septicemia virus (VHSV), a member of the Rhabdoviridae. Highly conserved domains were identified in the RNA-dependent RNA polymerase (L) between TV and other viruses within the order...... of Mononegavirales, and homology was found in particular with members of the Rhabdoviridae. The sequence similarities and the unique filovirus-like but nonidentical morphology unambiguously refer this newly identified virus to the order of Mononegavirales but to no family more than any to other within the order....

  8. Potential distribution of the endangered endemic lizard Liolaemus lutzae Mertens, 1938 (Liolaemidae: are there other suitable areas for a geographically restricted species?

    Directory of Open Access Journals (Sweden)

    GR. Winck

    Full Text Available In this study we attempted to access further information on the geographical distribution of the endangered lizard Liolaemus lutzae, estimating its potential distribution through the maximum entropy algorithm. For this purpose, we related its points of occurrence with matrices of environmental variables. After examining the correlation between environmental matrices, we selected 10 for model construction. The main variables influencing the current geographic distribution of L. lutzae were the diurnal temperature range and altitude. The species endemism seemed to be a consequence of a reduction of the original distribution area. Alternatively, the resulting model may reflect the geographic distribution of an ancestral lineage, since the model selected areas of occurrence of the two other species of Liolaemus from Brazil (L. arambarensis and L. occipitalis, all living in sand dune habitats and having psamophilic habits. Due to the high loss rate of habitat occupied by the species, the conservation and recovery of the remaining areas affected by human actions is essential.

  9. Identification and partial characterization of Taastrup virus: a newly identified member species of the Mononegavirales

    International Nuclear Information System (INIS)

    Bock, J.O.; Lundsgaard, T.; Pedersen, P.A.; Christensen, L.S.

    2004-01-01

    We present a 8904-nt sequence of the central part of the RNA genome of a novel virus with a filovirus-like, nonidentical morphology named Taastrup virus (TV) detected in the leafhopper Psammotettix alienus. Sequence analysis identified five potential open reading frames (ORFs) and a complex pattern of homologies to various members of the Mononegavirales suggests a genome organization with the following order of genes: 3'-N-P-M-G-L-5'. Sequence analyses reveal an unusually large glycoprotein (G) containing both potential O-linked (14) and N-linked (9) glycosylation sites--a feature shared with the glycoproteins of Filoviridae and Pneumovirinae, and a nucleoprotein (N) with homology to the nucleoprotein of viral hemorrhagic septicemia virus (VHSV), a member of the Rhabdoviridae. Highly conserved domains were identified in the RNA-dependent RNA polymerase (L) between TV and other viruses within the order of Mononegavirales, and homology was found in particular with members of the Rhabdoviridae. The sequence similarities and the unique filovirus-like but nonidentical morphology unambiguously refer this newly identified virus to the order of Mononegavirales but to no family more than any, to other within the order

  10. Role of dung beetle feeding mechanisms in limiting the suitability of species as hosts for the nematode Spirocerca lupi

    DEFF Research Database (Denmark)

    du Toit, C. A.; Holter, P.; Lutermann, H.

    2012-01-01

    Various species of dung beetle serve as intermediate hosts after ingesting the embryonated eggs (1115 x 3037 mu m) of Spirocerca lupi (Spirurida: Spirocercidae) in dog faeces. The feeding mechanisms of coprophagous dung beetles restrict the size of the food particles they can ingest and hence may...

  11. Identifying the principal driving factors of water ecosystem dependence and the corresponding indicator species in a pilot City, China

    Science.gov (United States)

    Zhao, C. S.; Shao, N. F.; Yang, S. T.; Xiang, H.; Lou, H. Z.; Sun, Y.; Yang, Z. Y.; Zhang, Y.; Yu, X. Y.; Zhang, C. B.; Yu, Q.

    2018-01-01

    The world's aquatic ecosystems yield numerous vital services, which are essential to human existence but have deteriorated seriously in recent years. By studying the mechanisms of interaction between ecosystems and habitat processes, the constraining factors can be identified, and this knowledge can be used to improve the success rate of ecological restoration initiatives. At present, there is insufficient data on the link between hydrological, water quality factors and the changes in the structure of aquatic communities to allow any meaningful study of driving factors of aquatic ecosystems. In this study, the typical monitoring stations were selected by fuzzy clustering analysis based on the spatial and temporal distribution characteristics of water ecology in Jinan City, the first pilot city for the construction of civilized aquatic ecosystems in China. The dominant species identification model was used to identify the dominant species of the aquatic community. The driving effect of hydrological and water quality factors on dominant species was analyzed by Canonical Correspondence Analysis. Then, the principal factors of aquatic ecosystem dependence were selected. The results showed that there were 10 typical monitoring stations out of 59 monitoring sites, which were representative of aquatic ecosystems, 9 dominant fish species, and 20 dominant invertebrate species. The selection of factors for aquatic ecosystem dependence in Jinan were highly influenced by its regional conditions. Chemical environmental parameters influence the temporal and spatial variation of invertebrate much more than that of fish in Jinan City. However, the methodologies coupling typical monitoring stations selection, dominant species determination and driving factors identification were certified to be a cost-effective way, which can provide in-deep theoretical and technical directions for the restoration of aquatic ecosystems elsewhere.

  12. Application of representational difference analysis to identify genomic differences between Bradyrhizobium elkanii and B. Japonicum species.

    Science.gov (United States)

    Soares, René Arderius; Passaglia, Luciane Maria Pereira

    2010-10-01

    Bradyrhizobium elkanii is successfully used in the formulation of commercial inoculants and, together with B. japonicum, it fully supplies the plant nitrogen demands. Despite the similarity between B. japonicum and B. elkanii species, several works demonstrated genetic and physiological differences between them. In this work Representational Difference Analysis (RDA) was used for genomic comparison between B. elkanii SEMIA 587, a crop inoculant strain, and B. japonicum USDA 110, a reference strain. Two hundred sequences were obtained. From these, 46 sequences belonged exclusively to the genome of B. elkanii strain, and 154 showed similarity to sequences from B. japonicum genome. From the 46 sequences with no similarity to sequences from B. japonicum, 39 showed no similarity to sequences in public databases and seven showed similarity to sequences of genes coding for known proteins. These seven sequences were divided in three groups: similar to sequences from other Bradyrhizobium strains, similar to sequences from other nitrogen-fixing bacteria, and similar to sequences from non nitrogen-fixing bacteria. These new sequences could be used as DNA markers in order to investigate the rates of genetic material gain and loss in natural Bradyrhizobium strains.

  13. Species-specific considerations in using the fish embryo test as an alternative to identify endocrine disruption.

    Science.gov (United States)

    Schiller, Viktoria; Zhang, Xiaowei; Hecker, Markus; Schäfers, Christoph; Fischer, Rainer; Fenske, Martina

    2014-10-01

    A number of regulations have been implemented that aim to control the release of potentially adverse endocrine disrupters into the aquatic environment based on evidence from laboratory studies. Currently, such studies rely on testing approaches with adult fish because reliable alternatives have not been validated so far. Fish embryo tests have been proposed as such an alternative, and here we compared two species (medaka and zebrafish) to determine their suitability for the assessment of substances with estrogenic and anti-androgenic activity. Changes in gene expression (in here the phrase gene expression is used synonymously to gene transcription, although it is acknowledged that gene expression is additionally regulated, e.g., by translation and protein stability) patterns between the two species were compared in short term embryo exposure tests (medaka: 7-day post fertilization [dpf]; zebrafish: 48 and 96h post fertilization [hpf]) by using relative quantitative real-time RT-PCR. The tested genes were related to the hypothalamic-gonadal-axis and early steroidogenesis. Test chemicals included 17α-ethinylestradiol and flutamide as estrogenic and anti-androgenic reference compounds, respectively, as well as five additional substances with endocrine activities, namely bisphenol A, genistein, prochloraz, linuron and propanil. Estrogenic responses were comparable in 7-dpf medaka and 48/96-hpf zebrafish embryos and included transcriptional upregulation of aromatase b, vitellogenin 1 as well as steroidogenic genes, suggesting that both species reliably detected exposure to estrogenic compounds. However, anti-androgenic responses differed between the two species, with each species providing specific information concerning the mechanism of anti-androgenic disruption in fish embryos. Although small but significant changes in the expression of selected genes was observed in 48-hpf zebrafish embryos, exposure prolonged to 96hpf was necessary to obtain a response indicative

  14. A Simple Key for Identifying the Sibling Species of the Malaria Vector Anopheles gambiae (Giles Complex by Polytene Chromosome Cytogenetics

    Directory of Open Access Journals (Sweden)

    Music Temitope OBEMBE

    2018-03-01

    Full Text Available It has been established that Anopheles gambiae complex sibling species are the major Plasmodium malaria vectors in Africa; however, not all the sibling species transmit the infection. Easier molecular methods, PCR-based assays, have been developed to distinguish the several members of the A. gambiae complex. However, malaria vector research in less developed countries, particularly sub-Saharan Africa, is being hampered by the lack of PCR facilities in laboratories and the cost of carrying out the assay within lack of funding. Hence, the present study was designed to develop a simple identification key, based on an affordable method of polytene chromosome cytotaxonomy, for identifying the major P. falciparum vectors. The Identification Key was successfully used to identify two members of the A. gambiae complex, A. gambiae sensu stricto and A. arabiensis, which are the most potent malaria vectors in Africa; even so, it could not be used to establish the infective and the refractory strains.

  15. Identifying areas suitable for wine tourism through the use of multi-criteria and geographic information system: the method and its application in the countryside around Mount Etna (Sicily

    Directory of Open Access Journals (Sweden)

    Lara Riguccio

    2017-06-01

    Full Text Available Vineyards are among the crops that shape quality landscapes. Many places in the world are famous for their unique wine landscapes which play an important role in the development of tourism in the rural areas. Among these, the wine landscape surrounding mount Etna (Sicily emerges due to its undisputed value, as it is an important component of the territory recognised as a World Heritage Site by UNESCO. This work was conducted with that in mind, in order to identify the most suitable areas for wine tourism on the slopes of our volcano. The method used assigns a great importance to the quality of the landscape, an indispensable resource for encouraging wine tourism, and considers it to be of equal importance with the production of the wines themselves. The present work uses multi-criteria analysis in combination with geographic information system (GIS. Numerous indicators describing local resources were weighed and spatialized. The GIS analysis allowed for the development of various intermediate maps, which allowed to draw up the final suitability map for wine tourism, identifying areas larger than those of the actual vineyards. The value of these areas and the quality of their landscapes are closely connected to the production of the wines in the zone. It could be the target for specific plans and projects aimed at using the available resources, to develop wine tourism in rural areas. Although the study only covers a limited geographical area, the methodology used has general validity and could be used in other contexts.

  16. Shortened Time to Identify Staphylococcus Species from Blood Cultures and Methicillin Resistance Testing Using CHROMAgar

    Directory of Open Access Journals (Sweden)

    Shingo Chihara

    2009-01-01

    Full Text Available The ability to rapidly differentiate coagulase-negative staphylococcus (CoNS from Staphylococcus aureus and to determine methicillin resistance is important as it affects the decision to treat empiric antibiotic selection. The objective of this study was to evaluate CHROMagar S. aureus and CHROMagar MRSA (Becton Dickinson for rapid identification of Staphylococcus spp. directly from blood cultures. Consecutive blood culture bottles (BacT Alert 3D SA and SN, bioMérieux growing gram-positive cocci in clusters were evaluated. An aliquot was plated onto CHROMagar MRSA (C-MRSA and CHROMagar S. aureus (C-SA plates, which were read at 12 to 16 hours. C-SA correctly identified 147/147 S. aureus (100% sensitivity; 2 CoNS were misidentified as S. aureus (98% specificity. C-MRSA correctly identified 74/77 MRSA (96% sensitivity. None of the MSSA isolates grew on C-MRSA (100% specificity. In conclusion, CHROMagar is a rapid and sensitive method to distinguish MRSA, MSSA, and coagulase-negative Staphylococcus and may decrease time of reporting positive results.

  17. Count your eggs before they invade: identifying and quantifying egg clutches of two invasive apple snail species (Pomacea.

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    Colin H Kyle

    Full Text Available Winning the war against invasive species requires early detection of invasions. Compared to terrestrial invaders, aquatic species often thrive undetected under water and do not garner notice until too late for early action. However, fortunately for managers, apple snails (Family Ampullariidae, Genus Pomacea provide their own conspicuous sign of invasion in the form of vibrantly colored egg clutches. Managers can potentially use egg clutches laid in the riparian zone as a means of early detection and species identification. To facilitate such efforts, we quantified differences in characteristics (length, width, depth, mass, egg number of field-laid clutches for the two most common invasive species of apple snail, P. canaliculata and P. maculata, in native and non-native populations. Pomacea canaliculata native and non-native populations differed noticeably only in width. Native P. maculata clutches possessed significantly greater width, mass and eggs numbers compared with native P. canaliculata. Non-native P. maculata clutches significantly exceeded all other populations in all measured characteristics. Consequently, these traits may successfully distinguish between species. Fecundity data also allowed us to develop models that accurately estimated the number of eggs per clutch for each species based on clutch dimensions. We tested one, two and three dimensional models of clutches, including rendering a clutch as either a complete ellipsoid or an ellipsoid intersected by a cylinder to represent the oviposition site. Model comparisons found the product of length and depth, with a different function for each population, best predicted egg number for both species. Comparisons of egg number to clutch volume and mass implied non-native P. canaliculata may be food limited, while non-native P. maculata appeared to produce such enormous clutches by having access to greater nutrients than the native population. With these new tools, researchers and

  18. Ochratoxigenic Black Species of Aspergilli in Grape Fruits of Northern Italy Identified by an Improved PCR-RFLP Procedure

    Directory of Open Access Journals (Sweden)

    Maria Lodovica Gullino

    2012-01-01

    Full Text Available A collection of 356 isolates of Aspergillus spp. collected during 2006 and 2007 from grapevines in northern Italy were identified through Internal Transcribed Spacer based Restriction Fragment Length Polymorphism (ITS-RFLP and tested for ochratoxin A (OTA production. Restriction endonuclease digestion of the ITS products using the endonucleases HhaI, HinfI and RsaI, distinguished five different RFLPs. From each pattern, three samples were sequenced and the nucleotide sequences showed different species corresponding to Aspergillus niger, A. carbonarius, A. tubingensis, A. japonicus and A. aculeatus. By comparing the sequences of the ITS regions, also the uniseriate species A. japonicus and A. aculeatus could be differentiated by HinfI digestion of the ITS products. Among the aspergilli, A. niger was the major species associated with grapes during 2006 (57.4%, while A. carbonarius was the major species during 2007 (46.6%. All the strains of Aspergillus were tested for their ability to produce OTA on Yeast extract sucrose medium (YES, as it was tested as an optimal substrate for the evaluation of OTA production by black aspergilli. Out of 356 isolates, 63 (17.7% isolates produced OTA ranging from 0.05 to 3.0 µg mL−1. Most of the ochratoxigenic isolates were A. carbonarius (46 in both years, but also some strains of A. tubingensis (11 and A. japonicus (6 produced lower amounts of OTA.

  19. Isolation of plant nuclei suitable for flow cytometry from species with extremely mucilaginous compounds: an example in the genus Viola L. (Violaceae

    Directory of Open Access Journals (Sweden)

    Fernández Prieto, José Antonio

    2011-12-01

    Full Text Available Flow cytometry analysis has been widely applied in the determination of nuclear DNA content and ploidy level in many organisms. Despite being the most appropriate method for DNA content measurement, flow cytometry also presents some limitations. A fairly common, but little-studied problem is the effect on measurements of the presence of secondary metabolites. A good example is the genus Viola, which is composed of 525-600 species distributed worldwide. These species have proved to be problematic for flow cytometric analyses due to the release of extremely mucilaginous compounds into the nuclear suspension. In this work, the genome size of 13 species of Viola using flow cytometry are presented for the first time. Despite obtaining histograms with high coefficients of variation, we here present an optimized protocol to remove cytoplasmic compounds, particularly mucilaginous ones, from plant nuclei that pave the way for its application to estimate the genome size of other species exhibiting similar problems. Statistical analyses revealed significant differences between sections Viola and Melanium, and within each section (P El análisis mediante citometría de flujo ha sido aplicado de modo general para determinar el contenido de ADN nuclear y el nivel de ploidía en muchos organismos. A pesar de ser el método más adecuado para medir la cantidad de ADN, esta técnica también presenta algunas limitaciones. Un problema bastante común, aunque poco estudiado, es el efecto de los metabolitos secundarios en los resultados obtenidos. Un ejemplo respecto a la presencia de estos compuestos se encuentra en el género Viola, compuesto por 525-600 especies distribuidas por todo el mundo. Las especies de este género ya han sido previamente descritas como problemáticas en los análisis de citometría de flujo debido a la presencia de compuestos extremadamente mucilaginosos en las suspensiones de núcleos. En el presente trabajo se analiza por primera vez

  20. Full genome sequencing and genetic characterization of Eubenangee viruses identify Pata virus as a distinct species within the genus Orbivirus.

    Directory of Open Access Journals (Sweden)

    Manjunatha N Belaganahalli

    Full Text Available Eubenangee virus has previously been identified as the cause of Tammar sudden death syndrome (TSDS. Eubenangee virus (EUBV, Tilligery virus (TILV, Pata virus (PATAV and Ngoupe virus (NGOV are currently all classified within the Eubenangee virus species of the genus Orbivirus, family Reoviridae. Full genome sequencing confirmed that EUBV and TILV (both of which are from Australia show high levels of aa sequence identity (>92% in the conserved polymerase VP1(Pol, sub-core VP3(T2 and outer core VP7(T13 proteins, and are therefore appropriately classified within the same virus species. However, they show much lower amino acid (aa identity levels in their larger outer-capsid protein VP2 (<53%, consistent with membership of two different serotypes - EUBV-1 and EUBV-2 (respectively. In contrast PATAV showed significantly lower levels of aa sequence identity with either EUBV or TILV (with <71% in VP1(Pol and VP3(T2, and <57% aa identity in VP7(T13 consistent with membership of a distinct virus species. A proposal has therefore been sent to the Reoviridae Study Group of ICTV to recognise 'Pata virus' as a new Orbivirus species, with the PATAV isolate as serotype 1 (PATAV-1. Amongst the other orbiviruses, PATAV shows closest relationships to Epizootic Haemorrhagic Disease virus (EHDV, with 80.7%, 72.4% and 66.9% aa identity in VP3(T2, VP1(Pol, and VP7(T13 respectively. Although Ngoupe virus was not available for these studies, like PATAV it was isolated in Central Africa, and therefore seems likely to also belong to the new species, possibly as a distinct 'type'. The data presented will facilitate diagnostic assay design and the identification of additional isolates of these viruses.

  1. Genotyping-by-sequencing in an orphan plant species Physocarpus opulifolius helps identify the evolutionary origins of the genus Prunus.

    Science.gov (United States)

    Buti, Matteo; Sargent, Daniel J; Mhelembe, Khethani G; Delfino, Pietro; Tobutt, Kenneth R; Velasco, Riccardo

    2016-05-11

    The Rosaceae family encompasses numerous genera exhibiting morphological diversification in fruit types and plant habit as well as a wide variety of chromosome numbers. Comparative genomics between various Rosaceous genera has led to the hypothesis that the ancestral genome of the family contained nine chromosomes, however, the synteny studies performed in the Rosaceae to date encompass species with base chromosome numbers x = 7 (Fragaria), x = 8 (Prunus), and x = 17 (Malus), and no study has included species from one of the many Rosaceous genera containing a base chromosome number of x = 9. A genetic linkage map of the species Physocarpus opulifolius (x = 9) was populated with sequence characterised SNP markers using genotyping by sequencing. This allowed for the first time, the extent of the genome diversification of a Rosaceous genus with a base chromosome number of x = 9 to be performed. Orthologous loci distributed throughout the nine chromosomes of Physocarpus and the eight chromosomes of Prunus were identified which permitted a meaningful comparison of the genomes of these two genera to be made. The study revealed a high level of macro-synteny between the two genomes, and relatively few chromosomal rearrangements, as has been observed in studies of other Rosaceous genomes, lending further support for a relatively simple model of genomic evolution in Rosaceae.

  2. A Literature Survey to Identify Potentially Volatile Iodine-Bearing Species Present in Off-Gas Streams

    Energy Technology Data Exchange (ETDEWEB)

    Bruffey, S. H. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Spencer, B. B. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Strachan, D. M. [Strata-G, Knoxville, TN (United States); Jubin, R. T. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Soelberg, N. R. [Idaho National Lab. (INL), Idaho Falls, ID (United States); Riley, B. J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-06-30

    Four radionuclides have been identified as being sufficiently volatile in the reprocessing of nuclear fuel that their gaseous release needs to be controlled to meet regulatory requirements (Jubin et al. 2011, 2012). These radionuclides are 3H, 14C, 85Kr, and 129I. Of these, 129I has the longest half-life and potentially high biological impact. Accordingly, control of the release of 129I is most critical with respect to the regulations for the release of radioactive material in stack emissions. It is estimated that current EPA regulations (EPA 2010) would require any reprocessing plant in the United States to limit 129I release to less than 0.05 Ci/MTIHM for a typical fuel burnup of 55 gigawatt days per metric tonne (GWd/t) (Jubin 2011). The study of inorganic iodide in off-gas systems has been almost exclusively limited to I2 and the focus of organic iodide studies has been CH3I. In this document, we provide the results of an examination of publically available literature that is relevant to the presence and sources of both inorganic and organic iodine-bearing species in reprocessing plants. We especially focus on those that have the potential to be poorly sequestered with traditional capture methodologies. Based on the results of the literature survey and some limited thermodynamic modeling, the inorganic iodine species hypoiodous acid (HOI) and iodine monochloride (ICl) were identified as potentially low-sorbing iodine species that could present in off-gas systems. Organic species of interest included both short chain alkyl iodides such as methyl iodide (CH3I) and longer alkyl iodides up to iodododecane (C10H21I). It was found that fuel dissolution may provide conditions conducive to HOI formation and has been shown to result in volatile long-chain alkyl iodides, though these may not volatilize until later in the reprocessing sequence. Solvent extraction processes were found to be significant sources of various organic iodine-bearing species; formation of these

  3. Nodule worm infection in humans and wild primates in Uganda: cryptic species in a newly identified region of human transmission.

    Directory of Open Access Journals (Sweden)

    Ria R Ghai

    Full Text Available Soil-transmitted helminths (STHs are a major health concern in tropical and sub-tropical countries. Oesophagostomum infection is considered endemic to West Africa but has also been identified in Uganda, East Africa, among primates (including humans. However, the taxonomy and ecology of Oesophagostomum in Uganda have not been studied, except for in chimpanzees (Pan troglodytes, which are infected by both O. bifurcum and O. stephanostomum.We studied Oesophagostomum in Uganda in a community of non-human primates that live in close proximity to humans. Prevalence estimates based on microscopy were lower than those based on polymerase chain reaction (PCR, indicating greater sensitivity of PCR. Prevalence varied among host species, with humans and red colobus (Procolobus rufomitratus infected at lowest prevalence (25% and 41% by PCR, respectively, and chimpanzees, olive baboons (Papio anubis, and l'hoest monkeys (Cercopithecus lhoesti infected at highest prevalence (100% by PCR in all three species. Phylogenetic regression showed that primates travelling further and in smaller groups are at greatest risk of infection. Molecular phylogenetic analyses revealed three cryptic clades of Oesophagostomum that were not distinguishable based on morphological characteristics of their eggs. Of these, the clade with the greatest host range had not previously been described genetically. This novel clade infects humans, as well as five other species of primates.Multiple cryptic forms of Oesophagostomum circulate in the people and primates of western Uganda, and parasite clades differ in host range and cross-species transmission potential. Our results expand knowledge about human Oesophagostomum infection beyond the West African countries of Togo and Ghana, where the parasite is a known public health concern. Oesophagostomum infection in humans may be common throughout Sub-Saharan Africa, and the transmission of this neglected STH among primates, including zoonotic

  4. High-Resolution Melting Curve Analysis of the 16S Ribosomal Gene to Detect and Identify Pathogenic and Saprophytic Leptospira Species in Colombian Isolates.

    Science.gov (United States)

    Peláez Sánchez, Ronald G; Quintero, Juan Álvaro López; Pereira, Martha María; Agudelo-Flórez, Piedad

    2017-05-01

    AbstractIt is important to identify the circulating Leptospira agent to enhance the performance of serodiagnostic tests by incorporating specific antigens of native species, develop vaccines that take into account the species/serovars circulating in different regions, and optimize prevention and control strategies. The objectives of this study were to develop a polymerase chain reaction (PCR)-high-resolution melting (HRM) assay for differentiating between species of the genus Leptospira and to verify its usefulness in identifying unknown samples to species level. A set of primers from the initial region of the 16S ribosomal gene was designed to detect and differentiate the 22 species of Leptospira . Eleven reference strains were used as controls to establish the reference species and differential melting curves. Twenty-five Colombian Leptospira isolates were studied to evaluate the usefulness of the PCR-HRM assay in identifying unknown samples to species level. This identification was confirmed by sequencing and phylogenetic analysis of the 16S ribosomal gene. Eleven Leptospira species were successfully identified, except for Leptospira meyeri / Leptospira yanagawae because the sequences were 100% identical. The 25 isolates from humans, animals, and environmental water sources were identified as Leptospira santarosai (twelve), Leptospira interrogans (nine), and L. meyeri / L. yanagawae (four). The species verification was 100% concordant between PCR-HRM and phylogenetic analysis of the 16S ribosomal gene. The PCR-HRM assay designed in this study is a useful tool for identifying Leptospira species from isolates.

  5. A Comparison of growth on mercuric chloride for three Lemnaceae species reveals differences in growth dynamics that effect their suitability for use in either monitoring or remediating ecosystems contaminated with mercury.

    Science.gov (United States)

    Yang, Jingjing; Li, Gaojie; Bishopp, Anthony; Heenatigala, P. P. M.; Hu, Shiqi; Chen, Yan; Wu, Zhigang; Kumar, Sunjeet; Duan, Pengfei; Yao, Lunguang; Hou, Hongwei

    2018-04-01

    Mercury (Hg) is a toxic heavy metal that can alter the ecological balance when it contaminates aquatic ecosystems. Previously, researchers have used various Lemnaceae species either to monitor and/or remove heavy metals from freshwater systems. As Hg contamination is a pressing issue for aquatic systems worldwide, we assessed its impact on the growth of three commonly species of Lemnaceae - Lemna gibba 6745, Lemna minor 6580 and Spirodela polyrhiza 5543. We exposed plants to different concentrations of mercuric chloride (HgCl2) and monitored their growth, including relative growth rate, frond number, and fresh weight. These data were coupled with measurements of starch content, levels of photosynthetic pigment and the activities of antioxidant substances. The growth of all three lines showed significant negative correlations with Hg concentrations, and starch content, photosynthetic pigment, soluble protein and antioxidant enzymes levels were all clearly affected. Our results indicate that the L. gibba line used in this study was the most suitable of the three for biomonitoring of water contaminated with Hg. Accumulation of Hg was highest in the S. polyrhiza line with a bioconcentration factor over 1000, making this line the most suitable of the three tested for use in an Hg bioremediation system.

  6. A Comparison of Growth on Mercuric Chloride for Three Lemnaceae Species Reveals Differences in Growth Dynamics That Effect Their Suitability for Use in Either Monitoring or Remediating Ecosystems Contaminated With Mercury

    Directory of Open Access Journals (Sweden)

    Jingjing Yang

    2018-04-01

    Full Text Available Mercury (Hg is a toxic heavy metal that can alter the ecological balance when it contaminates aquatic ecosystems. Previously, researchers have used various Lemnaceae species either to monitor and/or remove heavy metals from freshwater systems. As Hg contamination is a pressing issue for aquatic systems worldwide, we assessed its impact on the growth of three commonly species of Lemnaceae- Lemna gibba 6745, Lemna minor 6580 and Spirodela polyrhiza 5543. We exposed plants to different concentrations of mercuric chloride (HgCl2 and monitored their growth, including relative growth rate, frond number (FN, and fresh weight (FW. These data were coupled with measurements of starch content, levels of photosynthetic pigment and the activities of antioxidant substances. The growth of all three lines showed significant negative correlations with Hg concentrations, and starch content, photosynthetic pigment, soluble protein and antioxidant enzymes levels were all clearly affected. Our results indicate that the L. gibba line used in this study was the most suitable of the three for biomonitoring of water contaminated with Hg. Accumulation of Hg was highest in the S. polyrhiza line with a bioconcentration factor over 1,000, making this line the most suitable of the three tested for use in an Hg bioremediation system.

  7. Multiple nuclear and mitochondrial genotyping identifies emperors and large-eye breams (Teleostei : Lethrinidae) from New Caledonia and reveals new large-eye bream species

    OpenAIRE

    Borsa, Philippe; Collet, Adeline; Carassou, Laure; Ponton, Dominique; Chen, W. J.

    2010-01-01

    International audience; Species identification is fundamental to address questions about community ecology, biodiversity, conservation and resource management, at any life history stage. Current studies on fish larval ecology of tropical species are hampered by the lack of reliable and effective tools for identifying larvae at the species level. Emperors and large-eye breams comprise fish species from the perciform fish family Lethrinidae. They inhabit coastal and coral-reef habitats of the t...

  8. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

    KAUST Repository

    Abdel-Haleem, Alyaa M.; Hefzi, Hooman; Mineta, Katsuhiko; Gao, Xin; Gojobori, Takashi; Palsson, Bernhard O.; Lewis, Nathan E.; Jamshidi, Neema

    2018-01-01

    and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species

  9. Cross-sectional study to identify staphylococcal species isolated from teat and inguinal skin of different-aged dairy heifers.

    Science.gov (United States)

    Adkins, P R F; Dufour, S; Spain, J N; Calcutt, M J; Reilly, T J; Stewart, G C; Middleton, J R

    2018-04-01

    The purpose of this study was to describe the prevalence and distribution of staphylococcal species on the teat and inguinal skin of dairy heifers across the various stages of the heifer life cycle. The cross-sectional study included 106 Holstein heifers with an age range of 0 d to 27 mo that were selected from 11 different groups, based on housing type and age, on a single dairy operation. A composite swabbing sample including all 4 teats and a second composite sample including both inguinal regions of each heifer were collected using gas-sterilized electrostatic dusters (Swiffers; Procter and Gamble, Cincinnati, OH). Swabbing samples were mixed with 10 mL of sterile saline, agitated, and cultured on mannitol salt agar plates. At 24 h, plates were read and up to 10 staphylococcal colonies were saved for further analysis. Staphylococcal isolates were speciated using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or PCR amplification and partial sequencing of rpoB or tuf. The prevalence of staphylococci was compared between the inguinal and teat regions using the chi-squared or Fisher's exact test, as applicable. Logistic regression models were used to investigate the relationship between a heifer's age (treated as a quantitative continuous variable) and the probability of isolating a given staphylococcal species from a given body site (inguinal region or teats). Overall, the most common species identified were Staphylococcus haemolyticus followed by Staphylococcus chromogenes, Staphylococcus xylosus, Staphylococcus devriesei, and Staphylococcus sciuri. Staphylococcus aureus was more prevalent on the teat than in the inguinal region, whereas Staphylococcus arlettae was more prevalent in the inguinal region than on the teat. All other staphylococcal species were as likely to be found on the teat skin as the inguinal region skin. Isolation from the inguinal and teat skin was associated with age for Staphylococcus agnetis, S. chromogenes

  10. Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis.

    Science.gov (United States)

    O'Flynn, Ciaran; Deusch, Oliver; Darling, Aaron E; Eisen, Jonathan A; Wallis, Corrin; Davis, Ian J; Harris, Stephen J

    2015-11-13

    Porphyromonads play an important role in human periodontal disease and recently have been shown to be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions characterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from 18 Porphyromonad species from dogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to synthesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood. Other pathway differences such as the ability to synthesize siroheme and vitamin B12 point to enhanced metabolic flexibility for P. cangingivalis, which may underlie its prevalence in the canine oral cavity. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  11. Native Plant Species Suitable for Ecological Restoration

    Science.gov (United States)

    2011-05-10

    8217§ e "’ "’ ~ ::::> ~ ~ 3: 0 ~r c:... E- ~ ::r: ::r: ::r: ::c "’-! . . . . . . . . . Varieties "Aldous," "C:unper," ’’Cinunaron," ’" Pastura " and

  12. Cross-species global and subset gene expression profiling identifies genes involved in prostate cancer response to selenium

    Directory of Open Access Journals (Sweden)

    Dhir Rajiv

    2004-08-01

    Full Text Available Abstract Background Gene expression technologies have the ability to generate vast amounts of data, yet there often resides only limited resources for subsequent validation studies. This necessitates the ability to perform sorting and prioritization of the output data. Previously described methodologies have used functional pathways or transcriptional regulatory grouping to sort genes for further study. In this paper we demonstrate a comparative genomics based method to leverage data from animal models to prioritize genes for validation. This approach allows one to develop a disease-based focus for the prioritization of gene data, a process that is essential for systems that lack significant functional pathway data yet have defined animal models. This method is made possible through the use of highly controlled spotted cDNA slide production and the use of comparative bioinformatics databases without the use of cross-species slide hybridizations. Results Using gene expression profiling we have demonstrated a similar whole transcriptome gene expression patterns in prostate cancer cells from human and rat prostate cancer cell lines both at baseline expression levels and after treatment with physiologic concentrations of the proposed chemopreventive agent Selenium. Using both the human PC3 and rat PAII prostate cancer cell lines have gone on to identify a subset of one hundred and fifty-four genes that demonstrate a similar level of differential expression to Selenium treatment in both species. Further analysis and data mining for two genes, the Insulin like Growth Factor Binding protein 3, and Retinoic X Receptor alpha, demonstrates an association with prostate cancer, functional pathway links, and protein-protein interactions that make these genes prime candidates for explaining the mechanism of Selenium's chemopreventive effect in prostate cancer. These genes are subsequently validated by western blots showing Selenium based induction and using

  13. Identifying barriers to effective management of widespread invasive alien trees: Prosopis species (mesquite) in South Africa as a case study

    CSIR Research Space (South Africa)

    Shackleton, RT

    2016-05-01

    Full Text Available and in some cases improve the benefits that some invasive species can provide. This study assesses the barriers that hinder the effective management of widespread tree invasions, drawing insights from a case study of invasions of Prosopis species (mesquite...

  14. Learning from Nature: the use of non-model species to identify novel acclimations to flooding stress

    NARCIS (Netherlands)

    Voesenek, Laurentius|info:eu-repo/dai/nl/074850849; van Veen, Hans|info:eu-repo/dai/nl/330541897; Sasidharan, Rashmi|info:eu-repo/dai/nl/313968594

    2014-01-01

    Excess water in the form of waterlogged soil or deeper submergence (generically termed ‘flooding’) influences plant growth, survival and species distribution in many natural ecosystems. It also has a negative impact on crop growth and yield since many agricultural species are flooding intolerant.

  15. Quantitative Real-Time PCR Assays To Identify and Quantify Fecal Bifidobacterium Species in Infants Receiving a Prebiotic Infant Formula

    OpenAIRE

    Haarman, Monique; Knol, Jan

    2005-01-01

    A healthy intestinal microbiota is considered to be important for priming of the infants' mucosal and systemic immunity. Breast-fed infants typically have an intestinal microbiota dominated by different Bifidobacterium species. It has been described that allergic infants have different levels of specific Bifidobacterium species than healthy infants. For the accurate quantification of Bifidobacterium adolescentis, Bifidobacterium angulatum, Bifidobacterium bifidum, Bifidobacterium breve, Bifid...

  16. Using empirical models of species colonization under multiple threatening processes to identify complementary threat-mitigation strategies.

    Science.gov (United States)

    Tulloch, Ayesha I T; Mortelliti, Alessio; Kay, Geoffrey M; Florance, Daniel; Lindenmayer, David

    2016-08-01

    Approaches to prioritize conservation actions are gaining popularity. However, limited empirical evidence exists on which species might benefit most from threat mitigation and on what combination of threats, if mitigated simultaneously, would result in the best outcomes for biodiversity. We devised a way to prioritize threat mitigation at a regional scale with empirical evidence based on predicted changes to population dynamics-information that is lacking in most threat-management prioritization frameworks that rely on expert elicitation. We used dynamic occupancy models to investigate the effects of multiple threats (tree cover, grazing, and presence of an hyperaggressive competitor, the Noisy Miner (Manorina melanocephala) on bird-population dynamics in an endangered woodland community in southeastern Australia. The 3 threatening processes had different effects on different species. We used predicted patch-colonization probabilities to estimate the benefit to each species of removing one or more threats. We then determined the complementary set of threat-mitigation strategies that maximized colonization of all species while ensuring that redundant actions with little benefit were avoided. The single action that resulted in the highest colonization was increasing tree cover, which increased patch colonization by 5% and 11% on average across all species and for declining species, respectively. Combining Noisy Miner control with increasing tree cover increased species colonization by 10% and 19% on average for all species and for declining species respectively, and was a higher priority than changing grazing regimes. Guidance for prioritizing threat mitigation is critical in the face of cumulative threatening processes. By incorporating population dynamics in prioritization of threat management, our approach helps ensure funding is not wasted on ineffective management programs that target the wrong threats or species. © 2016 Society for Conservation Biology.

  17. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.

    Directory of Open Access Journals (Sweden)

    Alyaa M Abdel-Haleem

    2018-01-01

    Full Text Available Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale metabolic models (GeMMs of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1, choline, and pantothenate (vitamin B5 metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models.

  18. Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting

    KAUST Repository

    Abdel-Haleem, Alyaa M.

    2018-01-04

    Several antimalarial drugs exist, but differences between life cycle stages among malaria species pose challenges for developing more effective therapies. To understand the diversity among stages and species, we reconstructed genome-scale models (GEMs) of metabolism for five life cycle stages and five species of Plasmodium spanning the blood, transmission, and mosquito stages. The stage-specific models of Plasmodium falciparum uncovered stage-dependent changes in central carbon metabolism and predicted potential targets that could affect several life cycle stages. The species-specific models further highlight differences between experimental animal models and the human-infecting species. Comparisons between human- and rodent-infecting species revealed differences in thiamine (vitamin B1), choline, and pantothenate (vitamin B5) metabolism. Thus, we show that genome-scale analysis of multiple stages and species of Plasmodium can prioritize potential drug targets that could be both anti-malarials and transmission blocking agents, in addition to guiding translation from non-human experimental disease models.

  19. A new species of Casmaria H. Adams & A. Adams, 1853 (Gastropoda, Cassidae from the Philippines identified by molecular data

    Directory of Open Access Journals (Sweden)

    Alexander Fedosov

    2014-03-01

    Full Text Available The genus Casmaria H. Adams & A. Adams, 1853 (family Cassidae is widespread in the tropical Indo-Pacific and has been documented from some Atlantic localities as well. Two Casmaria species, C. erinaceus (Linnaeus, 1758 and C. ponderosa (Gmelin, 1791, are common in Indo-Pacific shallow-water sandy bottom communities and are characterized by high morphological variability; both species encompass multiple, often sympatric forms of uncertain status. In the present study we carry out a phylogenetic analysis of some Philippine Casmaria morphs and demonstrate that one of the distinctive morphs earlier assigned to Casmaria ponderosa is in fact a different species, which we describe as Casmaria boblehmani sp. nov. The smooth form of Casmaria ponderosa, C. ponderosa ponderosa, and the solid nodulose form, widely called “form nodulosa” despite being strikingly different in shell morphology, are shown to be conspecific. Studied specimens of these two morphs even from different localities share the same haplotype of the CO1 gene. In light of these new data on the morphological variability of Casmaria species, we discuss criteria of species delimitation in the genus Casmaria and possible affinities of Casmaria boblehmani sp. nov. within the genus.

  20. Using SSR-HRM to Identify Closely Related Species in Herbal Medicine Products: A Case Study on Licorice.

    Science.gov (United States)

    Li, Jingjian; Xiong, Chao; He, Xia; Lu, Zhaocen; Zhang, Xin; Chen, Xiaoyang; Sun, Wei

    2018-01-01

    Traditional herbal medicines have played important roles in the ways of life of people around the world since ancient times. Despite the advanced medical technology of the modern world, herbal medicines are still used as popular alternatives to synthetic drugs. Due to the increasing demand for herbal medicines, plant species identification has become an important tool to prevent substitution and adulteration. Here we propose a method for biological assessment of the quality of prescribed species in the Chinese Pharmacopoeia by use of high resolution melting (HRM) analysis of microsatellite loci. We tested this method on licorice, a traditional herbal medicine with a long history. Results showed that nine simple sequence repeat (SSR) markers produced distinct melting curve profiles for the five licorice species investigated using HRM analysis. These results were validated by capillary electrophoresis. We applied this protocol to commercially available licorice products, thus enabling the consistent identification of 11 labels with non-declared Glycyrrhiza species. This novel strategy may thus facilitate DNA barcoding as a method of identification of closely related species in herbal medicine products. Based on this study, a brief operating procedure for using the SSR-HRM protocol for herbal authentication is provided.

  1. Development of standardized methodology for identifying toxins in clinical samples and fish species associated with tetrodotoxin-borne poisoning incidents

    Directory of Open Access Journals (Sweden)

    Tai-Yuan Chen

    2016-01-01

    Full Text Available Tetrodotoxin (TTX is a naturally occurring toxin in food, especially in puffer fish. TTX poisoning is observed frequently in South East Asian regions. In TTX-derived food poisoning outbreaks, the amount of TTX recovered from suspicious fish samples or leftovers, and residual levels from biological fluids of victims are typically trace. However, liquid chromatography–mass spectrometry and liquid chromatography–tandem mass spectrometry methods have been demonstrated to qualitatively and quantitatively determine TTX in clinical samples from victims. Identification and validation of the TTX-originating seafood species responsible for a food poisoning incident is needed. A polymerase chain reaction-based method on mitochondrial DNA analysis is useful for identification of fish species. This review aims to collect pertinent information available on TTX-borne food poisoning incidents with a special emphasis on the analytical methods employed for TTX detection in clinical laboratories as well as for the identification of TTX-bearing species.

  2. Rapid approach to identify the presence of Arabica and Robusta species in coffee using 1H NMR spectroscopy.

    Science.gov (United States)

    Monakhova, Yulia B; Ruge, Winfried; Kuballa, Thomas; Ilse, Maren; Winkelmann, Ole; Diehl, Bernd; Thomas, Freddy; Lachenmeier, Dirk W

    2015-09-01

    NMR spectroscopy was used to verify the presence of Arabica and Robusta species in coffee. Lipophilic extracts of authentic roasted and green coffees showed the presence of established markers for Robusta (16-O-methylcafestol (16-OMC)) and for Arabica (kahweol). The integration of the 16-OMC signal (δ 3.165 ppm) was used to estimate the amount of Robusta in coffee blends with an approximate limit of detection of 1-3%. The method was successfully applied for the analysis of 77 commercial coffee samples (coffee pods, coffee capsules, and coffee beans). Furthermore, principal component analysis (PCA) was applied to the spectra of lipophilic and aqueous extracts of 20 monovarietal authentic samples. Clusters of the two species were observed. NMR spectroscopy can be used as a rapid prescreening tool to discriminate Arabica and Robusta coffee species before the confirmation applying the official method. Copyright © 2015 Elsevier Ltd. All rights reserved.

  3. Citizen science identifies the effects of nitrogen deposition, climate and tree species on epiphytic lichens across the UK.

    Science.gov (United States)

    Welden, N A; Wolseley, P A; Ashmore, M R

    2018-01-01

    A national citizen survey quantified the abundance of epiphytic lichens that are known to be either sensitive or tolerant to nitrogen (N) deposition. Records were collected across the UK from over 10,000 individual trees of 22 deciduous species. Mean abundance of tolerant and sensitive lichens was related to mean N deposition rates and climatic variables at a 5 km scale, and the response of lichens was compared on the three most common trees (Quercus, Fraxinus and Acer) and by assigning all 22 tree species to three bark pH groups. The abundance of N-sensitive lichens on trunks decreased with increasing total N deposition, while that of N-tolerant lichens increased. The abundance of N-sensitive lichens on trunks was reduced close to a busy road, while the abundance of N-tolerant lichens increased. The abundance of N-tolerant lichen species on trunks was lower on Quercus and other low bark pH species, but the abundance of N-sensitive lichens was similar on different tree species. Lichen abundance relationships with total N deposition did not differ between tree species or bark pH groups. The response of N-sensitive lichens to reduced nitrogen was greater than to oxidised N, and the response of N-tolerant lichens was greater to oxidised N than to reduced N. There were differences in the response of N-sensitive and N-tolerant lichens to rainfall, humidity and temperature. Relationships with N deposition and climatic variables were similar for lichen presence on twigs as for lichen abundance on trunks, but N-sensitive lichens increased, rather than decreased, on twigs of Quercus/low bark pH species. The results demonstrate the unique power of citizen science to detect and quantify the air pollution impacts over a wide geographical range, and specifically to contribute to understanding of lichen responses to different chemical forms of N deposition, local pollution sources and bark chemistry. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Application of CHD1 Gene and EE0.6 Sequences to Identify Sexes of Several Protected Bird Species in Taiwan

    Directory of Open Access Journals (Sweden)

    E.-C. Lin

    2011-06-01

    Full Text Available Many bird species, for example: Crested Serpent Eagle (Spilornis cheela hoya, Collared Scops (Owl Otus bakkamoena, Tawny Fish Owl (Ketupa flavipes, Crested Goshawk (Accipiter trivirgatus, and Grass Owl (Tyto longimembris... etc, are monomorphic, which is difficult to identify their sex simply by their outward appearance. Especially for those monomorphic endangered species, finding an effective tool to identify their sex beside outward appearance is needed for further captive breeding programs or other conservation plans. In this study, we collected samples of Black Swan (Cygmus atratus and Nicobar Pigeon (Caloenas nicobarica, two aviaries introduced monomorphic species served as control group, and Crested Serpent Eagle, Collared Scops Owl, Tawny Fish Owl, Crested Goshawk, and Grass Owl, five protected monomorphic species in Taiwan. We used sex-specific primers of avian CHD1 (chromo-helicase-DNA-binding gene and EE0.6 (EcoRI 0.6-kb fragment sequences to identify the sex of these birds. The results showed that CHD1 gene primers could be used to correctly identify the sex of Black Swans, Nicobar Pigeons and Crested Serpent Eagles, but it could not be used to correctly identify sex in Collared Scops Owls, Tawny Fish Owls, and Crested Goshawks. In the sex identification using EE0.6 sequence fragment, A, C, D and E primer sets could be used for sexing Black Swans; A, B, C, and D primer sets could be used for sexing Crested Serpent Eagles; and E primer set could be used for sexing Nicobar Pigeons and the two owl species. Correct determination of sex is the first step if a captive breeding measure is required. We have demonstrated that several of the existing primer sets can be used for sex determination of several captive breeding and indigenous bird species.

  5. Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera.

    Directory of Open Access Journals (Sweden)

    Nuttika Suwannasai

    Full Text Available Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI, we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1 Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2 Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3 Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in

  6. Fungi in Thailand: a case study of the efficacy of an ITS barcode for automatically identifying species within the Annulohypoxylon and Hypoxylon genera.

    Science.gov (United States)

    Suwannasai, Nuttika; Martín, María P; Phosri, Cherdchai; Sihanonth, Prakitsin; Whalley, Anthony J S; Spouge, John L

    2013-01-01

    Thailand, a part of the Indo-Burma biodiversity hotspot, has many endemic animals and plants. Some of its fungal species are difficult to recognize and separate, complicating assessments of biodiversity. We assessed species diversity within the fungal genera Annulohypoxylon and Hypoxylon, which produce biologically active and potentially therapeutic compounds, by applying classical taxonomic methods to 552 teleomorphs collected from across Thailand. Using probability of correct identification (PCI), we also assessed the efficacy of automated species identification with a fungal barcode marker, ITS, in the model system of Annulohypoxylon and Hypoxylon. The 552 teleomorphs yielded 137 ITS sequences; in addition, we examined 128 GenBank ITS sequences, to assess biases in evaluating a DNA barcode with GenBank data. The use of multiple sequence alignment in a barcode database like BOLD raises some concerns about non-protein barcode markers like ITS, so we also compared species identification using different alignment methods. Our results suggest the following. (1) Multiple sequence alignment of ITS sequences is competitive with pairwise alignment when identifying species, so BOLD should be able to preserve its present bioinformatics workflow for species identification for ITS, and possibly therefore with at least some other non-protein barcode markers. (2) Automated species identification is insensitive to a specific choice of evolutionary distance, contributing to resolution of a current debate in DNA barcoding. (3) Statistical methods are available to address, at least partially, the possibility of expert misidentification of species. Phylogenetic trees discovered a cryptic species and strongly supported monophyletic clades for many Annulohypoxylon and Hypoxylon species, suggesting that ITS can contribute usefully to a barcode for these fungi. The PCIs here, derived solely from ITS, suggest that a fungal barcode will require secondary markers in Annulohypoxylon and

  7. A GIS model of habitat suitability for Solanum conocarpum (Solanaceae) in St. John, US Virgin Islands

    Science.gov (United States)

    Palumbo, Matthew D.; Fleming, Jonathan P.; Monsegur, Omar A.; Vilella, Francisco

    2016-01-01

    Solanum conocarpum (Solanaceae) (Marron Bacora) is a rare, dry-forest shrub endemic to the island of St. John, US Virgin Islands, considered for listing under the Endangered Species Act. Given its status as a species of conservation concern, we incorporated environmental characteristics of 3 observed populations and 5 additional known locations into a geographic information system (GIS) analysis to create a habitat-suitability model for the species on the island of St. John. Our model identified 1929.87 ha of highly suitable and moderately suitable habitat. Of these, 1161.20 ha (60.2%) occurred within the boundaries of Virgin Islands National Park. Our model provides spatial information on potential locations for future surveys and restoration sites for this endemic species of the US Virgin Islands.

  8. Using otolith morphometric and morphology characteristics to identify carangids species in the Persian Gulf and Oman Sea

    OpenAIRE

    Mansourkiaei, Ana

    2010-01-01

    In a survey on 524 specimens from 18 different species belonging to the Carangidae family collected from The Persian Gulf, otolithes (Sagittae) are extracted from under gills region. After washing, their morphometric parameters measured. These parameters are otolith length, width, weight and length of antirostrum, width and length of rostrum, width in right and left sagittae. In addition to the otolith outline, mode position and mode opening of the Sulcus acusticus was examined. Data indicate...

  9. PRE-CLINICAL EVALUATION OF EXTRACTS AND ESSENTIAL OILS FROM BETEL-LIKE SCENT PIPER SPECIES IDENTIFIED POTENTIAL CANCER TREATMENT.

    Science.gov (United States)

    Sanubol, Arisa; Chaveerach, Arunrat; Tanee, Tawatchai; Sudmoon, Runglawan

    2017-01-01

    Nine Piper species with betel-like scents are sources of industrial and medicinal aromatic chemicals, but there is lack of information on cytotoxicity and genotoxicity for human safety, including how these plants impact human cervical cancer cell line. Plant leaves were extracted with hexane and hydro-distilled for essential oils. The extracts and oils were pre-clinically studied based on cyto - and genotoxicity using microculture tetrazolium (MTT) and comet assays. The crude extracts showed an IC 50 in leukocytes and HeLa cells of 58.59-97.31 mg/ml and 34.91-101.79 mg/ml, the LD 50 is higher than 5000 mg/kg. With lower values than the crude extracts, the essential oils showed an IC 50 in leukocytes and HeLa cells of 0.023-0.059 μg/ml and 0.025-0.043 μg/ml the LD 50 is less than 50 mg/kg. IC 50 values showed that the essential oils were highly toxic than the crude extracts. At the level of human genetic materials, the crude extracts of two species, including P. betloides and P. crocatum , showed a significant toxicity ( p Piper species showed insignificant toxicity in leukocytes. For HeLa cells, the eight-studied species showed significant toxicity in HeLa cells, whereas only P. submultinerve showed insignificant toxicity. The crude extracts and essential oils should be tested as putative cervical cancer treatments due to less toxicity in human normal cells.

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

    Science.gov (United States)

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

    2010-01-01

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

  11. Use of Whole-Genus Genome Sequence Data To Develop a Multilocus Sequence Typing Tool That Accurately Identifies Yersinia Isolates to the Species and Subspecies Levels

    Science.gov (United States)

    Hall, Miquette; Chattaway, Marie A.; Reuter, Sandra; Savin, Cyril; Strauch, Eckhard; Carniel, Elisabeth; Connor, Thomas; Van Damme, Inge; Rajakaruna, Lakshani; Rajendram, Dunstan; Jenkins, Claire; Thomson, Nicholas R.

    2014-01-01

    The genus Yersinia is a large and diverse bacterial genus consisting of human-pathogenic species, a fish-pathogenic species, and a large number of environmental species. Recently, the phylogenetic and population structure of the entire genus was elucidated through the genome sequence data of 241 strains encompassing every known species in the genus. Here we report the mining of this enormous data set to create a multilocus sequence typing-based scheme that can identify Yersinia strains to the species level to a level of resolution equal to that for whole-genome sequencing. Our assay is designed to be able to accurately subtype the important human-pathogenic species Yersinia enterocolitica to whole-genome resolution levels. We also report the validation of the scheme on 386 strains from reference laboratory collections across Europe. We propose that the scheme is an important molecular typing system to allow accurate and reproducible identification of Yersinia isolates to the species level, a process often inconsistent in nonspecialist laboratories. Additionally, our assay is the most phylogenetically informative typing scheme available for Y. enterocolitica. PMID:25339391

  12. Is Switzerland suitable for the invasion of Aedes albopictus [corrected]?

    Science.gov (United States)

    Neteler, Markus; Metz, Markus; Rocchini, Duccio; Rizzoli, Annapaola; Flacio, Eleonora; Engeler, Luca; Guidi, Valeria; Lüthy, Peter; Tonolla, Mauro

    2013-01-01

    Over the last 30 years, the Asian tiger mosquito, Aedes albopictus, has rapidly spread around the world. The European distribution comprises the Mediterranean basin with a first appearance in Switzerland in 2003. Early identification of the most suitable areas in Switzerland allowing progressive invasion by this species is considered crucial to suggest adequate surveillance and control plans. We identified the most suitable areas for invasion and establishment of Ae. albopictus in Switzerland. The potential distribution areas linked to the current climatic suitability were assessed using remotely sensed land surface temperature data recorded by the MODIS satellite sensors. Suitable areas for adult survival and overwintering of diapausing eggs were also identified for future climatic conditions, considering two different climate change scenarios (A1B, A2) for the periods 2020-2049 and 2045-2074. At present, the areas around Lake Geneva in western Switzerland provide suitable climatic conditions for Ae. albopictus. In northern Switzerland, parts of the Rhine valley, around Lake Constance, as well as the surroundings of Lake Neuchâtel, appear to be suitable for the survival at least of adult Ae. albopictus. However, these areas are characterized by winters currently being too cold for survival and development of diapausing eggs. In southern Switzerland, Ae. albopictus is already well-established, especially in the Canton of Ticino. For the years 2020-2049, the predicted possible spread of the tiger mosquito does not differ significantly from its potential current distribution. However, important expansions are obtained if the period is extended to the years 2045-2074, when Ae. albopictus may invade large new areas. Several parts of Switzerland provide suitable climatic conditions for invasion and establishment of Ae. albopictus. The current distribution and rapid spread in other European countries suggest that the tiger mosquito will colonize new areas in Switzerland

  13. Is Switzerland Suitable for the Invasion of Aedes albopictus?

    Science.gov (United States)

    Neteler, Markus; Metz, Markus; Rocchini, Duccio; Rizzoli, Annapaola; Flacio, Eleonora; Engeler, Luca; Guidi, Valeria; Lüthy, Peter; Tonolla, Mauro

    2013-01-01

    Background Over the last 30 years, the Asian tiger mosquito, Aedes albopictus, has rapidly spread around the world. The European distribution comprises the Mediterranean basin with a first appearance in Switzerland in 2003. Early identification of the most suitable areas in Switzerland allowing progressive invasion by this species is considered crucial to suggest adequate surveillance and control plans. Methodology/Principal Findings We identified the most suitable areas for invasion and establishment of Ae. albopictus in Switzerland. The potential distribution areas linked to the current climatic suitability were assessed using remotely sensed land surface temperature data recorded by the MODIS satellite sensors. Suitable areas for adult survival and overwintering of diapausing eggs were also identified for future climatic conditions, considering two different climate change scenarios (A1B, A2) for the periods 2020–2049 and 2045–2074. At present, the areas around Lake Geneva in western Switzerland provide suitable climatic conditions for Ae. albopictus. In northern Switzerland, parts of the Rhine valley, around Lake Constance, as well as the surroundings of Lake Neuchâtel, appear to be suitable for the survival at least of adult Ae. albopictus. However, these areas are characterized by winters currently being too cold for survival and development of diapausing eggs. In southern Switzerland, Ae. albopictus is already well-established, especially in the Canton of Ticino. For the years 2020–2049, the predicted possible spread of the tiger mosquito does not differ significantly from its potential current distribution. However, important expansions are obtained if the period is extended to the years 2045–2074, when Ae. albopictus may invade large new areas. Conclusions/Significance Several parts of Switzerland provide suitable climatic conditions for invasion and establishment of Ae. albopictus. The current distribution and rapid spread in other European

  14. Vertebrae classification models - Validating classification models that use morphometrics to identify ancient salmonid (Oncorhynchus spp.) vertebrae to species

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Using morphometric characteristics of modern salmonid (Oncorhynchus spp.) vertebrae, we have developed classification models to identify salmonid vertebrae to the...

  15. Niche suitability affects development: skull asymmetry increases in less suitable areas.

    Directory of Open Access Journals (Sweden)

    Renan Maestri

    Full Text Available For conservation purposes, it is important to take into account the suitability of a species to particular habitats; this information may predict the long-term survival of a species. In this sense, morphological measures of developmental stress, such as fluctuating asymmetry, can be proxies for an individual's performance in different regions. In this study, we conducted tests to determine whether areas with different levels of suitability for a species (generated by ecological niche models were congruent with morphological markers that reflect environmental stress and morphological variance. We generated a Maxent niche model and compared the suitability assessments of several areas with the skull morphology data (fluctuating asymmetry and morphological disparity of populations of the Atlantic forest endemic to Brazil rodent Akodon cursor. Our analyses showed a significant negative relationship between suitability levels and fluctuating asymmetry levels, which indicates that in less suitable areas, the individuals experience numerous disturbances during skull ontogeny. We have not found an association between morphological variance and environmental suitability. As expected, these results suggest that in environments with a lower suitability, developmental stress is increased. Such information is helpful in the understanding of the species evolution and in the selection of priority areas for the conservation of species.

  16. Potential bacterial core species associated with digital dermatitis in cattle herds identified by molecular profiling of interdigital skin samples

    DEFF Research Database (Denmark)

    Weiss Nielsen, Martin; Strube, Mikael Lenz; Isbrand, Anastasia

    2016-01-01

    of different molecular methods. Deep sequencing of the 16S rRNA gene variable regions V1–V2 showed that Treponema, Mycoplasma, Fusobacterium and Porphyromonas were the genera best differentiating the DD samples from the controls. Additional deep sequencing analysis of the most abundant genus, Treponema...... in the epidermal lesions and were present in only a subset of samples. RT-qPCR analysis showed that treponemes were also actively expressing a panel of virulence factors at the site of infection. Our results further support the hypothesis that species belonging to the genus Treponema are major pathogens of DD...... and also provide sufficient clues to motivate additional research into the role of M. fermentans, F. necrophorum and P. levii in the etiology of DD....

  17. Mild soaps and radiotherapy: a survey of the UK public to identify brands of soap considered mild and analysis of these to ascertain suitability for recommendation in radiotherapy departments.

    Science.gov (United States)

    Robertson, K; Brown, P

    2011-05-01

    Cancer agencies recommend that patients use mild soap when undergoing external beam radiotherapy to minimise skin reactions. They define 'mild soap' as non-alkaline, lanolin free, unperfumed soap with a neutral pH. This study aimed to identify which soaps the UK public perceive as mild and ascertain if these were clinically mild and could potentially be recommended within radiotherapy departments. A survey of 237 participants identified eight top brands of mild soap, which were then tested for pH and analysed for potential irritants. All soaps were lanolin free and non-alkaline, with Simple and Johnson's the closest to pH 5.5. All contained fragrances except Simple and E45. Dove, Pears and Imperial Leather contained the highest concentration of fragrances. All soaps except E45 contained potential irritants. Only Simple and E45 fit the cancer agencies' definition of mild soap and could therefore be recommended for radiotherapy patients. Future research should identify current practices and recommendations in the UK as anecdotal evidence suggests large variations in skin care advice. Further scientific analysis could potentially identify cheaper brands that fit the definition of 'mild'. UK recommendations should be standardised and consistent with best practice to reduce skin reaction severity in radiotherapy patients. © 2010 Blackwell Publishing Ltd.

  18. Clinical characteristics and persistence of bovine mastitis caused by different species of coagulase-negative staphylococci identified with API or AFLP

    DEFF Research Database (Denmark)

    Taponen, S.; Simojoki, H.; Haveri, M.

    2006-01-01

    The coagulase-negative staphylococcal species causing mastitis in lactating cattle were identified and possible differences in the clinical characteristics or persistence of mastitis caused by different CNS were evaluated. The effect of antimicrobial treatment was also assessed. In addition, AFLP...... of these species. Approximately half of the mastitis cases were clinical, and in the majority clinical signs were mild. The severity and persistence of intramammary infection were unaffected by CNS species. Fifty-nine percent of the quarter cases were treated with antimicrobials, and the rest were left without...... treatment. Mastitis due to P-lactamase-negative CNS was treated with penicillin G and that due to beta-lactamase-positive CNS with cloxacillin. Nineteen percent of the isolates were P-lactamase-positive. The bacterial cure rate for quarters treated with antimicrobials was high, 85.9%, as opposed to only 45...

  19. Reactive Oxygen Species (ROS)-Activated ATM-Dependent Phosphorylation of Cytoplasmic Substrates Identified by Large-Scale Phosphoproteomics Screen*

    Science.gov (United States)

    Kozlov, Sergei V.; Waardenberg, Ashley J.; Engholm-Keller, Kasper; Arthur, Jonathan W.; Graham, Mark E.; Lavin, Martin

    2016-01-01

    Ataxia-telangiectasia, mutated (ATM) protein plays a central role in phosphorylating a network of proteins in response to DNA damage. These proteins function in signaling pathways designed to maintain the stability of the genome and minimize the risk of disease by controlling cell cycle checkpoints, initiating DNA repair, and regulating gene expression. ATM kinase can be activated by a variety of stimuli, including oxidative stress. Here, we confirmed activation of cytoplasmic ATM by autophosphorylation at multiple sites. Then we employed a global quantitative phosphoproteomics approach to identify cytoplasmic proteins altered in their phosphorylation state in control and ataxia-telangiectasia (A-T) cells in response to oxidative damage. We demonstrated that ATM was activated by oxidative damage in the cytoplasm as well as in the nucleus and identified a total of 9,833 phosphorylation sites, including 6,686 high-confidence sites mapping to 2,536 unique proteins. A total of 62 differentially phosphorylated peptides were identified; of these, 43 were phosphorylated in control but not in A-T cells, and 19 varied in their level of phosphorylation. Motif enrichment analysis of phosphopeptides revealed that consensus ATM serine glutamine sites were overrepresented. When considering phosphorylation events, only observed in control cells (not observed in A-T cells), with predicted ATM sites phosphoSerine/phosphoThreonine glutamine, we narrowed this list to 11 candidate ATM-dependent cytoplasmic proteins. Two of these 11 were previously described as ATM substrates (HMGA1 and UIMCI/RAP80), another five were identified in a whole cell extract phosphoproteomic screens, and the remaining four proteins had not been identified previously in DNA damage response screens. We validated the phosphorylation of three of these proteins (oxidative stress responsive 1 (OSR1), HDGF, and ccdc82) as ATM dependent after H2O2 exposure, and another protein (S100A11) demonstrated ATM

  20. Ensemble modeling to predict habitat suitability for a large-scale disturbance specialist

    Science.gov (United States)

    Quresh S. Latif; Victoria A. Saab; Jonathan G. Dudley; Jeff P. Hollenbeck

    2013-01-01

    To conserve habitat for disturbance specialist species, ecologists must identify where individuals will likely settle in newly disturbed areas. Habitat suitability models can predict which sites at new disturbances will most likely attract specialists. Without validation data from newly disturbed areas, however, the best approach for maximizing predictive accuracy can...

  1. Periodontitis-associated septic pulmonary embolism caused by Actinomyces species identified by anaerobic culture of bronchoalveolar lavage fluid: a case report.

    Science.gov (United States)

    Endo, Shun; Mishima, Eikan; Takeuchi, Yoichi; Ohi, Takashi; Ishida, Masatsugu; Yanai, Masaru; Kiyomoto, Hideyasu; Nagasawa, Tasuku; Ito, Sadayoshi

    2015-12-01

    Periodontal disease is a less common but important cause of septic pulmonary embolism (SPE). However, the pathogens causing periodontal disease-associated SPE (PD-SPE) have been poorly understood. Actinomyces species are resident microbiota in the oral cavity. Here we report a case of PD-SPE caused by Actinomyces species, which was identified by anaerobic culture of bronchoalveolar lavage fluid (BAL). A 64-year-old Asian man, complicated with severe chronic periodontitis, was admitted with chest pain and fever. Chest CT revealed multiple bilateral pulmonary nodules located subpleurally. We diagnosed the case as SPE associated with periodontitis. Although blood cultures were negative for the usual 5-day incubation, anaerobic culture of the BAL fluid sample yielded Actinomyces species. Antibacterial therapy alone did not ameliorate the symptoms; however, additional dental treatment, including tooth extraction, promptly did. The patient was discharged 23 days after admission. The 3-month follow-up revealed no recurrence of the symptoms and complete resolution of the lung lesions. This case demonstrated that Actinomyces species can cause PD-SPE. Additionally, clinicians should consider performing appropriate anaerobic culture of BAL fluid to identify the pathogen of SPE, and to ordering dental treatment, if necessary, in addition to antibiotics for the initial management of PD-SPE.

  2. A comprehensive DNA barcode database for Central European beetles with a focus on Germany: adding more than 3500 identified species to BOLD.

    Science.gov (United States)

    Hendrich, Lars; Morinière, Jérôme; Haszprunar, Gerhard; Hebert, Paul D N; Hausmann, Axel; Köhler, Frank; Balke, Michael

    2015-07-01

    Beetles are the most diverse group of animals and are crucial for ecosystem functioning. In many countries, they are well established for environmental impact assessment, but even in the well-studied Central European fauna, species identification can be very difficult. A comprehensive and taxonomically well-curated DNA barcode library could remedy this deficit and could also link hundreds of years of traditional knowledge with next generation sequencing technology. However, such a beetle library is missing to date. This study provides the globally largest DNA barcode reference library for Coleoptera for 15 948 individuals belonging to 3514 well-identified species (53% of the German fauna) with representatives from 97 of 103 families (94%). This study is the first comprehensive regional test of the efficiency of DNA barcoding for beetles with a focus on Germany. Sequences ≥500 bp were recovered from 63% of the specimens analysed (15 948 of 25 294) with short sequences from another 997 specimens. Whereas most specimens (92.2%) could be unambiguously assigned to a single known species by sequence diversity at CO1, 1089 specimens (6.8%) were assigned to more than one Barcode Index Number (BIN), creating 395 BINs which need further study to ascertain if they represent cryptic species, mitochondrial introgression, or simply regional variation in widespread species. We found 409 specimens (2.6%) that shared a BIN assignment with another species, most involving a pair of closely allied species as 43 BINs were involved. Most of these taxa were separated by barcodes although sequence divergences were low. Only 155 specimens (0.97%) show identical or overlapping clusters. © 2014 John Wiley & Sons Ltd.

  3. Cross-Genome Comparisons of Newly Identified Domains in Mycoplasma gallisepticum and Domain Architectures with Other Mycoplasma species

    Directory of Open Access Journals (Sweden)

    Chandra Sekhar Reddy Chilamakuri

    2011-01-01

    Full Text Available Accurate functional annotation of protein sequences is hampered by important factors such as the failure of sequence search methods to identify relationships and the inherent diversity in function of proteins related at low sequence similarities. Earlier, we had employed intermediate sequence search approach to establish new domain relationships in the unassigned regions of gene products at the whole genome level by taking Mycoplasma gallisepticum as a specific example and established new domain relationships. In this paper, we report a detailed comparison of the conservation status of the domain and domain architectures of the gene products that bear our newly predicted domains amongst 14 other Mycoplasma genomes and reported the probable implications for the organisms. Some of the domain associations, observed in Mycoplasma that afflict humans and other non-human primates, are involved in regulation of solute transport and DNA binding suggesting specific modes of host-pathogen interactions.

  4. ApicoAP: the first computational model for identifying apicoplast-targeted proteins in multiple species of Apicomplexa.

    Directory of Open Access Journals (Sweden)

    Gokcen Cilingir

    Full Text Available Most of the parasites of the phylum Apicomplexa contain a relict prokaryotic-derived plastid called the apicoplast. This organelle is important not only for the survival of the parasite, but its unique properties make it an ideal drug target. The majority of apicoplast-associated proteins are nuclear encoded and targeted post-translationally to the organellar lumen via a bipartite signaling mechanism that requires an N-terminal signal and transit peptide (TP. Attempts to define a consensus motif that universally identifies apicoplast TPs have failed.In this study, we propose a generalized rule-based classification model to identify apicoplast-targeted proteins (ApicoTPs that use a bipartite signaling mechanism. Given a training set specific to an organism, this model, called ApicoAP, incorporates a procedure based on a genetic algorithm to tailor a discriminating rule that exploits the known characteristics of ApicoTPs. Performance of ApicoAP is evaluated for four labeled datasets of Plasmodium falciparum, Plasmodium yoelii, Babesia bovis, and Toxoplasma gondii proteins. ApicoAP improves the classification accuracy of the published dataset for P. falciparum to 94%, originally 90% using PlasmoAP.We present a parametric model for ApicoTPs and a procedure to optimize the model parameters for a given training set. A major asset of this model is that it is customizable to different parasite genomes. The ApicoAP prediction software is available at http://code.google.com/p/apicoap/ and http://bcb.eecs.wsu.edu.

  5. Evaluation of 5.8S rRNA to identify Penaeus semisulcatus and its subspecies, Penaeus semisulcatus persicus (Penaeidae and some Decapoda species

    Directory of Open Access Journals (Sweden)

    Zahra Noroozi

    2015-10-01

    Full Text Available The green tiger prawn, Penaeus semisulcatus is one of the most important members of the family Penaeidae in the Persian Gulf. Based on the morphological characteristics, two groups, including P. semisulcatus and its subspecies viz. P. s. persicus are recognized. This study was conducted to investigate the genetic distance between P. semisulcatus and P. s. persicus by analyzing partial sequence of 5.8S rRNA. Another objective of this study is to evaluate the ability of 5.8S rRNA to identify the species of Decapoda. The results indicated that the 5.8S rRNA gene of both P. semisulcatus and P. s. persicus were exactly identical, and sequence variation was not observed. The results also indicated that 5.8S rRNA sequences between species of the same genus of analysed species of Decapoda are conserved, and no genetic distance was observed in species level. The low evolutionary rate and efficient conservation of the 5.8S rRNA can be attributed to its role in the translation process.

  6. Identifying the Achilles heel of multi-host pathogens: the concept of keystone ‘host’ species illustrated by Mycobacterium ulcerans transmission

    International Nuclear Information System (INIS)

    Roche, Benjamin; Eric Benbow, M; Merritt, Richard; Kimbirauskas, Ryan; McIntosh, Mollie; Small, Pamela L C; Williamson, Heather; Guégan, Jean-François

    2013-01-01

    Pathogens that use multiple host species are an increasing public health issue due to their complex transmission, which makes them difficult to mitigate. Here, we explore the possibility of using networks of ecological interactions among potential host species to identify the particular disease-source species to target to break down transmission of such pathogens. We fit a mathematical model on prevalence data of Mycobacterium ulcerans in western Africa and we show that removing the most abundant taxa for this category of pathogen is not an optimal strategy to decrease the transmission of the mycobacterium within aquatic ecosystems. On the contrary, we reveal that the removal of some taxa, especially Oligochaeta worms, can clearly reduce rates of pathogen transmission, and these should be considered as keystone organisms for its transmission because they lead to a substantial reduction in pathogen prevalence regardless of the network topology. Besides their potential application for the understanding of M. ulcerans ecology, we discuss how networks of species interactions can modulate transmission of multi-host pathogens. (letter)

  7. Characterization of Staphylococcus spp. strains in milk from buffaloes with mastitis in Brazil: the need to identify to species level to avoid misidentification

    Directory of Open Access Journals (Sweden)

    V. Coimbra-e-Souza

    Full Text Available ABSTRACT Mastitis is an inflammation of the mammary gland that affects dairy cattle worldwide causing economic losses. Coagulase-negative staphylococci (CNS are the predominant cause of this type of infection. We have recently showed that coagulase-positive staphylococci could be misidentified. So, the aim of this study was to characterize the Staphylococcus spp. strains initially classified as coagulase-negative Staphylococci, isolated from buffalo with subclinical mastitis. Milk of buffaloes with mastitis in herds was collected and 9 strains were identified as CNS by phenotypic tests. Molecular methodologies latter identified the strains as coagulase-negative Staphylococcus chromogenes (5, coagulase-positive Staphylococcus hyicus (2 and coagulase-positive Staphylococcus aureus (2. Our results strongly support the need to identify the isolates to a species level in order to avoid misidentification and to be aware of the classification using the coagulase test alone.

  8. EcoIP: An Open Source Image Analysis Toolkit to Identify Different Stages of Plant Phenology for Multiple Species with Pan-Tilt-Zoom Cameras

    DEFF Research Database (Denmark)

    Granados, Joel; Bonnet, Philippe

    2013-01-01

    Because of the increased number of cameras employed in environmental sensing and the tremendous image output they produce, we have created a flexible, open-source software solution called EcoIP to help automatically determine different phenophases for different species from digital image sequences....... Onset and ending dates are calculated through an iterative process: (1) training images are chosen and areas of interest identified, (2) separation of foreground and background is accomplished based on a naive Bayesian method, (3) a signal is created based on the separation model and (4) it is then fit...... to a sigmoid that contains the dates of interest. Results using different phenological events of different species indicate that estimated dates fall within a few days of the observed dates for most cases. Our experiments indicate that color separability and scene illumination are contributing factors...

  9. Linking the Salt Transcriptome with Physiological Responses of a Salt-Resistant Populus Species as a Strategy to Identify Genes Important for Stress Acclimation1[W][OA

    Science.gov (United States)

    Brinker, Monika; Brosché, Mikael; Vinocur, Basia; Abo-Ogiala, Atef; Fayyaz, Payam; Janz, Dennis; Ottow, Eric A.; Cullmann, Andreas D.; Saborowski, Joachim; Kangasjärvi, Jaakko; Altman, Arie; Polle, Andrea

    2010-01-01

    To investigate early salt acclimation mechanisms in a salt-tolerant poplar species (Populus euphratica), the kinetics of molecular, metabolic, and physiological changes during a 24-h salt exposure were measured. Three distinct phases of salt stress were identified by analyses of the osmotic pressure and the shoot water potential: dehydration, salt accumulation, and osmotic restoration associated with ionic stress. The duration and intensity of these phases differed between leaves and roots. Transcriptome analysis using P. euphratica-specific microarrays revealed clusters of coexpressed genes in these phases, with only 3% overlapping salt-responsive genes in leaves and roots. Acclimation of cellular metabolism to high salt concentrations involved remodeling of amino acid and protein biosynthesis and increased expression of molecular chaperones (dehydrins, osmotin). Leaves suffered initially from dehydration, which resulted in changes in transcript levels of mitochondrial and photosynthetic genes, indicating adjustment of energy metabolism. Initially, decreases in stress-related genes were found, whereas increases occurred only when leaves had restored the osmotic balance by salt accumulation. Comparative in silico analysis of the poplar stress regulon with Arabidopsis (Arabidopsis thaliana) orthologs was used as a strategy to reduce the number of candidate genes for functional analysis. Analysis of Arabidopsis knockout lines identified a lipocalin-like gene (AtTIL) and a gene encoding a protein with previously unknown functions (AtSIS) to play roles in salt tolerance. In conclusion, by dissecting the stress transcriptome of tolerant species, novel genes important for salt endurance can be identified. PMID:20959419

  10. Linking the salt transcriptome with physiological responses of a salt-resistant Populus species as a strategy to identify genes important for stress acclimation.

    Science.gov (United States)

    Brinker, Monika; Brosché, Mikael; Vinocur, Basia; Abo-Ogiala, Atef; Fayyaz, Payam; Janz, Dennis; Ottow, Eric A; Cullmann, Andreas D; Saborowski, Joachim; Kangasjärvi, Jaakko; Altman, Arie; Polle, Andrea

    2010-12-01

    To investigate early salt acclimation mechanisms in a salt-tolerant poplar species (Populus euphratica), the kinetics of molecular, metabolic, and physiological changes during a 24-h salt exposure were measured. Three distinct phases of salt stress were identified by analyses of the osmotic pressure and the shoot water potential: dehydration, salt accumulation, and osmotic restoration associated with ionic stress. The duration and intensity of these phases differed between leaves and roots. Transcriptome analysis using P. euphratica-specific microarrays revealed clusters of coexpressed genes in these phases, with only 3% overlapping salt-responsive genes in leaves and roots. Acclimation of cellular metabolism to high salt concentrations involved remodeling of amino acid and protein biosynthesis and increased expression of molecular chaperones (dehydrins, osmotin). Leaves suffered initially from dehydration, which resulted in changes in transcript levels of mitochondrial and photosynthetic genes, indicating adjustment of energy metabolism. Initially, decreases in stress-related genes were found, whereas increases occurred only when leaves had restored the osmotic balance by salt accumulation. Comparative in silico analysis of the poplar stress regulon with Arabidopsis (Arabidopsis thaliana) orthologs was used as a strategy to reduce the number of candidate genes for functional analysis. Analysis of Arabidopsis knockout lines identified a lipocalin-like gene (AtTIL) and a gene encoding a protein with previously unknown functions (AtSIS) to play roles in salt tolerance. In conclusion, by dissecting the stress transcriptome of tolerant species, novel genes important for salt endurance can be identified.

  11. Blind to morphology: Genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)

    KAUST Repository

    Pinzón, Jorge H C

    2013-04-05

    Aim: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. Location: Indo-Pacific, Red Sea, Arabian/Persian Gulf. Methods: Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus. Results: Between five and eight genetically distinct lineages comparable to species were identified with minimal or no hybridization between them. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (about seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder. Main conclusions: The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the

  12. Blind to morphology: Genetics identifies several widespread ecologically common species and few endemics among Indo-Pacific cauliflower corals (Pocillopora, Scleractinia)

    KAUST Repository

    Pinzó n, Jorge H C; Sampayo, Eugenia M.; Cox, Evelyn F.; Chauka, Leonard J.; Chen, Chaolun Allen; Voolstra, Christian R.; LaJeunesse, Todd C.

    2013-01-01

    Aim: Using high-resolution genetic markers on samples gathered from across their wide distributional range, we endeavoured to delimit species diversity in reef-building Pocillopora corals. They are common, ecologically important, and widespread throughout the Indo-Pacific, but their phenotypic plasticity in response to environmental conditions and their nearly featureless microskeletal structures confound taxonomic assignments and limit an understanding of their ecology and evolution. Location: Indo-Pacific, Red Sea, Arabian/Persian Gulf. Methods: Sequence analysis of nuclear ribosomal (internal transcribed spacer 2, ITS2) and mitochondrial (open reading frame) loci were combined with population genetic data (seven microsatellite loci) for Pocillopora samples collected throughout the Indo-Pacific, Red Sea and Arabian Gulf, in order to assess the evolutionary divergence, reproductive isolation, frequency of hybridization and geographical distributions of the genus. Results: Between five and eight genetically distinct lineages comparable to species were identified with minimal or no hybridization between them. Colony morphology was generally incongruent with genetics across the full range of sampling, and the total number of species is apparently consistent with lower estimates from competing morphologically based hypotheses (about seven or eight taxa). The most commonly occurring genetic lineages were widely distributed and exhibited high dispersal and gene flow, factors that have probably minimized allopatric speciation. Uniquely among scleractinian genera, this genus contains a monophyletic group of broadcast spawners that evolved recently from an ancestral brooder. Main conclusions: The delineation of species diversity guided by genetics fundamentally advances our understanding of Pocillopora geographical distributions, ecology and evolution. Because traditional diagnostic features of colony and branch morphology are proving to be of limited utility, the

  13. HOW DO WE IDENTIFY MICRONYCTERIS (SCHIZONYCETRIS SANBORNI SIMMONS, 1996 (CHIROPTERA, PHYLLOSTOMIDAE RELIABLY AND WHERE WE CAN FIND THIS SPECIES IN BRAZIL?

    Directory of Open Access Journals (Sweden)

    ANDERSON FEIJÓ

    2015-01-01

    Full Text Available Micronycteris is divided into four subgenera, Micronycteris, Leuconycteris, Xenoctenes, and Schizonycteris. The latter includes Micronycteris (Schizonycteris minuta, Micronycteris (S. schmidtorum, Micronycteris (S. sanborni and Micronycteris (S. yatesi. Little is known of the biology of M. (S. sanborni, which is widely distributed in the dry forests of South America, but is known from only few sites. The scarcity of records of M. sanborni appears to be at least partly related to the difficulty of differentiating this species from the other members of the subgenus Schizonycteris. The present study identifies the key traits that distinguish this species from other Schizonycteris, reviews the geographic distribution of the species, and presents some notes on breeding patterns. Six new localities are presented for M. sanborni, and are analyzed together with those available in the literature, providing new insights into ecological and zoogeographic patterns. A number of the diagnostic features established by Simmons (1996 in the description of M. sanborni proved to have little taxonomic value, especially for the differentiation of M. minuta and M. yatesi, which it closely resembles. The primary external difference is the pure white color of the ventral pelage and the proportion of the white base (2/3-4/5 of the dorsal hair in M. sanborni, in contrast with dirty white or pale gray and a much shorter white base of the dorsal hair in the other species. A number of cranial traits are also important. The distributional data now indicate that M. sanborni occurs mainly in mesic and open areas, including disturbed habitats, in the Caatinga scrublands and the Cerrado savannas of northeastern Brazil, especially in areas with rocky outcrops. Micronycteris sanborni appears to be monoestrous, with births coinciding with the rainy season.

  14. Faecal corticosterone metabolite concentrations are not a good predictor of habitat suitability for common gartersnakes.

    Science.gov (United States)

    Halliday, William D; Gilmour, Kathleen M; Blouin-Demers, Gabriel

    2015-01-01

    Measuring habitat suitability is important in conservation and in wildlife management. Measuring the abundance or presence-absence of a species in various habitats is not sufficient to measure habitat suitability because these metrics can be poor predictors of population success. Therefore, having some measure of population success is essential in assessing habitat suitability, but estimating population success is difficult. Identifying suitable proxies for population success could thus be beneficial. We examined whether faecal corticosterone metabolite (fCM) concentrations could be used as a proxy for habitat suitability in common gartersnakes (Thamnophis sirtalis). We conducted a validation study and confirmed that fCM concentrations indeed reflect circulating corticosterone concentrations. We estimated abundance, reproductive output and growth rate of gartersnakes in field and in forest habitat and we also measured fCM concentrations of gartersnakes from these same habitats. Common gartersnakes were more abundant and had higher reproductive outputs and higher growth rates in field habitat than in forest habitat, but fCM concentrations did not differ between the same two habitats. Our results suggest either that fCM concentrations are not a useful metric of habitat suitability in common gartersnakes or that the difference in suitability between the two habitats was too small to induce changes in fCM concentrations. Incorporating fitness metrics in estimates of habitat suitability is important, but these metrics of fitness have to be sensitive enough to vary between habitats.

  15. Mapping anuran habitat suitability to estimate effects of grassland and wetland conservation programs

    Science.gov (United States)

    Mushet, David M.; Euliss, Ned H.; Stockwell, Craig A.

    2012-01-01

    The conversion of the Northern Great Plains of North America to a landscape favoring agricultural commodity production has negatively impacted wildlife habitats. To offset impacts, conservation programs have been implemented by the U.S. Department of Agriculture and other agencies to restore grassland and wetland habitat components. To evaluate effects of these efforts on anuran habitats, we used call survey data and environmental data in ecological niche factor analyses implemented through the program Biomapper to quantify habitat suitability for five anuran species within a 196 km2 study area. Our amphibian call surveys identified Northern Leopard Frogs (Lithobates pipiens), Wood Frogs (Lithobates sylvaticus), Boreal Chorus Frogs (Pseudacris maculata), Great Plains Toads (Anaxyrus cognatus), and Woodhouse’s Toads (Anaxyrus woodhousii) occurring within the study area. Habitat suitability maps developed for each species revealed differing patterns of suitable habitat among species. The most significant findings of our mapping effort were 1) the influence of deep-water overwintering wetlands on suitable habitat for all species encountered except the Boreal Chorus Frog; 2) the lack of overlap between areas of core habitat for both the Northern Leopard Frog and Wood Frog compared to the core habitat for both toad species; and 3) the importance of conservation programs in providing grassland components of Northern Leopard Frog and Wood Frog habitat. The differences in habitats suitable for the five species we studied in the Northern Great Plains, i.e., their ecological niches, highlight the importance of utilizing an ecosystem based approach that considers the varying needs of multiple species in the development of amphibian conservation and management plans.

  16. BLAST screening of chlamydial genomes to identify signature proteins that are unique for the Chlamydiales, Chlamydiaceae, Chlamydophila and Chlamydia groups of species

    Directory of Open Access Journals (Sweden)

    Gupta Radhey S

    2006-01-01

    Full Text Available Abstract Background Chlamydiae species are of much importance from a clinical viewpoint. Their diversity both in terms of their numbers as well as clinical involvement are presently believed to be significantly underestimated. The obligate intracellular nature of chlamydiae has also limited their genetic and biochemical studies. Thus, it is of importance to develop additional means for their identification and characterization. Results We have carried out analyses of available chlamydiae genomes to identify sets of unique proteins that are either specific for all Chlamydiales genomes, or different Chlamydiaceae family members, or members of the Chlamydia and Chlamydophila genera, or those unique to Protochlamydia amoebophila, but which are not found in any other bacteria. In total, 59 Chlamydiales-specific proteins, 79 Chlamydiaceae-specific proteins, 20 proteins each that are specific for both Chlamydia and Chlamydophila and 445 ORFs that are Protochlamydia-specific were identified. Additionally, 33 cases of possible gene loss or lateral gene transfer were also detected. Conclusion The identified chlamydiae-lineage specific proteins, many of which are highly conserved, provide novel biomarkers that should prove of much value in the diagnosis of these bacteria and in exploration of their prevalence and diversity. These conserved protein sequences (CPSs also provide novel therapeutic targets for drugs that are specific for these bacteria. Lastly, functional studies on these chlamydiae or chlamydiae subgroup-specific proteins should lead to important insights into lineage-specific adaptations with regards to development, infectivity and pathogenicity.

  17. High throughput phenotypic selection of Mycobacterium tuberculosis mutants with impaired resistance to reactive oxygen species identifies genes important for intracellular growth.

    Directory of Open Access Journals (Sweden)

    Olga Mestre

    Full Text Available Mycobacterium tuberculosis has the remarkable capacity to survive within the hostile environment of the macrophage, and to resist potent antibacterial molecules such as reactive oxygen species (ROS. Thus, understanding mycobacterial resistance mechanisms against ROS may contribute to the development of new anti-tuberculosis therapies. Here we identified genes involved in such mechanisms by screening a high-density transposon mutant library, and we show that several of them are involved in the intracellular lifestyle of the pathogen. Many of these genes were found to play a part in cell envelope functions, further strengthening the important role of the mycobacterial cell envelope in protection against aggressions such as the ones caused by ROS inside host cells.

  18. Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach

    DEFF Research Database (Denmark)

    Bothwell, H.; Bisbing, S.; Therkildsen, Nina Overgaard

    2013-01-01

    It is generally accepted that most plant populations are locally adapted. Yet, understanding how environmental forces give rise to adaptive genetic variation is a challenge in conservation genetics and crucial to the preservation of species under rapidly changing climatic conditions. Environmental...... loci, we compared outlier locus detection methods with a recently-developed landscape genetic approach. We analyzed 157 loci from samples of the alpine herb Gentiana nivalis collected across the European Alps. Principle coordinates of neighbor matrices (PCNM), eigenvectors that quantify multi...... variables identified eight more potentially adaptive loci than models run without spatial variables. 3) When compared to outlier detection methods, the landscape genetic approach detected four of the same loci plus 11 additional loci. 4) Temperature, precipitation, and solar radiation were the three major...

  19. Fungal Peritonitis Due to Fusarium solani Species Complex Sequential Isolates Identified with DNA Sequencing in a Kidney Transplant Recipient in Brazil.

    Science.gov (United States)

    da Silva-Rocha, Walicyranison Plinio; Zuza-Alves, Diana Luzia; Melo, Analy Salles de Azevedo; Chaves, Guilherme Maranhão

    2015-12-01

    Fungal peritonitis is a rare serious complication most commonly observed in immunocompromised patients under peritoneal dialysis. Nevertheless, this clinical condition is more difficult to treat than bacterial peritonitis. Bacterial peritonitis followed by the use of antibiotics is the main risk factor for developing fungal peritonitis. Candida spp. are more frequently isolated, and the isolation of filamentous fungi is only occasional. Here we describe a case of Fusarium solani species complex peritonitis associated with bacterial peritonitis in a female kidney transplant recipient with previous history of nephrotic syndrome. The patient has had Enterobacter sp. endocarditis and was hypertensive and diabetic. Two sequential isolates of F. solani were recovered from cultures and identified with different molecular techniques. She was successfully treated with 50 mg daily amphotericin B for 4 weeks.

  20. Characteristics and suitability of waste dump sites in Owerri, Nigeria ...

    African Journals Online (AJOL)

    A five point criteria screening of the three major waste dumpsites in Owerri Municipality was identified, and a ranking procedure adopted to determine the suitability or otherwise of the dumpsites. The sites were screened and ranked hydro-geologically and geo-technically in order of suitable, moderately suitable, and not ...

  1. Global habitat suitability for framework-forming cold-water corals.

    Directory of Open Access Journals (Sweden)

    Andrew J Davies

    Full Text Available Predictive habitat models are increasingly being used by conservationists, researchers and governmental bodies to identify vulnerable ecosystems and species' distributions in areas that have not been sampled. However, in the deep sea, several limitations have restricted the widespread utilisation of this approach. These range from issues with the accuracy of species presences, the lack of reliable absence data and the limited spatial resolution of environmental factors known or thought to control deep-sea species' distributions. To address these problems, global habitat suitability models have been generated for five species of framework-forming scleractinian corals by taking the best available data and using a novel approach to generate high resolution maps of seafloor conditions. High-resolution global bathymetry was used to resample gridded data from sources such as World Ocean Atlas to produce continuous 30-arc second (∼1 km(2 global grids for environmental, chemical and physical data of the world's oceans. The increased area and resolution of the environmental variables resulted in a greater number of coral presence records being incorporated into habitat models and higher accuracy of model predictions. The most important factors in determining cold-water coral habitat suitability were depth, temperature, aragonite saturation state and salinity. Model outputs indicated the majority of suitable coral habitat is likely to occur on the continental shelves and slopes of the Atlantic, South Pacific and Indian Oceans. The North Pacific has very little suitable scleractinian coral habitat. Numerous small scale features (i.e., seamounts, which have not been sampled or identified as having a high probability of supporting cold-water coral habitat were identified in all ocean basins. Field validation of newly identified areas is needed to determine the accuracy of model results, assess the utility of modelling efforts to identify vulnerable marine

  2. Web page classification on child suitability

    NARCIS (Netherlands)

    C. Eickhoff (Carsten); P. Serdyukov; A.P. de Vries (Arjen)

    2010-01-01

    htmlabstractChildren spend significant amounts of time on the Internet. Recent studies showed, that during these periods they are often not under adult supervision. This work presents an automatic approach to identifying suitable web pages for children based on topical and non-topical web page

  3. LC-QTOF-MS identification of porcine-specific peptide in heat treated pork identifies candidate markers for meat species determination.

    Science.gov (United States)

    Sarah, S A; Faradalila, W N; Salwani, M S; Amin, I; Karsani, S A; Sazili, A Q

    2016-05-15

    The purpose of this study was to identify porcine-specific peptide markers from thermally processed meat that could differentiate pork from beef, chevon and chicken meat. In the initial stage, markers from tryptic digested protein of chilled, boiled and autoclaved pork were identified using LC-QTOF-MS. An MRM method was then established for verification. A thorough investigation of LC-QTOF-MS data showed that only seven porcine-specific peptides were consistently detected. Among these peptides, two were derived from lactate dehydrogenase, one from creatine kinase, and four from serum albumin protein. However, MRM could only detect four peptides (EVTEFAK, LVVITAGAR, FVIER and TVLGNFAAFVQK) that were consistently present in pork samples. In conclusion, meat species determination through a tandem mass spectrometry platform shows high potential in providing scientifically valid and reliable results even at peptide level. Besides, the specificity and selectivity offered by the proteomics approach also provide a robust platform for Halal authentication. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Developing and testing a landscape habitat suitability model for fisher (Martes pennanti) in forests of interior northern California

    Science.gov (United States)

    W.J. Zielinski; J. R. Dunk; J. S. Yaeger; D. W. LaPlante

    2010-01-01

    The fisher is warranted for protection under the Endangered Species Act in the western United States and, as such, it is especially important that conservation and management actions are based on sound scientific information. We developed a landscape-scale suitability model for interior northern California to predict the probability of detecting fishers and to identify...

  5. Rock suitability classification RSC 2012

    Energy Technology Data Exchange (ETDEWEB)

    McEwen, T. (ed.) [McEwen Consulting, Leicester (United Kingdom); Kapyaho, A. [Geological Survey of Finland, Espoo (Finland); Hella, P. [Saanio and Riekkola, Helsinki (Finland); Aro, S.; Kosunen, P.; Mattila, J.; Pere, T.

    2012-12-15

    This report presents Posiva's Rock Suitability Classification (RSC) system, developed for locating suitable rock volumes for repository design and construction. The RSC system comprises both the revised rock suitability criteria and the procedure for the suitability classification during the construction of the repository. The aim of the classification is to avoid such features of the host rock that may be detrimental to the favourable conditions within the repository, either initially or in the long term. This report also discusses the implications of applying the RSC system for the fulfilment of the regulatory requirements concerning the host rock as a natural barrier and the site's overall suitability for hosting a final repository of spent nuclear fuel.

  6. Rock suitability classification RSC 2012

    International Nuclear Information System (INIS)

    McEwen, T.; Kapyaho, A.; Hella, P.; Aro, S.; Kosunen, P.; Mattila, J.; Pere, T.

    2012-12-01

    This report presents Posiva's Rock Suitability Classification (RSC) system, developed for locating suitable rock volumes for repository design and construction. The RSC system comprises both the revised rock suitability criteria and the procedure for the suitability classification during the construction of the repository. The aim of the classification is to avoid such features of the host rock that may be detrimental to the favourable conditions within the repository, either initially or in the long term. This report also discusses the implications of applying the RSC system for the fulfilment of the regulatory requirements concerning the host rock as a natural barrier and the site's overall suitability for hosting a final repository of spent nuclear fuel

  7. Quantitative validation of a habitat suitability index for oyster restoration

    Directory of Open Access Journals (Sweden)

    Seth eTheuerkauf

    2016-05-01

    Full Text Available Habitat suitability index (HSI models provide spatially explicit information on the capacity of a given habitat to support a species of interest, and their prevalence has increased dramatically in recent years. Despite caution that the reliability of HSIs must be validated using independent, quantitative data, most HSIs intended to inform terrestrial and marine species management remain unvalidated. Furthermore, of the eight HSI models developed for eastern oyster (Crassostrea virginica restoration and fishery production, none has been validated. Consequently, we developed, calibrated, and validated an HSI for the eastern oyster to identify optimal habitat for restoration in a tributary of Chesapeake Bay, the Great Wicomico River (GWR. The GWR harbors a high density, restored oyster population, and therefore serves as an excellent model system for assessing the validity of the HSI. The HSI was derived from GIS layers of bottom type, salinity, and water depth (surrogate for dissolved oxygen, and was tested using live adult oyster density data from a survey of high vertical relief reefs (HRR and low vertical relief reefs (LRR in the sanctuary network. Live adult oyster density was a statistically-significant sigmoid function of the HSI, which validates the HSI as a robust predictor of suitable oyster reef habitat for rehabilitation or restoration. In addition, HRR had on average 103-116 more adults m^−2 than LRR at a given level of the HSI. For HRR, HSI values ≥0.3 exceeded the accepted restoration target of 50 live adult oysters m^−2. For LRR, the HSI was generally able to predict live adult oyster densities that meet or exceed the target at HSI values ≥0.3. The HSI indicated that there remain large areas of suitable habitat for restoration in the GWR. This study provides a robust framework for HSI model development and validation, which can be refined and applied to other systems and previously developed HSIs to improve the efficacy of

  8. Elk habitat suitability map for North Carolina

    Science.gov (United States)

    Williams, Steven G.; Cobb, David T.; Collazo, Jaime A.

    2015-01-01

    Although eastern elk (Cervus elaphus canadensis) were extirpated from the eastern United States in the 19th century, they were successfully reintroduced in the North Carolina portion of the Great Smoky Mountains National Park in the early 2000s. The North Carolina Wildlife Resources Commission (NCWRC) is evaluating the prospect of reintroducing the species in other locations in the state to augment recreational opportunities. As a first step in the process, we created a state-wide elk habitat suitability map. We used medium-scale data sets and a two-component approach to iden- tify areas of high biological value for elk and exclude from consideration areas where elk-human conflicts were more likely. Habitats in the state were categorized as 66% unsuitable, 16.7% low, 17% medium, and <1% high suitability for elk. The coastal plain and Piedmont contained the most suitable habitat, but prospective reintroduction sites were largely excluded from consideration due to extensive agricultural activities and pervasiveness of secondary roads. We ranked 31 areas (≥ 500 km2) based on their suitability for reintroduction. The central region of the state contained the top five ranked areas. The Blue Ridge Mountains, where the extant population of elk occurs, was ranked 21st. Our work provides a benchmark for decision makers to evaluate potential consequences and trade-offs associated with the selection of prospective elk reintroduction sites.

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Natasha A Hamilton

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

  11. Habitat suitability and movement corridors of grey wolf (Canis lupus) in Northern Pakistan

    Science.gov (United States)

    Kabir, Muhammad; Hameed, Shoaib; Ali, Hussain; Bosso, Luciano; Din, Jaffar Ud; Bischof, Richard; Redpath, Steve

    2017-01-01

    Habitat suitability models are useful to understand species distribution and to guide management and conservation strategies. The grey wolf (Canis lupus) has been extirpated from most of its historic range in Pakistan primarily due to its impact on livestock and livelihoods. We used non-invasive survey data from camera traps and genetic sampling to develop a habitat suitability model for C. lupus in northern Pakistan and to explore the extent of connectivity among populations. We detected suitable habitat of grey wolf using a maximum entropy approach (Maxent ver. 3.4.0) and identified suitable movement corridors using the Circuitscape 4.0 tool. Our model showed high levels of predictive performances, as seen from the values of area under curve (0.971±0.002) and true skill statistics (0.886±0.021). The main predictors for habitat suitability for C. lupus were distances to road, mean temperature of the wettest quarter and distance to river. The model predicted ca. 23,129 km2 of suitable areas for wolf in Pakistan, with much of suitable habitat in remote and inaccessible areas that appeared to be well connected through vulnerable movement corridors. These movement corridors suggest that potentially the wolf range can expand in Pakistan’s Northern Areas. However, managing protected areas with stringent restrictions is challenging in northern Pakistan, in part due to heavy dependence of people on natural resources. The habitat suitability map provided by this study can inform future management strategies by helping authorities to identify key conservation areas. PMID:29121089

  12. Agroforestry suitability analysis based upon nutrient availability mapping: a GIS based suitability mapping

    Directory of Open Access Journals (Sweden)

    Firoz Ahmad

    2017-05-01

    Full Text Available Agroforestry has drawn the attention of researchers due to its capacity to reduce the poverty and land degradation, improve food security and mitigate the climate change. However, the progress in promoting agroforestry is held back due to the lack of reliable data sets and appropriate tools to accurately map and to have an adequate decision making system for agroforestry modules. Agroforestry suitability being one special form of land suitability is very pertinent to study in the current times when there is tremendous pressure on the land as it is a limited commodity. The study aims for applying the geo-spatial tools towards visualizing various soil and environmental data to reveal the trends and interrelationships and to achieve a nutrient availability and agroforestry suitability map. Using weight matrix and ranks, individual maps were developed in ArcGIS 10.1 platform to generate nutrient availability map, which was later used to develop agroforestry suitability map. Watersheds were delineated using DEM in some part of the study area and were evaluated for prioritizing it and agroforestry suitability of the watersheds were also done as per the schematic flowchart. Agroforestry suitability regions were delineated based upon the weight and ranks by integrated mapping. The total open area was identified 42.4% out of which 21.6% area was found to have high suitability towards agroforestry. Within the watersheds, 22 village points were generated for creating buffers, which were further evaluated showing its proximity to high suitable agroforestry sites thus generating tremendous opportunity to the villagers to carry out agroforestry projects locally. This research shows the capability of remote sensing in studying agroforestry practices and in estimating the prominent factors for its optimal productivity. The ongoing agroforestry projects can be potentially diverted in the areas of high suitability as an extension. The use of ancillary data in GIS

  13. DNA from the past informs ex situ conservation for the future: an "extinct" species of Galápagos tortoise identified in captivity.

    Directory of Open Access Journals (Sweden)

    Michael A Russello

    2010-01-01

    Full Text Available Although not unusual to find captive relicts of species lost in the wild, rarely are presumed extinct species rediscovered outside of their native range. A recent study detected living descendents of an extinct Galápagos tortoise species (Chelonoidis elephantopus once endemic to Floreana Island on the neighboring island of Isabela. This finding adds to the growing cryptic diversity detected among these species in the wild. There also exists a large number of Galápagos tortoises in captivity of ambiguous origin. The recently accumulated population-level haplotypic and genotypic data now available for C. elephantopus add a critical reference population to the existing database of 11 extant species for investigating the origin of captive individuals of unknown ancestry.We reanalyzed mitochondrial DNA control region haplotypes and microsatellite genotypes of 156 captive individuals using an expanded reference database that included all extant Galápagos tortoise species as well as the extinct species from Floreana. Nine individuals (six females and three males exhibited strong signatures of Floreana ancestry and a high probability of assignment to C. elephantopus as detected by Bayesian assignment and clustering analyses of empirical and simulated data. One male with high assignment probability to C. elephantopus based on microsatellite genotypic data also possessed a "Floreana-like" mitochondrial DNA haplotype.Historical DNA analysis of museum specimens has provided critical spatial and temporal components to ecological, evolutionary, taxonomic and conservation-related research, but rarely has it informed ex situ species recovery efforts. Here, the availability of population-level genotypic data from the extinct C. elephantopus enabled the identification of nine Galápagos tortoise individuals of substantial conservation value that were previously misassigned to extant species of varying conservation status. As all captive individuals of C

  14. Identifying the best season for mapping evergreen swamp and mangrove species using leaf-level spectra in an estuarine system in KwaZulu-Natal, South Africa

    CSIR Research Space (South Africa)

    Van Deventer, Heidi

    2014-10-01

    Full Text Available would provide the best discrimination of six evergreen tree species, associated with swamp (Ficus Trichopoda), mangrove (Avicennia marina, Bruguiera gymnorrhiza, Hibiscus tiliaceus), wetlands in adjacent woodlands (Syzygium cordatum) and coastal...

  15. Morphology, songs and genetics identify two new cicada species from Morocco: Tettigettalna afroamissa sp. nov. and Berberigetta dimelodica gen. nov. & sp. nov. (Hemiptera: Cicadettini).

    Science.gov (United States)

    Costa, Gonçalo João; Nunes, Vera L; Marabuto, Eduardo; Mendes, Raquel; Laurentino, Telma G; Quartau, José Alberto; Paulo, Octávio S; Simões, Paula Cristina

    2017-03-01

    Morocco has been the subject of very few expeditions on the last century with the objective of studying small cicadas. In the summer of 2014 an expedition was carried out to Morocco to update our knowledge with acoustic recordings and genetic data of these poorly known species. We describe here two new small-sized cicadas that could not be directly assigned to any species of North African cicadas: Tettigettalna afroamissa sp. nov. and Berberigetta dimelodica gen. nov. & sp. nov. In respect to T. afroamissa it is the first species of the genus to be found outside Europe and we frame this taxon within the evolutionary history of the genus. Acoustic analysis of this species allows us to confidently separate T. afroamissa from its congeners. With B. dimelodica, a small species showing a remarkable calling song characterized by an abrupt frequency modulation, a new genus had to be erected. Bayesian inference and maximum likelihood phylogenetic analyses with DNA-barcode sequences of Cytochrome C Oxidase 1 support the monophyly of both species, their distinctness and revealed genetic structure within B. dimelodica. Alongside the descriptions we also provide GPS coordinates of collection points, distributions and habitat preferences.

  16. Evaluation of Land Suitability for Selected Tree Species in the ...

    African Journals Online (AJOL)

    Kassa T

    The study watershed is located at Korir village, in Tigray (Fig 1). The total size ..... contributed to 78% of the local market economy for firewood, 100% each for construction poles and .... Socio-economics and Policy Research Working Paper 54.

  17. Evaluation of Land Suitability for Selected Tree Species in the ...

    African Journals Online (AJOL)

    Kassa T

    The major limiting factors were the steep slope and shallow soil depth in major part of the area. ... appropriately selected, arranged and managed are through land quality measurement. (Venema and Vargas, 2007; ... area of the catchment into eleven land units, set of pixels characterized by the same value for the diagnostic ...

  18. Comparing habitat suitability and connectivity modeling methods for conserving pronghorn migrations.

    Directory of Open Access Journals (Sweden)

    Erin E Poor

    Full Text Available Terrestrial long-distance migrations are declining globally: in North America, nearly 75% have been lost. Yet there has been limited research comparing habitat suitability and connectivity models to identify migration corridors across increasingly fragmented landscapes. Here we use pronghorn (Antilocapra americana migrations in prairie habitat to compare two types of models that identify habitat suitability: maximum entropy (Maxent and expert-based (Analytic Hierarchy Process. We used distance to wells, distance to water, NDVI, land cover, distance to roads, terrain shape and fence presence to parameterize the models. We then used the output of these models as cost surfaces to compare two common connectivity models, least-cost modeling (LCM and circuit theory. Using pronghorn movement data from spring and fall migrations, we identified potential migration corridors by combining each habitat suitability model with each connectivity model. The best performing model combination was Maxent with LCM corridors across both seasons. Maxent out-performed expert-based habitat suitability models for both spring and fall migrations. However, expert-based corridors can perform relatively well and are a cost-effective alternative if species location data are unavailable. Corridors created using LCM out-performed circuit theory, as measured by the number of pronghorn GPS locations present within the corridors. We suggest the use of a tiered approach using different corridor widths for prioritizing conservation and mitigation actions, such as fence removal or conservation easements.

  19. Comparing habitat suitability and connectivity modeling methods for conserving pronghorn migrations.

    Science.gov (United States)

    Poor, Erin E; Loucks, Colby; Jakes, Andrew; Urban, Dean L

    2012-01-01

    Terrestrial long-distance migrations are declining globally: in North America, nearly 75% have been lost. Yet there has been limited research comparing habitat suitability and connectivity models to identify migration corridors across increasingly fragmented landscapes. Here we use pronghorn (Antilocapra americana) migrations in prairie habitat to compare two types of models that identify habitat suitability: maximum entropy (Maxent) and expert-based (Analytic Hierarchy Process). We used distance to wells, distance to water, NDVI, land cover, distance to roads, terrain shape and fence presence to parameterize the models. We then used the output of these models as cost surfaces to compare two common connectivity models, least-cost modeling (LCM) and circuit theory. Using pronghorn movement data from spring and fall migrations, we identified potential migration corridors by combining each habitat suitability model with each connectivity model. The best performing model combination was Maxent with LCM corridors across both seasons. Maxent out-performed expert-based habitat suitability models for both spring and fall migrations. However, expert-based corridors can perform relatively well and are a cost-effective alternative if species location data are unavailable. Corridors created using LCM out-performed circuit theory, as measured by the number of pronghorn GPS locations present within the corridors. We suggest the use of a tiered approach using different corridor widths for prioritizing conservation and mitigation actions, such as fence removal or conservation easements.

  20. Initiation of simian virus 40 DNA replication in vitro: Pulse-chase experiments identify the first labeled species as topologically unwound

    International Nuclear Information System (INIS)

    Bullock, P.A.; Seo, Yeon Soo; Hurwitz, J.

    1989-01-01

    A distinct unwound form of DNA containing the simian virus 40 (SV40) origin is produced in replication reactions carried out in mixtures containing crude fractions prepared from HeLa cells. This species, termed form U R , comigrates on chloroquine-containing agarose gels with the upper part of the previously described heterogeneous highly unwound circular DNA, form U. As with form U, formation of form U R is dependent upon the SV40 tumor (T) antigen. Pulse-chase experiments demonstrate that the first species to incorporate labeled deoxyribonucleotides comigrates with form U R . Restriction analyses of the products of the pulse-chase experiments show that initiation occurs at the SV40 origin and then proceeds outward in a bidirectional manner. These experiments establish form U R as the earliest detectable substrate for SV40 DNA replication and suggest that SV40 DNA replication initiates on an unwound species

  1. The Spatial Suitable Habitat Model of Acacia decurrens in Mount Merbabu National Park

    Directory of Open Access Journals (Sweden)

    Yoko Untoro

    2017-09-01

    Full Text Available Green wattle (Acacia decurrens is an invasive alien species (IAS found in the Mount Merbabu National Park (TNGMb. This study aim to obtain spatially studies on habitat suitability models of A. decurrens in TNGMb region. In fact, this species became as a high invasive and dominance in the TNGMb and contributes the negative impact to the ecosystem. In addition, the result of this study should be useful for controling activities of A. decurrens. Predictor variables in this research were (altitude, slope, rainfall, air temperature, distance from river, NDVI, NDMI, distance from hiking trail, and distance from burnt area. The survey was conducted with random sampling of presence or absence of A. decurrens by marking the coordinate point of location using GPS. Data analysis in this research was used binary logistic regression enter method. Binary logistic regression involves the data acquisition of the presence and absence of A. decurrens as the y variable, while the predictor variable map as the variable x. The type of spatial distribution of A. decurrens in the TNGMb was identified as clumped. The Nagelkerke R2 values obtained in the model was 39,2%, while 60,8% was explained by other variables were not used in the model. The results of the logistic regression model showed a high percentage of suitability of 64,29%, a medium suitability of 28,57%, and a low suitability of 7.14% then the Implications for controlling activities of A. decurrens in TNGMb could be prioritized in high suitability habitat. Keywords: Acacia decurrens, green wattle, invasive, spatial suitable habitat 

  2. Linking functional traits and species preferences to species’ abundance and occupancy trends through time to identify habitat changes in coastal ecosystems

    DEFF Research Database (Denmark)

    Pakeman, Robin J.; Hewison, Richard; Lewis, Robert John

    2017-01-01

    . In general, there has been a shift towards taller species with more exploitative growth forms and an increase in indicators of unfavourable habitat condition according to criteria for assessing sites designated for nature protection as part of the EU Natura 2000 network, particularly tall grasses...

  3. Alternative polymerase chain reaction method to identify Plasmodium species in human blood samples: the semi-nested multiplex malaria PCR (SnM-PCR)

    NARCIS (Netherlands)

    Rubio, J.M.; Post, R.J.; Docters van Leeuwen, W.M.; Henry, M.C.; Lindergard, G.; Hommel, M.

    2002-01-01

    A simplified protocol for the identification of Plasmodium species by semi-nested multiplex polymerase chain reaction (SnM-PCR) in human blood samples is compared with microscopical examination of thin and thick blood films in 2 field trials in Côte d'Ivoire and Cameroon. Also, dried blood spots or

  4. What does it take to resolve relationships and to identify species with molecular markers? An example from the epiphytic Rhipsalideae (Cactaceae).

    Science.gov (United States)

    Korotkova, Nadja; Borsch, Thomas; Quandt, Dietmar; Taylor, Nigel P; Müller, Kai F; Barthlott, Wilhelm

    2011-09-01

    The Cactaceae are a major New World plant family and popular in horticulture. Still, taxonomic units and species limits have been difficult to define, and molecular phylogenetic studies so far have yielded largely unresolved trees, so relationships within Cactaceae remain insufficiently understood. This study focuses on the predominantly epiphytic tribe Rhipsalideae and evaluates the utility of a spectrum of plastid genomic regions. • We present a phylogenetic study including 52 of the 53 Rhipsalideae species and all the infraspecific taxa. Seven regions (trnK intron, matK, rbcL, rps3-rpl16, rpl16 intron, psbA-trnH, trnQ-rps16), ca. 5600 nucleotides (nt) were sequenced per sample. The regions used were evaluated for their phylogenetic performance and performance in DNA-based species recognition based on operational taxonomic units (OTUs) defined beforehand. • The Rhipsalideae are monophyletic and contain five clades that correspond to the genera Rhipsalis, Lepismium, Schlumbergera, Hatiora, and Rhipsalidopsis. The species-level tree was well resolved and supported; the rpl16 and trnK introns yielded the best phylogenetic signal. Although the psbA-trnH and trnQ-rps16 spacers were the most successful individual regions for OTU identification, their success rate did not significantly exceed 70%. The highest OTU identification rate of 97% was found using the combination of psbA-trnH, rps3-rpl16, trnK intron, and trnQ-rps16 as a minimum possible marker length (ca. 1660 nt). • The phylogenetic performance of a marker is not determined by the level of sequence variability, and species discrimination power does not necessarily correlate with phylogenetic utility.

  5. Preliminary geological suitability assessment for LILW disposal

    International Nuclear Information System (INIS)

    Tomse, P.; Mele, I.

    2001-01-01

    outcome of this stage a number of potentially suitable areas is expected. The final confirmation of site suitability will be gained by detailed field investigations during the site characterisation and site confirmation stages. The progress of this phase of site selection process will strongly depend on the response of local communities where potentially suitable areas will be identified, and on the successfulness and efficiency of the mediator conducting the negotiations with local communities. According to the most optimistic scenario the final site will be selected and confirmed by the period 2004 -2005.(author)

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

    Science.gov (United States)

    Lance Craighead; Baden Cross

    2007-01-01

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

  7. Assessment of Climate Suitability of Maize in South Korea

    Science.gov (United States)

    Hyun, S.; Choi, D.; Seo, B.

    2017-12-01

    Assessing suitable areas for crops would be useful to design alternate cropping systems as an adaptation option to climate change adaptation. Although suitable areas could be identified by using a crop growth model, it would require a number of input parameters including cultivar and soil. Instead, a simple climate suitability model, e.g., EcoCrop model, could be used for an assessment of climate suitability for a major grain crop. The objective of this study was to assess of climate suitability for maize using the EcoCrop model under climate change conditions in Korea. A long term climate data from 2000 - 2100 were compiled from weather data source. The EcoCrop model implemented in R was used to determine climate suitability index at each grid cell. Overall, the EcoCrop model tended to identify suitable areas for maize production near the coastal areas whereas the actual major production areas located in inland areas. It is likely that the discrepancy between assessed and actual crop production areas would result from the socioeconomic aspects of maize production. Because the price of maize is considerably low, maize has been grown in an area where moisture and temperature conditions would be less than optimum. In part, a simple algorithm to predict climate suitability for maize would caused a relatively large error in climate suitability assessment under the present climate conditions. In 2050s, the climate suitability for maize increased in a large areas in southern and western part of Korea. In particular, the plain areas near the coastal region had considerably greater suitability index in the future compared with mountainous areas. The expansion of suitable areas for maize would help crop production policy making such as the allocation of rice production area for other crops due to considerably less demand for the rice in Korea.

  8. [(≡SiO)TaV (=CH2)Cl2], the first tantalum methylidene species prepared and identified on the silica surface

    KAUST Repository

    Chen, Yin

    2013-11-01

    A novel surface tantalum methylidene [(≡SiO)TaV (=CH 2)Cl2] was obtained via thermal decomposition of the well-defined surface species [(≡SiO)TaVCl2Me 2]. This first surface tantalum methylidene ever synthesized has been fully characterized and the kinetics of the a-hydrogen abstraction reaction has also been investigated in the heterogeneous system. © 2013 Elsevier B.V. All rights reserved.

  9. [(≡SiO)TaV (=CH2)Cl2], the first tantalum methylidene species prepared and identified on the silica surface

    KAUST Repository

    Chen, Yin; Callens, Emmanuel; Abou-Hamad, Edy; Basset, Jean-Marie

    2013-01-01

    A novel surface tantalum methylidene [(≡SiO)TaV (=CH 2)Cl2] was obtained via thermal decomposition of the well-defined surface species [(≡SiO)TaVCl2Me 2]. This first surface tantalum methylidene ever synthesized has been fully characterized and the kinetics of the a-hydrogen abstraction reaction has also been investigated in the heterogeneous system. © 2013 Elsevier B.V. All rights reserved.

  10. Predicting patch occupancy in fragmented landscapes at the rangewide scale for an endangered species: an example of an American warbler

    KAUST Repository

    Collier, Bret A.; Groce, Julie E.; Morrison, Michael L.; Newnam, John C.; Campomizzi, Andrew J.; Farrell, Shannon L.; Mathewson, Heather A.; Snelgrove, Robert T.; Carroll, Raymond J.; Wilkins, Robert N.

    2011-01-01

    -makers in identifying suitable habitat across the species breeding range on which conservation or mitigation activities can be focused and thus prioritize management and conservation planning. LOCATION: Texas, USA. METHODS: We used repeated double-observer detection

  11. Sediment Dwelling Benthos as Indicator Species for Pollution Monitoring of Mamala Bay, Oahu, Hawaii, 1993-1994 (NODC Accession 9900121)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — A multifaceted study of the sediment dwelling benthos was conducted in Mamala Bay to identify suitable species as indicators of sewage enrichment. There are five...

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

    Directory of Open Access Journals (Sweden)

    Hanlie E K Winterbach

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

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

    Science.gov (United States)

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

    2014-01-01

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

  14. Integrative research identifies 71 new plant species records in the state of Rio Grande do Norte (Brazil) and enhances a small herbarium collection during a funding shortage.

    Science.gov (United States)

    Versieux, Leonardo M; Dávila, Nállarett; Delgado, Geadelande C; de Sousa, Valdeci F; de Moura, Edweslley Otaviano; Filgueiras, Tarciso; Alves, Marccus V; Carvalho, Eric; Piotto, Daniel; Forzza, Rafaela C; Calvente, Alice; Jardim, Jomar G

    2017-01-01

    A National Forest Inventory (NFI) encompassing the entire territory of Brazil is in progress. It is coordinated and promoted by the Brazilian Forest Service of the Ministry of Environment. In each state, the NFI collaborates with local herbaria by receiving collected plant material and performing species identification. Consultants are hired by the NFI and work at the local herbaria under the supervision of a curator. In exchange for curatorial assistance, the NFI provides equipment and consumables for the herbarium. Other public projects collaborating with NFI are Reflora and the Brazilian Biodiversity Information System (SiBBr). Both projects have online platforms that seek to connect herbaria and make all their data freely available, including high quality digital images of specimens. Through inter-institutional collaboration, the joint interests of NFI, Reflora, SiBBr and local herbaria have improved collections, expanded the online Reflora database, and provided the NFI with verified species lists. These strategic uses of public funding are positively affecting Botany, particularly during a period of economic crisis and cuts in research. Here, we illustrate the increase in floristic knowledge through the improvement of a herbarium collection in Rio Grande do Norte (RN) - the Brazilian state with the lowest levels of plant richness. We report 71 new occurrences of vascular plants for RN, belonging mainly to the Poaceae, Fabaceae and Malvaceae. Most of the species with new occurrences have a Neotropical distribution (21 spp.) and only seven are restricted to the Brazilian Northeast. Our findings highlight previous gaps in RN's floristic knowledge. The partnership NFI, Reflora, SiBBr and the UFRN herbarium improved herbarium curation, digital collection, and quality of data. Finally, a fellowship provided by Reflora and SiBBr allowed improving curation by distributing duplicates and incorporating the Herbarium of Câmara Cascudo Museum.

  15. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

    Directory of Open Access Journals (Sweden)

    O'Gara Fergal

    2010-11-01

    Full Text Available Abstract Background Catabolite repression control (CRC is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas

  16. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria.

    Science.gov (United States)

    Browne, Patrick; Barret, Matthieu; O'Gara, Fergal; Morrissey, John P

    2010-11-25

    Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate nutritional status cues with the regulation

  17. Molecular analysis of the genus Asparagus based on matK sequences and its application to identify A. racemosus, a medicinally phytoestrogenic species.

    Science.gov (United States)

    Boonsom, Teerawat; Waranuch, Neti; Ingkaninan, Kornkanok; Denduangboripant, Jessada; Sukrong, Suchada

    2012-07-01

    The plant Asparagus racemosus is one of the most widely used sources of phytoestrogens because of its high content of the steroidal saponins, shatavarins I-IV, in roots. The dry root of A. racemosus, known as "Rak-Sam-Sip" in Thai, is one of the most popular herbal medicines, used as an anti-inflammatory, an aphrodisiac and a galactagogue. Recently, the interest in plant-derived estrogens has increased tremendously, making A. racemosus particularly important and a possible target for fraudulent labeling. However, the identification of A. racemosus is generally difficult due to its similar morphology to other Asparagus spp. Thus, accurate authentication of A. racemosus is essential. In this study, 1557-bp nucleotide sequences of the maturase K (matK) gene of eight Asparagus taxa were analyzed. A phylogenetic relationship based on the matK gene was also constructed. Ten polymorphic sites of nucleotide substitutions were found within the matK sequences. A. racemosus showed different nucleotide substitutions to the other species. A polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of the matK gene was developed to discriminate A. racemosus from others. Only the 650-bp PCR product from A. racemosus could be digested with BssKI into two fragments of 397 and 253-bp while the products of other species remained undigested. Ten commercially crude drugs were analyzed and revealed that eight samples were derived from A. racemosus while two samples of that were not. Thus, the PCR-RFLP analysis of matK gene was shown to be an effective method for authentication of the medicinally phytoestrogenic species, A. racemosus. Copyright © 2012 Elsevier B.V. All rights reserved.

  18. Phylogenetic analysis and protein structure modelling identifies distinct Ca(2+)/Cation antiporters and conservation of gene family structure within Arabidopsis and rice species.

    Science.gov (United States)

    Pittman, Jon K; Hirschi, Kendal D

    2016-12-01

    The Ca(2+)/Cation Antiporter (CaCA) superfamily is an ancient and widespread family of ion-coupled cation transporters found in nearly all kingdoms of life. In animals, K(+)-dependent and K(+)-indendent Na(+)/Ca(2+) exchangers (NCKX and NCX) are important CaCA members. Recently it was proposed that all rice and Arabidopsis CaCA proteins should be classified as NCX proteins. Here we performed phylogenetic analysis of CaCA genes and protein structure homology modelling to further characterise members of this transporter superfamily. Phylogenetic analysis of rice and Arabidopsis CaCAs in comparison with selected CaCA members from non-plant species demonstrated that these genes form clearly distinct families, with the H(+)/Cation exchanger (CAX) and cation/Ca(2+) exchanger (CCX) families dominant in higher plants but the NCKX and NCX families absent. NCX-related Mg(2+)/H(+) exchanger (MHX) and CAX-related Na(+)/Ca(2+) exchanger-like (NCL) proteins are instead present. Analysis of genomes of ten closely-related rice species and four Arabidopsis-related species found that CaCA gene family structures are highly conserved within related plants, apart from minor variation. Protein structures were modelled for OsCAX1a and OsMHX1. Despite exhibiting broad structural conservation, there are clear structural differences observed between the different CaCA types. Members of the CaCA superfamily form clearly distinct families with different phylogenetic, structural and functional characteristics, and therefore should not be simply classified as NCX proteins, which should remain as a separate gene family.

  19. Computational prediction of the Crc regulon identifies genus-wide and species-specific targets of catabolite repression control in Pseudomonas bacteria

    LENUS (Irish Health Repository)

    Browne, Patrick

    2010-11-25

    Abstract Background Catabolite repression control (CRC) is an important global control system in Pseudomonas that fine tunes metabolism in order optimise growth and metabolism in a range of different environments. The mechanism of CRC in Pseudomonas spp. centres on the binding of a protein, Crc, to an A-rich motif on the 5\\' end of an mRNA resulting in translational down-regulation of target genes. Despite the identification of several Crc targets in Pseudomonas spp. the Crc regulon has remained largely unexplored. Results In order to predict direct targets of Crc, we used a bioinformatics approach based on detection of A-rich motifs near the initiation of translation of all protein-encoding genes in twelve fully sequenced Pseudomonas genomes. As expected, our data predict that genes related to the utilisation of less preferred nutrients, such as some carbohydrates, nitrogen sources and aromatic carbon compounds are targets of Crc. A general trend in this analysis is that the regulation of transporters is conserved across species whereas regulation of specific enzymatic steps or transcriptional activators are often conserved only within a species. Interestingly, some nucleoid associated proteins (NAPs) such as HU and IHF are predicted to be regulated by Crc. This finding indicates a possible role of Crc in indirect control over a subset of genes that depend on the DNA bending properties of NAPs for expression or repression. Finally, some virulence traits such as alginate and rhamnolipid production also appear to be regulated by Crc, which links nutritional status cues with the regulation of virulence traits. Conclusions Catabolite repression control regulates a broad spectrum of genes in Pseudomonas. Some targets are genus-wide and are typically related to central metabolism, whereas other targets are species-specific, or even unique to particular strains. Further study of these novel targets will enhance our understanding of how Pseudomonas bacteria integrate

  20. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability.

    Science.gov (United States)

    Joardar, Vinita; Abrams, Natalie F; Hostetler, Jessica; Paukstelis, Paul J; Pakala, Suchitra; Pakala, Suman B; Zafar, Nikhat; Abolude, Olukemi O; Payne, Gary; Andrianopoulos, Alex; Denning, David W; Nierman, William C

    2012-12-12

    The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25-36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population

  1. Suitable footwear for enhanced safety

    CERN Document Server

    2004-01-01

    Safety shoes are the theme of a new safety campaign. Always remember that accidents can happen - even to your feet! When entering hazardous areas such as underground halls, work sites, experiment assembly sites, workshops etc., sandals, ordinary shoes or similar light footwear should not be worn. Whatever the risks to which you may be exposed, always think safety and wear suitable footwear, i.e. safety shoes, which have non-slip soles and steel reinforcements to protect your feet from being crushed, fractured or pierced. Is it serious, Doctor? "Some traumas resulting from foot-related accidents - open fractures for instance - can be quite serious," explains CERN Works Doctor Véronique Fassnacht. "But the most common injuries are sprained ankles sustained during simple falls caused by differences in floor-levels (e.g. false floors). Fractures, bruising, surface wounds or deep wounds caused by objects falling onto the top of the foot are also quite common." ...

  2. Habitat Suitability Index Models: Yellow-headed blackbird

    Science.gov (United States)

    Schroeder, Richard L.

    1982-01-01

    Habitat preferences of the yellow-headed blackbird (Xanthocephalus xanthocephalus) are described in this publication. It is one of a series of Habitat Suitability Index (HSI) models and was developed through an analysis of available infomration on the species-habitat requirements of the species. Habitat use information is presented in a review of the literature, followed by the development of an HSI model, designed for use in impact assessment and habitat management activities.

  3. Comparative Genomics of H. pylori and Non-Pylori Helicobacter Species to Identify New Regions Associated with Its Pathogenicity and Adaptability

    Directory of Open Access Journals (Sweden)

    De-Min Cao

    2016-01-01

    Full Text Available The genus Helicobacter is a group of Gram-negative, helical-shaped pathogens consisting of at least 36 bacterial species. Helicobacter pylori (H. pylori, infecting more than 50% of the human population, is considered as the major cause of gastritis, peptic ulcer, and gastric cancer. However, the genetic underpinnings of H. pylori that are responsible for its large scale epidemic and gastrointestinal environment adaption within human beings remain unclear. Core-pan genome analysis was performed among 75 representative H. pylori and 24 non-pylori Helicobacter genomes. There were 1173 conserved protein families of H. pylori and 673 of all 99 Helicobacter genus strains. We found 79 genome unique regions, a total of 202,359bp, shared by at least 80% of the H. pylori but lacked in non-pylori Helicobacter species. The operons, genes, and sRNAs within the H. pylori unique regions were considered as potential ones associated with its pathogenicity and adaptability, and the relativity among them has been partially confirmed by functional annotation analysis. However, functions of at least 54 genes and 10 sRNAs were still unclear. Our analysis of protein-protein interaction showed that 30 genes within them may have the cooperation relationship.

  4. Matrix-assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a Reliable Tool to Identify Species of Catalase-negative Gram-positive Cocci not Belonging to the Streptococcus Genus.

    Science.gov (United States)

    Almuzara, Marisa; Barberis, Claudia; Velázquez, Viviana Rojas; Ramirez, Maria Soledad; Famiglietti, Angela; Vay, Carlos

    2016-01-01

    To evaluate the performance of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) by using 190 Catalase-negative Gram-Positive Cocci (GPC) clinical isolates. All isolates were identified by conventional phenotypic tests following the proposed scheme by Ruoff and Christensen and MALDI-TOF MS (Bruker Daltonics, BD, Bremen, Germany). Two different extraction methods (direct transfer formic acid method on spot and ethanol formic acid extraction method) and different cut-offs for genus/specie level identification were used. The score cut-offs recommended by the manufacturer (≥ 2.000 for species-level, 1.700 to 1.999 for genus level and genus level, ≥ 1.700 for species-level and score genus or species. MALDI-TOF MS identification was considered correct when the result obtained from MS database agreed with the phenotypic identification result. When both methods gave discordant results, the 16S rDNA or sodA genes sequencing was considered as the gold standard identification method. The results obtained by MS concordant with genes sequencing, although discordant with conventional phenotyping, were considered correct. MS results discordant with 16S or sod A identification were considered incorrect. Using the score cut-offs recommended by the manufacturer, 97.37% and 81.05% were correctly identified to genus and species level, respectively. On the other hand, using lower cut-off scores for identification, 97.89% and 94.21% isolates were correctly identified to genus and species level respectively by MALDI-TOF MS and no significant differences between the results obtained with two extraction methods were obtained. The results obtained suggest that MALDI-TOF MS has the potential of being an accurate tool for Catalase-negative GPC identification even for those species with difficult diagnosis as Helcococcus , Abiotrophia , Granulicatella , among others. Nevertheless, expansion of the library, especially including more strains with

  5. Leaf morphology in Cowpea [Vigna unguiculata (L.) Walp]: QTL analysis, physical mapping and identifying a candidate gene using synteny with model legume species.

    Science.gov (United States)

    Pottorff, Marti; Ehlers, Jeffrey D; Fatokun, Christian; Roberts, Philip A; Close, Timothy J

    2012-06-12

    Cowpea [Vigna unguiculata (L.) Walp] exhibits a considerable variation in leaf shape. Although cowpea is mostly utilized as a dry grain and animal fodder crop, cowpea leaves are also used as a high-protein pot herb in many countries of Africa. Leaf morphology was studied in the cowpea RIL population, Sanzi (sub-globose leaf shape) x Vita 7 (hastate leaf shape). A QTL for leaf shape, Hls (hastate leaf shape), was identified on the Sanzi x Vita 7 genetic map spanning from 56.54 cM to 67.54 cM distance on linkage group 15. SNP marker 1_0910 was the most significant over the two experiments, accounting for 74.7% phenotypic variance (LOD 33.82) in a greenhouse experiment and 71.5% phenotypic variance (LOD 30.89) in a field experiment. The corresponding Hls locus was positioned on the cowpea consensus genetic map on linkage group 4, spanning from 25.57 to 35.96 cM. A marker-trait association of the Hls region identified SNP marker 1_0349 alleles co-segregating with either the hastate or sub-globose leaf phenotype. High co-linearity was observed for the syntenic Hls region in Medicago truncatula and Glycine max. One syntenic locus for Hls was identified on Medicago chromosome 7 while syntenic regions for Hls were identified on two soybean chromosomes, 3 and 19. In all three syntenic loci, an ortholog for the EZA1/SWINGER (AT4G02020.1) gene was observed and is the candidate gene for the Hls locus. The Hls locus was identified on the cowpea physical map via SNP markers 1_0910, 1_1013 and 1_0992 which were identified in three BAC contigs; contig926, contig821 and contig25. This study has demonstrated how integrated genomic resources can be utilized for a candidate gene approach. Identification of genes which control leaf morphology may be utilized to improve the quality of cowpea leaves for vegetable and or forage markets as well as contribute to more fundamental research understanding the control of leaf shape in legumes.

  6. Land suitability assessment on a watershed of Loess Plateau using the analytic hierarchy process.

    Directory of Open Access Journals (Sweden)

    Xiaobo Yi

    Full Text Available In order to reduce soil erosion and desertification, the Sloping Land Conversion Program has been conducted in China for more than 15 years, and large areas of farmland have been converted to forest and grassland. However, this large-scale vegetation-restoration project has faced some key problems (e.g. soil drying that have limited the successful development of the current ecological-recovery policy. Therefore, it is necessary to know about the land use, vegetation, and soil, and their inter-relationships in order to identify the suitability of vegetation restoration. This study was conducted at the watershed level in the ecologically vulnerable region of the Loess Plateau, to evaluate the land suitability using the analytic hierarchy process (AHP. The results showed that (1 the area unsuitable for crops accounted for 73.3% of the watershed, and the main factors restricting cropland development were soil physical properties and soil nutrients; (2 the area suitable for grassland was about 86.7% of the watershed, with the remaining 13.3% being unsuitable; (3 an area of 3.95 km(2, accounting for 66.7% of the watershed, was unsuitable for forest. Overall, the grassland was found to be the most suitable land-use to support the aims of the Sloping Land Conversion Program in the Liudaogou watershed. Under the constraints of soil water shortage and nutrient deficits, crops and forests were considered to be inappropriate land uses in the study area, especially on sloping land. When selecting species for re-vegetation, non-native grass species with high water requirements should be avoided so as to guarantee the sustainable development of grassland and effective ecological functioning. Our study provides local land managers and farmers with valuable information about the inappropriateness of growing trees in the study area along with some information on species selection for planting in the semi-arid area of the Loess Plateau.

  7. Land suitability assessment on a watershed of Loess Plateau using the analytic hierarchy process.

    Science.gov (United States)

    Yi, Xiaobo; Wang, Li

    2013-01-01

    In order to reduce soil erosion and desertification, the Sloping Land Conversion Program has been conducted in China for more than 15 years, and large areas of farmland have been converted to forest and grassland. However, this large-scale vegetation-restoration project has faced some key problems (e.g. soil drying) that have limited the successful development of the current ecological-recovery policy. Therefore, it is necessary to know about the land use, vegetation, and soil, and their inter-relationships in order to identify the suitability of vegetation restoration. This study was conducted at the watershed level in the ecologically vulnerable region of the Loess Plateau, to evaluate the land suitability using the analytic hierarchy process (AHP). The results showed that (1) the area unsuitable for crops accounted for 73.3% of the watershed, and the main factors restricting cropland development were soil physical properties and soil nutrients; (2) the area suitable for grassland was about 86.7% of the watershed, with the remaining 13.3% being unsuitable; (3) an area of 3.95 km(2), accounting for 66.7% of the watershed, was unsuitable for forest. Overall, the grassland was found to be the most suitable land-use to support the aims of the Sloping Land Conversion Program in the Liudaogou watershed. Under the constraints of soil water shortage and nutrient deficits, crops and forests were considered to be inappropriate land uses in the study area, especially on sloping land. When selecting species for re-vegetation, non-native grass species with high water requirements should be avoided so as to guarantee the sustainable development of grassland and effective ecological functioning. Our study provides local land managers and farmers with valuable information about the inappropriateness of growing trees in the study area along with some information on species selection for planting in the semi-arid area of the Loess Plateau.

  8. Evaluation of didactic suitability indicators from curricular orientations

    Directory of Open Access Journals (Sweden)

    Pedro Arteaga

    2012-12-01

    Full Text Available Assessment of didactic suitability of mathematics teaching and learning processes requires suitable instruments to guide and support it. This paper presents a methodology for progressive improvement of such instruments to evaluate the suitability of mathematical instruction processes based on the analysis of curricular orientations. Analysis units are classifi ed according to the facets and components proposed by the Didactic Suitability Theory to identify norms and suitability indicators,which are compared with the system proposed by this theory, in order to point out agreements and complementarities. This methodology is exemplified through its application to the principles and standards of the National Council of Teachers of Mathematics (NCTM in the statistics content area at the level K-8.

  9. Digital data for Quick Response (QR) codes of thermophiles to identify and compare the bacterial species isolated from Unkeshwar hot springs (India)

    Science.gov (United States)

    Rekadwad, Bhagwan N.; Khobragade, Chandrahasya N.

    2015-01-01

    16S rRNA sequences of morphologically and biochemically identified 21 thermophilic bacteria isolated from Unkeshwar hot springs (19°85′N and 78°25′E), Dist. Nanded (India) has been deposited in NCBI repository. The 16S rRNA gene sequences were used to generate QR codes for sequences (FASTA format and full Gene Bank information). Diversity among the isolates is compared with known isolates and evaluated using CGR, FCGR and PCA i.e. visual comparison and evaluation respectively. Considerable biodiversity was observed among the identified bacteria isolated from Unkeshwar hot springs. The hyperlinked QR codes, CGR, FCGR and PCA of all the isolates are made available to the users on a portal https://sites.google.com/site/bhagwanrekadwad/. PMID:26793757

  10. Flavonols and ellagic acid derivatives in peels of different species of jabuticaba (Plinia spp.) identified by HPLC-DAD-ESI/MSn.

    Science.gov (United States)

    Neves, Nathália de Andrade; Stringheta, Paulo César; Gómez-Alonso, Sergio; Hermosín-Gutiérrez, Isidro

    2018-06-30

    Extracts of jabuticaba peels show complex chromatographic profiles at 360 nm, with some peaks presenting UV-Vis spectra resembling those of flavonol glycosides and others resembling that of ellagic acid. The presence and tentative identification of these phenolic compounds were comprehensively studied in four species of Brazilian jabuticaba fruit - Plinia trunciflora, variety 'jabuticaba de cabinho'; P. caulifora, varieties 'jabuticaba paulista' and 'jabuticaba canaã-açu'; P. jaboticaba, variety 'jabuticaba sabará'; and P. phitrantha, variety 'jabuticaba branca-vinho' - using HPLC-DAD-ESI-MS n . Seventeen flavonols derived from quercetin and three from myricetin and eighteen derivatives of ellagic acid and eleven of methyl ellagic acid were detected. Most of them were newly described and mainly occurred in glycosylated and acylglycosylated forms. Some compounds were missing in one variety, such as the absence of methyl ellagic acid derivatives in 'jabuticaba branca-vinho', and others only appeared in one variety, thus suggesting potential capacity for varietal differentiation. Copyright © 2018 Elsevier Ltd. All rights reserved.

  11. Chemical fingerprinting identifies Echium vulgare, Eupatorium cannabinum and Senecio spp. as plant species mainly responsible for pyrrolizidine alkaloids in bee-collected pollen.

    Science.gov (United States)

    Kast, Christina; Kilchenmann, Verena; Reinhard, Hans; Droz, Benoit; Lucchetti, Matteo Angelo; Dübecke, Arne; Beckh, Gudrun; Zoller, Otmar

    2018-02-01

    Various studies have shown that bee-collected pollen sold as nutritional supplements may contain toxic pyrrolizidine alkaloids (PAs) and, thus, pose a potential health risk for consumers. The level of contamination may vary according to its geographical and botanical origin. Here, the PA content of pollen produced in Switzerland was studied and 32 commercially available bee-collected pollen supplements produced between 2010 and 2014 were analysed. In addition, at what time period bees collect PA-containing pollen was investigated. Hence, this study looked into the occurrence of PAs in pollen samples collected daily during two-to-three consecutive seasons. Furthermore, the PA spectrum in pollen was compared to the spectrum found in flower heads of PA-plants to unambiguously identify plants responsible for PA contamination of pollen. The PA concentration of commercial and daily collected pollen was determined by target analysis using an HPLC-MS/MS system, allowing the detection of 18 different PAs and PA N-oxides found in the genera Echium, Eupatorium and Senecio, while the comparison of the PA spectrum in pollen and flower heads was performed by LC-HR-MS, allowing the detection of all PA types in a sample, including saturated, non-carcinogenic PAs. Of the commercially available pollen, 31% contained PAs with a mean concentration of 319 ng/g, mainly Echium- and Eupatorium-type PAs, while the PA concentrations were below the limit of quantitation (LOQ) in 69% of the pollen samples. Bees collected pollen containing Echium-type PAs mainly in June and July, while they gathered pollen containing Eupatorium-type PAs from mid-July to August. Senecio-type PAs appeared from June to September. Comparison of the PA array in pollen and plants identified E. vulgare and E. cannabinum as the main plants responsible for PA contamination of Swiss bee-collected pollen, and to a lesser extent also identified plants belonging to the genus Senecio.

  12. Shifting suitability for malaria vectors across Africa with warming climates

    Directory of Open Access Journals (Sweden)

    Peterson A Townsend

    2009-05-01

    Full Text Available Abstract Background Climates are changing rapidly, producing warm climate conditions globally not previously observed in modern history. Malaria is of great concern as a cause of human mortality and morbidity, particularly across Africa, thanks in large part to the presence there of a particularly competent suite of mosquito vector species. Methods I derive spatially explicit estimates of human populations living in regions newly suitable climatically for populations of two key Anopheles gambiae vector complex species in Africa over the coming 50 years, based on ecological niche model projections over two global climate models, two scenarios of climate change, and detailed spatial summaries of human population distributions. Results For both species, under all scenarios, given the changing spatial distribution of appropriate conditions and the current population distribution, the models predict a reduction of 11.3–30.2% in the percentage of the overall population living in areas climatically suitable for these vector species in coming decades, but reductions and increases are focused in different regions: malaria vector suitability is likely to decrease in West Africa, but increase in eastern and southern Africa. Conclusion Climate change effects on African malaria vectors shift their distributional potential from west to east and south, which has implications for overall numbers of people exposed to these vector species. Although the total is reduced, malaria is likely to pose novel public health problems in areas where it has not previously been common.

  13. Ecological suitability modeling for anthrax in the Kruger National Park, South Africa.

    Directory of Open Access Journals (Sweden)

    Pieter Johan Steenkamp

    Full Text Available The spores of the soil-borne bacterium, Bacillus anthracis, which causes anthrax are highly resistant to adverse environmental conditions. Under ideal conditions, anthrax spores can survive for many years in the soil. Anthrax is known to be endemic in the northern part of Kruger National Park (KNP in South Africa (SA, with occasional epidemics spreading southward. The aim of this study was to identify and map areas that are ecologically suitable for the harboring of B. anthracis spores within the KNP. Anthrax surveillance data and selected environmental variables were used as inputs to the maximum entropy (Maxent species distribution modeling method. Anthrax positive carcasses from 1988-2011 in KNP (n = 597 and a total of 40 environmental variables were used to predict and evaluate their relative contribution to suitability for anthrax occurrence in KNP. The environmental variables that contributed the most to the occurrence of anthrax were soil type, normalized difference vegetation index (NDVI and precipitation. Apart from the endemic Pafuri region, several other areas within KNP were classified as ecologically suitable. The outputs of this study could guide future surveillance efforts to focus on predicted suitable areas for anthrax, since the KNP currently uses passive surveillance to detect anthrax outbreaks.

  14. A passive radon dosemeter suitable for workplaces

    International Nuclear Information System (INIS)

    Orlando, C.; Orlando, P.; Patrizii, L.; Tommasino, L.; Tonnarini, S.; Trevisi, R.; Viola, P.

    2002-01-01

    The results obtained in different international intercomparisons on passive radon monitors have been analysed with the aim of identifying a suitable radon monitoring device for workplaces. From this analysis, the passive radon device, first developed for personal dosimetry in mines by the National Radiation Protection Board, UK (NRPB), has shown the most suitable set of characteristics. This radon monitor consists of a diffusion chamber, made of conductive plastic with less than 2 cm height, containing a CR-39 film (Columbia Resin 1939), as track detector. Radon detectors in workplaces may be exposed only during the working hours, thus requiring the storage of the detectors in low-radon zones when not exposed. This paper describes how this problem can be solved. Since track detectors are also efficient neutron dosemeters, care should be taken when radon monitors are used in workplaces, where they may be exposed to neutrons, such as on high altitude mountains, in the surroundings of high energy X ray facilities (where neutrons are produced by (gamma, n) reactions) or around high energy particle accelerators. To this end, the response of these passive radon monitors to high energy neutron fields has been investigated. (author)

  15. Suitability Analysis and Projected Climate Change Impact on Banana and Coffee Production Zones in Nepal

    Science.gov (United States)

    Sujakhu, Nani M.; Merz, Juerg; Kindt, Roeland; Xu, Jianchu; Matin, Mir A.; Ali, Mostafa; Zomer, Robert J.

    2016-01-01

    The Government of Nepal has identified opportunities in agricultural commercialization, responding to a growing internal demand and expansion of export markets to reduce the immense trade deficit. Several cash crops, including coffee and bananas, have been identified in the recently approved Agriculture Development Strategy. Both of these crops have encouraged smallholder farmers to convert their subsistence farming practices to more commercial cultivation. Identification of suitable agro-ecological zones and understanding climate-related issues are important for improved production and livelihoods of smallholder farmers. Here, the suitability of coffee and banana crops is analyzed for different agro-ecological zones represented by Global Environmental Stratification (GEnS). Future shifts in these suitability zones are also predicted. Plantation sites in Nepal were geo-referenced and used as input in species distribution modelling. The multi-model ensemble model suggests that climate change will reduce the suitable growing area for coffee by about 72% across the selected emission scenarios from now to 2050. Impacts are low for banana growing, with a reduction in suitability by about 16% by 2050. Bananas show a lot of potential for playing an important role in Nepal as a sustainable crop in the context of climate change, as this study indicates that the amount of area suited to banana growing will grow by 40% by 2050. Based on our analysis we recommend possible new locations for coffee plantations and one method for mitigating climate change-related problems on existing plantations. These findings are expected to support planning and policy dialogue for mitigation and support better informed and scientifically based decision-making relating to these two crops. PMID:27689354

  16. Assessing the suitable habitat for reintroduction of brown trout (Salmo trutta forma fario) in a lowland river: A modeling approach.

    Science.gov (United States)

    Boets, Pieter; Gobeyn, Sacha; Dillen, Alain; Poelman, Eddy; Goethals, Peter L M

    2018-05-01

    Huge efforts have been made during the past decades to improve the water quality and to restore the physical habitat of rivers and streams in western Europe. This has led to an improvement in biological water quality and an increase in fish stocks in many countries. However, several rheophilic fish species such as brown trout are still categorized as vulnerable in lowland streams in Flanders (Belgium). In order to support cost-efficient restoration programs, habitat suitability modeling can be used. In this study, we developed an ensemble of habitat suitability models using metaheuristic algorithms to explore the importance of a large number of environmental variables, including chemical, physical, and hydromorphological characteristics to determine the suitable habitat for reintroduction of brown trout in the Zwalm River basin (Flanders, Belgium), which is included in the Habitats Directive. Mean stream velocity, water temperature, hiding opportunities, and presence of pools or riffles were identified as the most important variables determining the habitat suitability. Brown trout mainly preferred streams with a relatively high mean reach stream velocity (0.2-1 m/s), a low water temperature (7-15°C), and the presence of pools. The ensemble of models indicated that most of the tributaries and headwaters were suitable for the species. Synthesis and applications . Our results indicate that this modeling approach can be used to support river management, not only for brown trout but also for other species in similar geographical regions. Specifically for the Zwalm River basin, future restoration of the physical habitat, removal of the remaining migration barriers and the development of suitable spawning grounds could promote the successful restoration of brown trout.

  17. [Ecology suitability study of Chinese materia medica Gentianae Macrophyllae Radix].

    Science.gov (United States)

    Lu, You-Yuan; Yang, Yan-Mei; Ma, Xiao-Hui; Zhang, Xiao-Bo; Zhu, Shou-Dong; Jin, Ling

    2016-09-01

    This paper is aimed to predict ecology suitability distribution of Gentianae Macrophyllae Radix and search the main ecological factors affecting the suitability distribution. The 313 distribution information about G. macrophylla, 186 distribution information about G. straminea, 343 distribution information about G. dauricaand 131 distribution information about G. crasicaulis were collected though investigation and network sharing platform data . The ecology suitable distribution factors for production Gentianae Macrophyllae Radix was analyzed respectively by the software of ArcGIS and MaxEnt with 55 environmental factors. The result of MaxEnt prediction was very well (AUC was above 0.9). The results of predominant factors analysis showed that precipitation and altitude were all the major factors impacting the ecology suitable of Getiana Macrophylla Radix production. G. macrophylla ecology suitable region was mainly concentrated in south of Gansu, Shanxi, central of Shaanxi and east of Qinghai provinces. G. straminea ecology suitable region was mainly concentrated in southwest of Gansu, east of Qinghai, north and northwest of Sichuan, east of Xizang province. G. daurica ecology suitable region was mainly concentrated in south and southwest of Gansu, east of Qinghai, Shanxi and north of Shaanxi province. G. crasicaulis ecology suitable region was mainly concentrated in Sichuan and north of Yunnan, east of Xizang, south of Gansu and east of Qinghai province. The ecological suitability distribution result of Gentianae Macrophyllae Radix was consistent with each species actual distribution. The study could provide reference for the collection and protection of wild resources, meanwhile, provide the basis for the selection of cultivation area of Gentiana Macrophylla Radix. Copyright© by the Chinese Pharmaceutical Association.

  18. Transferability of habitat suitability criteria for fishes in warmwater streams

    Science.gov (United States)

    Freeman, Mary C.; Bowen, Z.H.; Crance, J.H.

    1997-01-01

    We developed habitat suitability criteria and tested their transferability for nine fishes inhabiting unregulated Piedmont and Coastal Plain streams in Alabama. Cr iteria for optimal habitat were defined as ranges of depth, velocity, substrate type and cover type for which a species' suitability index (proportional abundance divided by proportional habitat availability, scaled from 0 to 1) equalled or exceeded 0.4. We evaluated the transferability of criteria between study sites by testing the null hypothesis that species occurrence in a sample was independent of whether or not the sample was taken in optimal habitat. We also tested criteria transference to a large, flow-regulated river sampled during low flow periods. Depth, velocity and most substrate criteria developed for the bronze darter Percina palmaris successfully transferred between unregulated streams and to the flow-regulated river samples. All criteria developed for a pair of closely related, allopatric darter species, Etheostoma chuckwachattee and E. jordani, transferred sucessfully when applied between species (in the unregulated sites) and to the regulated river samples. In contrast, criteria for the Alabama shiner Cyprinella callistia failed nearly all tests of transferability. Criteria for E. stigmaeum, P. nigrofasciata, an undescribed Percina species, and a pair of related, allopatric Cyprinella species transferred inconsistently. The species with good criteria transference had high suitability indices for shallow depths, fast current velocities and coarse substrates, characteristic of riffle species. We suggest that microhabitat criteria for riffle fishes are more likely to provide a transferable measure of habitat quality than criteria for fishes that, although restricted to fluvial habitats, commonly occupy a variety of pool and riffle habitats.

  19. Glass compositions suitable for PFR wastes

    International Nuclear Information System (INIS)

    Boult, K.A.; Dalton, J.T.; Eccles, E.W.; Hough, A.; Marples, J.A.C.; Paige, E.L.; Sutcliffe, P.W.

    1988-03-01

    Previous work had identified glass compositions that were suitable for vitrifying current and future high level wastes from the Prototype Fast Reactor (PFR) fuel reprocessing plant. Further work on these glasses has shown that: a) Foaming and crystallisation can occur under certain conditions, both probably associated with the presence of iron in the waste. Either of these could lead to greater difficulties in processing. b) Inconel 690, the preferred JCM (Joule-heated Ceramic Melter) electrode material has an acceptable corrosion rate at 1200 0 C: ca 0.6mm.y -1 . c) The leach rates are unaffected by radiation damage. The density of the glass decreases slightly with α-dose, with a dependency that extrapolates, at infinite time, to an 0.13% linear expansion. d) The concentrations of the radiologically important elements Tc, Np, Pu and Am, observed in a 'repository simulation' leach test, were satisfactorily low. (author)

  20. Larvicidal activity and possible mode of action of four flavonoids and two fatty acids identified in Millettia pinnata seed toward three mosquito species.

    Science.gov (United States)

    Perumalsamy, Haribalan; Jang, Myung Jin; Kim, Jun-Ran; Kadarkarai, Murugan; Ahn, Young-Joon

    2015-04-19

    extract or hydrodistillate applied as 10% liquid provided 100% mortality toward the three mosquito species larvae and the efficacy of the liquids was comparable to that of temephos 200 g/L EC. Further studies will warrant possible applications of M. pinnata seed-derived products as potential larvicides for the control of mosquito populations.

  1. Evaluation of reference gene suitability for quantitative expression analysis by quantitative polymerase chain reaction in the mandibular condyle of sheep.

    Science.gov (United States)

    Jiang, Xin; Xue, Yang; Zhou, Hongzhi; Li, Shouhong; Zhang, Zongmin; Hou, Rui; Ding, Yuxiang; Hu, Kaijin

    2015-10-01

    Reference genes are commonly used as a reliable approach to normalize the results of quantitative polymerase chain reaction (qPCR), and to reduce errors in the relative quantification of gene expression. Suitable reference genes belonging to numerous functional classes have been identified for various types of species and tissue. However, little is currently known regarding the most suitable reference genes for bone, specifically for the sheep mandibular condyle. Sheep are important for the study of human bone diseases, particularly for temporomandibular diseases. The present study aimed to identify a set of reference genes suitable for the normalization of qPCR data from the mandibular condyle of sheep. A total of 12 reference genes belonging to various functional classes were selected, and the expression stability of the reference genes was determined in both the normal and fractured area of the sheep mandibular condyle. RefFinder, which integrates the following currently available computational algorithms: geNorm, NormFinder, BestKeeper, and the comparative ΔCt method, was used to compare and rank the candidate reference genes. The results obtained from the four methods demonstrated a similar trend: RPL19, ACTB, and PGK1 were the most stably expressed reference genes in the sheep mandibular condyle. As determined by RefFinder comprehensive analysis, the results of the present study suggested that RPL19 is the most suitable reference gene for studies associated with the sheep mandibular condyle. In addition, ACTB and PGK1 may be considered suitable alternatives.

  2. 45 CFR 12a.4 - Suitability determination.

    Science.gov (United States)

    2010-10-01

    ... underutilized will be reviewed for suitability no earlier than six months prior to the expected date when the... following: (1) The suitability determination for a particular piece of property, and the reasons for that...

  3. Identifying some pathogenic Vibrio/Photobacterium species during mass mortalities of cultured Gilthead seabream (Sparus aurata and European seabass (Dicentrarchus labrax from some Egyptian coastal provinces

    Directory of Open Access Journals (Sweden)

    Mohammed Abdel-Aziz

    2013-12-01

    Full Text Available Vibrio alginolyticus, Vibrio parahemolyticus and Photobacterium damselae subsp damselae were isolated during recurrent episodes of mass mortalities among different stages of Gilthead sea bream (Sparus aurata and European seabass (Dicentrarchus labrax. The pathogens were recovered from the external/internal lesions of a total of 320 seeds, juvenile and adult fishes from the period of February 2013 through August 2013. Two hundred and sixty four bacterial isolates were retrieved and presumptively identified using morpho-chemical characterization and API®20NE. However, definitive molecular confirmation of V. alginolyticus was obtained through implementing collagenase gene based regular PCR technique. The total prevalence of V. alginolyticus, V. parahemolyticus and Photobacterium damselae subsp damselae among naturally infected Gilthead seabream and European seabass was 82.19%, 87.28% 10.27%, 6.79% and 7.54%, 5.93% respectively. Antibiogram has revealed that isolates were sensitive to ciprofloxacin, chloramphenicol, enrofloxacin, nalidixic acid and oxolinic acid while resistant to ampicillin, amoxicillin, and lincomycin.

  4. Milestone Report - M3FT-15OR03120213 - A Literature Survey to Identify Potentially Problematic Volatile Iodine-Bearing Species Present in Off-Gas Streams

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Brian [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Soelberg, Nick [Idaho National Lab. (INL), Idaho Falls, ID (United States); Jubin, Robert Thomas [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Bruffey, Stephanie H. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Strachan, Denis M. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

    2015-06-30

    Four radionuclides have been identified as being sufficiently volatile in the reprocessing of nuclear fuel that their gaseous release needs to be controlled to meet U.S. regulatory requirements (Jubin et al. 2011, 2012). These radionuclides are 3H, 14C, 85Kr, and 129I. Of these, 129I has the longest half-life and potentially highest biological impact. Accordingly, control of the release of 129I is most critical with respect to U.S. regulations for the release of radioactive material in stack emissions. Current U.S. Environmental Protection Agency regulation governing nuclear facilities (40 CFR 190) states that the total quantity of radioactive materials entering the general environment from the entire uranium fuel cycle, per gigawatt-year of electrical energy produced by the fuel cycle, must contain less than 5 mCi of 129I. The study of inorganic iodide in off-gas systems has been almost exclusively limited to I2, and the focus of organic iodide studies has been CH3I.

  5. [Climatic suitability of citrus in subtropical China].

    Science.gov (United States)

    Duan, Hai-Lai; Qian, Huai-Sui; Li, Ming-Xia; Du, Yao-Dong

    2010-08-01

    By applying the theories of ecological suitability and the methods of fuzzy mathematics, this paper established a climatic suitability model for citrus, calculated and evaluated the climatic suitability and its spatiotemporal differences for citrus production in subtropical China, and analyzed the climatic suitability of citrus at its different growth stages and the mean climatic suitability of citrus in different regions of subtropical China. The results showed that the citrus in subtropical China had a lower climatic suitability and a higher risk at its flower bud differentiation stage, budding stage, and fruit maturity stage, but a higher climatic suitability and a lower risk at other growth stages. Cold damage and summer drought were the key issues affecting the citrus production in subtropical China. The citrus temperature suitability represented a latitudinal zonal pattern, i. e., decreased with increasing latitude; its precipitation suitability was high in the line of "Sheyang-Napo", medium in the southeast of the line, low in the northwest of the line, and non in high mountainous area; while the sunlight suitability was in line with the actual duration of sunshine, namely, higher in high-latitude areas than in low-latitude areas, and higher in high-altitude areas than in plain areas. Limited by temperature factor, the climatic suitability was in accordance with temperature suitability, i. e., south parts had a higher suitability than north parts, basically representing latitudinal zonal pattern. From the analysis of the inter-annual changes of citrus climatic suitability, it could be seen that the citrus climatic suitability in subtropical China was decreasing, and had obvious regional differences, suggesting that climate change could bring about the changes in the regions suitable for citrus production and in the key stages of citrus growth.

  6. CHARACTERISTICS AND SUITABILITY EVALUATION OF THE ...

    African Journals Online (AJOL)

    Ifedotun Aina

    suggested that the soils were not currently suitable for the production of the two ... crop – land suitability analysis has been used for achieving optimum utilization of the available ... Two methods of land suitability evaluation (FAO frame work and parametric) ..... Characterization and Classification of Onwu River Floodplain.

  7. Mid-Atlantic elasmobranchs: Suitable metal scouts?

    International Nuclear Information System (INIS)

    Torres, Paulo; Tristão da Cunha, Regina; Rodrigues, Armindo dos Santos

    2017-01-01

    Heavy metals are a hazard to marine fauna and human health. In this study we assess stable isotopes and metal content in Prionace glauca and Isurus oxyrinchus and analyse these results within and among other species and across regions and geographical areas. Also, we evaluate their suitability, together with Raja clavata and Galeorhinus galeus, as Mid-Atlantic bioindicators. Prionace glauca and I. oxyrinchus shared the same trophic level in a pelagic food web and did not present significant differences between genders or metals, except for As. Arsenic and Hg accumulated while Cd and Pb were not detected. One I. oxyrinchus presented Hg values above regulatory limits. A high Hg exposure was associated with I. oxyrinchus since its maximum weekly intake was exceeded. Elasmobranchs can be used as metal sentinels, each presenting different key features which defines a good marine bioindicator, allowing long-term monitoring at different temporal and spatial scales. - Highlights: • We analysed P. glauca and I. oxyrinchus muscle from Mid-Atlantic. • We determined stable isotopes, trophic ecology and heavy metal content. • Results reflect bioaccumulation for As and Hg. • Oxyrinchus already presented Hg values above regulatory limits. • Mid-Atlantic elasmobranchs appear to be effective metal bioindicators.

  8. Modeling Habitat Suitability of Migratory Birds from Remote Sensing Images Using Convolutional Neural Networks

    Science.gov (United States)

    Su, Jin-He; Piao, Ying-Chao; Luo, Ze; Yan, Bao-Ping

    2018-01-01

    Simple Summary The understanding of the spatio-temporal distribution of the species habitats would facilitate wildlife resource management and conservation efforts. Existing methods have poor performance due to the limited availability of training samples. More recently, location-aware sensors have been widely used to track animal movements. The aim of the study was to generate suitability maps of bar-head geese using movement data coupled with environmental parameters, such as remote sensing images and temperature data. Therefore, we modified a deep convolutional neural network for the multi-scale inputs. The results indicate that the proposed method can identify the areas with the dense goose species around Qinghai Lake. In addition, this approach might also be interesting for implementation in other species with different niche factors or in areas where biological survey data are scarce. Abstract With the application of various data acquisition devices, a large number of animal movement data can be used to label presence data in remote sensing images and predict species distribution. In this paper, a two-stage classification approach for combining movement data and moderate-resolution remote sensing images was proposed. First, we introduced a new density-based clustering method to identify stopovers from migratory birds’ movement data and generated classification samples based on the clustering result. We split the remote sensing images into 16 × 16 patches and labeled them as positive samples if they have overlap with stopovers. Second, a multi-convolution neural network model is proposed for extracting the features from temperature data and remote sensing images, respectively. Then a Support Vector Machines (SVM) model was used to combine the features together and predict classification results eventually. The experimental analysis was carried out on public Landsat 5 TM images and a GPS dataset was collected on 29 birds over three years. The results

  9. Identifying Fishes through DNA Barcodes and Microarrays.

    Directory of Open Access Journals (Sweden)

    Marc Kochzius

    2010-09-01

    Full Text Available International fish trade reached an import value of 62.8 billion Euro in 2006, of which 44.6% are covered by the European Union. Species identification is a key problem throughout the life cycle of fishes: from eggs and larvae to adults in fisheries research and control, as well as processed fish products in consumer protection.This study aims to evaluate the applicability of the three mitochondrial genes 16S rRNA (16S, cytochrome b (cyt b, and cytochrome oxidase subunit I (COI for the identification of 50 European marine fish species by combining techniques of "DNA barcoding" and microarrays. In a DNA barcoding approach, neighbour Joining (NJ phylogenetic trees of 369 16S, 212 cyt b, and 447 COI sequences indicated that cyt b and COI are suitable for unambiguous identification, whereas 16S failed to discriminate closely related flatfish and gurnard species. In course of probe design for DNA microarray development, each of the markers yielded a high number of potentially species-specific probes in silico, although many of them were rejected based on microarray hybridisation experiments. None of the markers provided probes to discriminate the sibling flatfish and gurnard species. However, since 16S-probes were less negatively influenced by the "position of label" effect and showed the lowest rejection rate and the highest mean signal intensity, 16S is more suitable for DNA microarray probe design than cty b and COI. The large portion of rejected COI-probes after hybridisation experiments (>90% renders the DNA barcoding marker as rather unsuitable for this high-throughput technology.Based on these data, a DNA microarray containing 64 functional oligonucleotide probes for the identification of 30 out of the 50 fish species investigated was developed. It represents the next step towards an automated and easy-to-handle method to identify fish, ichthyoplankton, and fish products.

  10. Habitat Suitability analysis of Koklass (Pucrasia macrolopha) Pheasant in Churdhar Wildlife Sanctuary of Himachal Pradesh, India using Geospatial Technology

    Science.gov (United States)

    Eliza, K.; Sarma, K.

    2014-12-01

    Pheasants are at the brink of destruction due to degradation of forests, environmental pollution, climatic changes and extensive hunting of wild floras and faunas.The problem is more acute in the developing countries where wildlife and biodiversity conservation are often less prioritized due to more pressing demands of food security and poverty alleviation. Koklass Pheasant (Pucrasia macrolopha) species is distributed from Afghanistan and Pakistan in the east along the Himalayas to southeastern Tibet, western China and southeastern Mongolia.This species is grouped under endangered species in Red Data Book of Zoological Survey of India and also classified as least concern species according to IUCN Red List of Threatened Species.Conservation biologists and managers need a range of both classical analyses and specific modern tools to face the increasing threats to biodiversity. Among these tools, habitat-suitability modeling has recently emerged as a relevant technique to assess global impacts to define wide conservation priorities.The present study is carried out using remote sensing satellite imagery and GIS modeling technique for assessing habitat suitability of Koklass Pheasants and finding out the habitat factors influencing the Koklass distribution in Churdhar Wildlife Sanctuary, India. Effective management and conservation of wildlife populations and their habitats largely depend on our ability to understand and predict species-habitat interactions. Different thematic maps viz., land use/cover, forest types, drainage buffer, multiple ring buffers of sighting locations and multiple ring buffers of roads have been prepared to support the objective of the study. The Weighted Overlay Analysis model is used for identifying different potential areas of habitat for this endangered species. The most suitable area for Koklass Pheasant within the Wildlife Sanctuary is found to be about 23.8 percent of the total area which is due to favourable habitat conditions for the

  11. Land suitability maps for waste disposal siting

    International Nuclear Information System (INIS)

    Hrasna, M.

    1996-01-01

    The suitability of geoenvironment for waste disposal depends mainly on its stability and on the danger of groundwater pollution. Besides them, on the land suitability maps for the given purpose also those factors of the factors of the geoenvironment and the landscape should be taken into account, which enable another way of the land use, such as mineral resources, water resources, fertile soils, nature reserves, etc. On the base of the relevant factors influence evaluation - suitable, moderately suitable and unsuitable territorial units are delimited on the maps. The different way of various scale maps compilation is applied, taken into account their different representing feasibilities. (authors)

  12. A new cryptic species and review of the east-Andean leaf chafer genus Mesomerodon Ohaus, 1905 (Coleoptera, Scarabaeidae, Rutelinae).

    Science.gov (United States)

    Seidel, Matthias; Jameson, Mary L; Stone, Rachel L

    2017-01-01

    The Neotropical scarab beetle genus Mesomerodon Ohaus (Scarabaeidae: Rutelinae: Rutelini) is distributed in the western (lowland) Amazonian region from Colombia to Bolivia. Based on our research, the genus includes three species including a new cryptic species from Ecuador. We use niche modeling to predict potential suitable habitat and identify environmental factors associated with the distribution of Mesomerodon species. We characterize the genus, provide a key to species, diagnose each species, describe a new species, provide spatial and temporal distributions, and discuss distributions of the species in relation to Amazonian landscape biodiversity.

  13. Ecological variables governing habitat suitability and the distribution ...

    African Journals Online (AJOL)

    governed by soil particle size distribution), in combination with the cover provided by trees, as the two ecological factors that best explained habitat suitability for Juliana's golden mole at the three localities. An IndVal analysis failed to identify ...

  14. Using environmental niche modeling to find suitable habitats for the Hard-ground Barasingha in Madhya Pradesh, India

    Directory of Open Access Journals (Sweden)

    C. P. Singh

    2015-09-01

    Full Text Available The subspecies of Swamp Deer, the Hard-ground Barasingha (Rucervus duvaucelii branderi Pocock, is presently found only in Kanha Tiger Reserve (KTR in Madhya Pradesh, India. This subspecies is highly vulnerable to extinction, and reintroduction in suitable sites is the need of the hour.  Environmental niche models (GARP, SVM, ED, CSM aimed at providing a detailed prediction of species distribution by relating presence of species to 19 bioclimatic indices were developed, using swamp deer occurrence records in KTR. The predictions were appropriately weighted with the prevailing LU/LC classes to identify suitable habitats in Madhya Pradesh, India. The result shows that the southern region of Madhya Pradesh is suitable for the sustenance of Barasingha with varying degrees of habitability. Vicarious validation shows that most of these forest areas were the same as that of historical records dating back to 50 years. However, land use maps can help identify areas where this subspecies can be reintroduced. 

  15. Upward Altitudinal Shifts in Habitat Suitability of Mountain Vipers since the Last Glacial Maximum.

    Directory of Open Access Journals (Sweden)

    Masoud Yousefi

    Full Text Available We determined the effects of past and future climate changes on the distribution of the Montivipera raddei species complex (MRC that contains rare and endangered viper species limited to Iran, Turkey and Armenia. We also investigated the current distribution of MRC to locate unidentified isolated populations as well as to evaluate the effectiveness of the current network of protected areas for their conservation. Present distribution of MRC was modeled based on ecological variables and model performance was evaluated by field visits. Some individuals at the newly identified populations showed uncommon morphological characteristics. The distribution map of MRC derived through modeling was then compared with the distribution of protected areas in the region. We estimated the effectiveness of the current protected area network to be 10%, which would be sufficient for conserving this group of species, provided adequate management policies and practices are employed. We further modeled the distribution of MRC in the past (21,000 years ago and under two scenarios in the future (to 2070. These models indicated that climatic changes probably have been responsible for an upward shift in suitable habitats of MRC since the Last Glacial Maximum, leading to isolation of allopatric populations. Distribution will probably become much more restricted in the future as a result of the current rate of global warming. We conclude that climate change most likely played a major role in determining the distribution pattern of MRC, restricting allopatric populations to mountaintops due to habitat alterations. This long-term isolation has facilitated unique local adaptations among MRC populations, which requires further investigation. The suitable habitat patches identified through modeling constitute optimized solutions for inclusion in the network of protected areas in the region.

  16. Validation of suitable reference genes for expression normalization in Echinococcus spp. larval stages.

    Science.gov (United States)

    Espínola, Sergio Martin; Ferreira, Henrique Bunselmeyer; Zaha, Arnaldo

    2014-01-01

    In recent years, a significant amount of sequence data (both genomic and transcriptomic) for Echinococcus spp. has been published, thereby facilitating the analysis of genes expressed during a specific stage or involved in parasite development. To perform a suitable gene expression quantification analysis, the use of validated reference genes is strongly recommended. Thus, the aim of this work was to identify suitable reference genes to allow reliable expression normalization for genes of interest in Echinococcus granulosus sensu stricto (s.s.) (G1) and Echinococcus ortleppi upon induction of the early pre-adult development. Untreated protoscoleces (PS) and pepsin-treated protoscoleces (PSP) from E. granulosus s.s. (G1) and E. ortleppi metacestode were used. The gene expression stability of eleven candidate reference genes (βTUB, NDUFV2, RPL13, TBP, CYP-1, RPII, EF-1α, βACT-1, GAPDH, ETIF4A-III and MAPK3) was assessed using geNorm, Normfinder, and RefFinder. Our qPCR data showed a good correlation with the recently published RNA-seq data. Regarding expression stability, EF-1α and TBP were the most stable genes for both species. Interestingly, βACT-1 (the most commonly used reference gene), and GAPDH and ETIF4A-III (previously identified as housekeeping genes) did not behave stably in our assay conditions. We propose the use of EF-1α as a reference gene for studies involving gene expression analysis in both PS and PSP experimental conditions for E. granulosus s.s. and E. ortleppi. To demonstrate its applicability, EF-1α was used as a normalizer gene in the relative quantification of transcripts from genes coding for antigen B subunits. The same EF-1α reference gene may be used in studies with other Echinococcus sensu lato species. This report validates suitable reference genes for species of class Cestoda, phylum Platyhelminthes, thus providing a foundation for further validation in other epidemiologically important cestode species, such as those from the

  17. Validation of Suitable Reference Genes for Expression Normalization in Echinococcus spp. Larval Stages

    Science.gov (United States)

    Espínola, Sergio Martin; Ferreira, Henrique Bunselmeyer; Zaha, Arnaldo

    2014-01-01

    In recent years, a significant amount of sequence data (both genomic and transcriptomic) for Echinococcus spp. has been published, thereby facilitating the analysis of genes expressed during a specific stage or involved in parasite development. To perform a suitable gene expression quantification analysis, the use of validated reference genes is strongly recommended. Thus, the aim of this work was to identify suitable reference genes to allow reliable expression normalization for genes of interest in Echinococcus granulosus sensu stricto (s.s.) (G1) and Echinococcus ortleppi upon induction of the early pre-adult development. Untreated protoscoleces (PS) and pepsin-treated protoscoleces (PSP) from E. granulosus s.s. (G1) and E. ortleppi metacestode were used. The gene expression stability of eleven candidate reference genes (βTUB, NDUFV2, RPL13, TBP, CYP-1, RPII, EF-1α, βACT-1, GAPDH, ETIF4A-III and MAPK3) was assessed using geNorm, Normfinder, and RefFinder. Our qPCR data showed a good correlation with the recently published RNA-seq data. Regarding expression stability, EF-1α and TBP were the most stable genes for both species. Interestingly, βACT-1 (the most commonly used reference gene), and GAPDH and ETIF4A-III (previously identified as housekeeping genes) did not behave stably in our assay conditions. We propose the use of EF-1α as a reference gene for studies involving gene expression analysis in both PS and PSP experimental conditions for E. granulosus s.s. and E. ortleppi. To demonstrate its applicability, EF-1α was used as a normalizer gene in the relative quantification of transcripts from genes coding for antigen B subunits. The same EF-1α reference gene may be used in studies with other Echinococcus sensu lato species. This report validates suitable reference genes for species of class Cestoda, phylum Platyhelminthes, thus providing a foundation for further validation in other epidemiologically important cestode species, such as those from the

  18. Less is more: Strategic scale site suitability for concentrated solar thermal power in Western Australia

    International Nuclear Information System (INIS)

    Dawson, Lucas; Schlyter, Peter

    2012-01-01

    Concentrated Solar Thermal Power (CSP) represents a technology with a great deal of promise for low-emissions electricity generation. Several recent studies have identified large swathes of the world’s ‘sunbelt’ as technically suitable for the technology, but current estimates grossly overestimate site suitability for CSP. There is a need for more realistic suitability estimations in order to provide a more accurate basis for policy and investment decisions. This paper establishes a generally applicable GIS-based methodology to better enable identification of CSP-suitable sites at the continental scale. We test the methodology, identifying a large number of CSP suitable sites in Western Australia (WA). Our results indicate a 99.4% reduction from technically suitable areas to areas showing medium-to-very-high suitability in the current and near term in WA. The availability of infrastructure is critical to site suitability and the introduction of new major loads and infrastructure in currently under-developed regions is likely to open up further areas with medium to very high suitability. Despite the fact that current global/continental scale estimates of CSP potentials are likely overestimated by at least two orders of magnitude, truly CSP-suitable areas remain more than sufficient to motivate investment in utility-scale CSP and power potentials from this technology remain enormous. - Highlights: ► 1.78 million km 2 of Western Australia is identified as technically suitable. ► Hypothetical production potential of technically suitable area ≈908,000 TW h/year. ► Only 0.6% of technically suitable areas considered to be medium-very highly suitable. ► Site suitability highly dependent on availability of infrastructure and load. ► Suitable areas still more than sufficient to motivate CSP production.

  19. Land Suitability Assessment for Sugarcane in "Herois de Caxito" (Angola

    Directory of Open Access Journals (Sweden)

    Baert, G.

    2005-01-01

    Full Text Available The suitability of the soils surrounding the sugarcane plantation at "Herois de Caxito" (7068 ha is assessed. The main goal is to identify land suitability for the enlargement of the present plantation, using FAO land evaluation models (modified to suit Herois de Caxito conditions and GIS. Calculations of the radiationthermal production potential (RPP, land production potential (LPP, irrigation suitability index, and evaluation of the irrigation water quality are done. The water-limited production potential (WPP is found equal to the RPP, because water needs were fully met under irrigation. Maps showing the spatial distribution of the LPP and the suitability for irrigation are generated. The matching of irrigation and fertility indices has shown that, about 40% of the soils with good fertility for sugarcane production present low suitability for irrigation, the main limitations being the very fine texture and the drainage. The available surface water at Herois de Caxito (Dande river is of very good quality for irrigation of sugarcane.

  20. GIS-based rapid-assessment of bighead carp Hypophthalmichthys nobilis (Richardson, 1845) suitability in reservoirs

    Science.gov (United States)

    Long, James M.; Liang, Yu; Shoup, Daniel E.; Dzialowski, Andrew R.; Bidwell, Joseph R.

    2014-01-01

    Broad-scale niche models are good for examining the potential for invasive species occurrences, but can fall short in providing managers with site-specific locations for monitoring. Using Oklahoma as an example, where invasive bighead carp (Hypophthalmichthys nobilis) are established in certain reservoirs, but predicted to be widely distributed based on broad-scale niche models, we cast bighead carp reproductive ecology in a site-specific geospatial framework to determine their potential establishment in additional reservoirs. Because bighead carp require large, long free-flowing rivers with suitable hydrology for reproduction but can persist in reservoirs, we considered reservoir tributaries with mean annual daily discharge ≥8.5 cubic meters per second (m3 /s) and quantified the length of their unimpeded portions. In contrast to published broad-scale niche models that identified nearly the entire state as susceptible to invasion, our site-specific models showed that few reservoirs in Oklahoma (N = 9) were suitable for bighead carp establishment. Moreover, this method was rapid and identified sites that could be prioritized for increased study or scrutiny. Our results highlight the importance of considering the environmental characteristics of individual sites, which is often the level at which management efforts are implemented when assessing susceptibility to invasion.

  1. Relative availability of natural prey versus livestock predicts landscape suitability for cheetahs Acinonyx jubatus in Botswana

    Science.gov (United States)

    Winterbach, Christiaan W.; Boast, Lorraine K.; Klein, Rebecca; Somers, Michael J.

    2015-01-01

    Prey availability and human-carnivore conflict are strong determinants that govern the spatial distribution and abundance of large carnivore species and determine the suitability of areas for their conservation. For wide-ranging large carnivores such as cheetahs (Acinonyx jubatus), additional conservation areas beyond protected area boundaries are crucial to effectively conserve them both inside and outside protected areas. Although cheetahs prefer preying on wild prey, they also cause conflict with people by predating on especially small livestock. We investigated whether the distribution of cheetahs’ preferred prey and small livestock biomass could be used to explore the potential suitability of agricultural areas in Botswana for the long-term persistence of its cheetah population. We found it gave a good point of departure for identifying priority areas for land management, the threat to connectivity between cheetah populations, and areas where the reduction and mitigation of human-cheetah conflict is critical. Our analysis showed the existence of a wide prey base for cheetahs across large parts of Botswana’s agricultural areas, which provide additional large areas with high conservation potential. Twenty percent of wild prey biomass appears to be the critical point to distinguish between high and low probable levels of human-cheetah conflict. We identified focal areas in the agricultural zones where restoring wild prey numbers in concurrence with effective human-cheetah conflict mitigation efforts are the most immediate conservation strategies needed to maintain Botswana’s still large and contiguous cheetah population. PMID:26213646

  2. Relative availability of natural prey versus livestock predicts landscape suitability for cheetahs Acinonyx jubatus in Botswana.

    Science.gov (United States)

    Winterbach, Hanlie E K; Winterbach, Christiaan W; Boast, Lorraine K; Klein, Rebecca; Somers, Michael J

    2015-01-01

    Prey availability and human-carnivore conflict are strong determinants that govern the spatial distribution and abundance of large carnivore species and determine the suitability of areas for their conservation. For wide-ranging large carnivores such as cheetahs (Acinonyx jubatus), additional conservation areas beyond protected area boundaries are crucial to effectively conserve them both inside and outside protected areas. Although cheetahs prefer preying on wild prey, they also cause conflict with people by predating on especially small livestock. We investigated whether the distribution of cheetahs' preferred prey and small livestock biomass could be used to explore the potential suitability of agricultural areas in Botswana for the long-term persistence of its cheetah population. We found it gave a good point of departure for identifying priority areas for land management, the threat to connectivity between cheetah populations, and areas where the reduction and mitigation of human-cheetah conflict is critical. Our analysis showed the existence of a wide prey base for cheetahs across large parts of Botswana's agricultural areas, which provide additional large areas with high conservation potential. Twenty percent of wild prey biomass appears to be the critical point to distinguish between high and low probable levels of human-cheetah conflict. We identified focal areas in the agricultural zones where restoring wild prey numbers in concurrence with effective human-cheetah conflict mitigation efforts are the most immediate conservation strategies needed to maintain Botswana's still large and contiguous cheetah population.

  3. Relative availability of natural prey versus livestock predicts landscape suitability for cheetahs Acinonyx jubatus in Botswana

    Directory of Open Access Journals (Sweden)

    Hanlie E.K. Winterbach

    2015-07-01

    Full Text Available Prey availability and human-carnivore conflict are strong determinants that govern the spatial distribution and abundance of large carnivore species and determine the suitability of areas for their conservation. For wide-ranging large carnivores such as cheetahs (Acinonyx jubatus, additional conservation areas beyond protected area boundaries are crucial to effectively conserve them both inside and outside protected areas. Although cheetahs prefer preying on wild prey, they also cause conflict with people by predating on especially small livestock. We investigated whether the distribution of cheetahs’ preferred prey and small livestock biomass could be used to explore the potential suitability of agricultural areas in Botswana for the long-term persistence of its cheetah population. We found it gave a good point of departure for identifying priority areas for land management, the threat to connectivity between cheetah populations, and areas where the reduction and mitigation of human-cheetah conflict is critical. Our analysis showed the existence of a wide prey base for cheetahs across large parts of Botswana’s agricultural areas, which provide additional large areas with high conservation potential. Twenty percent of wild prey biomass appears to be the critical point to distinguish between high and low probable levels of human-cheetah conflict. We identified focal areas in the agricultural zones where restoring wild prey numbers in concurrence with effective human-cheetah conflict mitigation efforts are the most immediate conservation strategies needed to maintain Botswana’s still large and contiguous cheetah population.

  4. From Suitable Weak Solutions to Entropy Viscosity

    KAUST Repository

    Guermond, Jean-Luc; Pasquetti, Richard; Popov, Bojan

    2010-01-01

    This paper focuses on the notion of suitable weak solutions for the three-dimensional incompressible Navier-Stokes equations and discusses the relevance of this notion to Computational Fluid Dynamics. The purpose of the paper is twofold (i

  5. Obtaining shale oil suitable for lighting

    Energy Technology Data Exchange (ETDEWEB)

    Giraudel, M

    1851-11-12

    Treats with sulphuric acid and then with soda, obtaining 57 per cent of products suitable for lighting in place of the usual 35 to 40 per cent as obtained by present processes. The product has a less disagreeable odor.

  6. Using Machine Learning for Land Suitability Classification

    African Journals Online (AJOL)

    User

    West African Journal of Applied Ecology, vol. ... evidence for the utility of machine learning methods in land suitability classification especially MCS methods. ... Artificial intelligence tools. ..... Numerical values of index for the various classes.

  7. Projection of climatic suitability for Aedes albopictus Skuse (Culicidae) in Europe under climate change conditions

    Science.gov (United States)

    Fischer, Dominik; Thomas, Stephanie Margarete; Niemitz, Franziska; Reineking, Björn; Beierkuhnlein, Carl

    2011-07-01

    During the last decades the disease vector Aedes albopictus ( Ae. albopictus) has rapidly spread around the globe. The spread of this species raises serious public health concerns. Here, we model the present distribution and the future climatic suitability of Europe for this vector in the face of climate change. In order to achieve the most realistic current prediction and future projection, we compare the performance of four different modelling approaches, differentiated by the selection of climate variables (based on expert knowledge vs. statistical criteria) and by the geographical range of presence records (native range vs. global range). First, models of the native and global range were built with MaxEnt and were either based on (1) statistically selected climatic input variables or (2) input variables selected with expert knowledge from the literature. Native models show high model performance (AUC: 0.91-0.94) for the native range, but do not predict the European distribution well (AUC: 0.70-0.72). Models based on the global distribution of the species, however, were able to identify all regions where Ae. albopictus is currently established, including Europe (AUC: 0.89-0.91). In a second step, the modelled bioclimatic envelope of the global range was projected to future climatic conditions in Europe using two emission scenarios implemented in the regional climate model COSMO-CLM for three time periods 2011-2040, 2041-2070, and 2071-2100. For both global-driven models, the results indicate that climatically suitable areas for the establishment of Ae. albopictus will increase in western and central Europe already in 2011-2040 and with a temporal delay in eastern Europe. On the other hand, a decline in climatically suitable areas in southern Europe is pronounced in the Expert knowledge based model. Our projections appear unaffected by non-analogue climate, as this is not detected by Multivariate Environmental Similarity Surface analysis. The generated risk maps

  8. Suitability of Varicose Veins for Endovenous Treatments

    International Nuclear Information System (INIS)

    Goode, S. D.; Kuhan, G.; Altaf, N.; Simpson, R.; Beech, A.; Richards, T.; MacSweeney, S. T.; Braithwaite, B. D.

    2009-01-01

    The aim of the study was to assess the suitability of radiofrequency ablation (RFA), endovenous laser ablation (EVLA), and foam sclerotherapy (FS) for patients with symptomatic varicose veins (VVs). The study comprised 403 consecutive patients with symptomatic VVs. Data on 577 legs from 403 consecutive patients with symptomatic VVs were collected for the year 2006. Median patient age was 55 years (interquartile range 45-66), and 62% patients were women. A set of criteria based on duplex ultrasonography was used to select patients for each procedure. Great saphenous vein (GSV) reflux was present in 77% (446 of 577) of legs. Overall, 328 (73%) of the legs were suitable for at least one of the endovenous options. Of the 114 legs with recurrent GSV reflux disease, 83 (73%) were suitable to receive endovenous therapy. Patients with increasing age were less likely to be suitable for endovenous therapy (P = 0.03). Seventy-three percent of patients with VVs caused by GSV incompetence are suitable for endovenous therapy.

  9. Acceptance and suitability of novel trees for Orthotomicus erosus, an exotic bark beetle in North America

    Science.gov (United States)

    A.J. Walter; R.C. Venette; S.A. Kells

    2010-01-01

    To predict whether an herbivorous pest insect will establish in a new area, the potential host plants must be known. For invading bark beetles, adults must recognize and accept trees suitable for larval development. The preference-performance hypothesis predicts that adults will select host species that maximize the fitness of their offspring. We tested five species of...

  10. [Ecology suitability study of Ephedra intermedia].

    Science.gov (United States)

    Ma, Xiao-Hui; Lu, You-Yuan; Huang, De-Dong; Zhu, Tian-Tian; Lv, Pei-Lin; Jin, Ling

    2017-06-01

    The study aims at predicting ecological suitability of Ephedra intermedia in China by using maximum entropy Maxent model combined with GIS, and finding the main ecological factors affecting the distribution of E. intermedia suitability in appropriate growth area. Thirty-eight collected samples of E. intermedia and E. intermedia and 116 distribution information from CVH information using ArcGIS technology were analyzed. MaxEnt model was applied to forecast the E. intermedia in our country's ecology. E. intermedia MaxEnt ROC curve model training data and testing data sets the AUC value was 0.986 and 0.958, respectively, which were greater than 0.9, tending to be 1.The calculated E. intermedia habitat suitability by the model showed a high accuracy and credibility, which indicated that MaxEnt model could well predict the potential distribution area of E. intermedia in China. Copyright© by the Chinese Pharmaceutical Association.

  11. Impact of Alternative Environmental Flow Prescriptions on Hydropower Production and Fish Habitat Suitability

    Science.gov (United States)

    Castellarin, A.; Ceola, S.; Pugliese, A.; Galeati, G. A.

    2015-12-01

    Anthropogenic activities along streams and rivers are increasingly recognized to be a major concern for fluvial ecosystems. The management of water resources, by means of e.g. flow diversions and dams, for industrial, agricultural, water-supply, hydropower production and flood protection purposes induces significant changes to the natural streamflow regime of a river. Indeed, the river flow regime is known to be a major abiotic factor influencing fluvial ecosystems. An established approach aimed at preserving the behaviour and distribution of fluvial species relies on the definition of minimum streamflow requirements (i.e., environmental flows) downstream of dams and diversion structures. Such environmental flows are normally identified through methodologies that have an empirical nature and may not be representative of local ecological and hydraulic conditions. While the effect of imposing a minimum discharge release is easily predictable in terms of e.g. loss of hydropower production, the advantages in terms of species preferences are often poorly understood and seldom assessed. To analyze the interactions between flow releases and the behaviour and distribution of fluvial species (i.e., from periphyton, to benthic invertebrate and fish), one may use a habitat suitability curve, which is a fundamental tool capable of describing species preferences influenced by any generic environmental variable. The outcomes of a real case study applied to several Italian rivers, located in the Marche administrative district in Central Italy (∽10000km2), in which we quantitatively assess the effects of alternative environmental flow scenarios on the existing hydropower network and on two fish species that are quite abundant in the study area (i.e., Leuciscus cephalus cabeda and Barbus barbus plebejus), will be presented and discussed. The proposed analysis, which can be easily adapted to different riparian habitats and hydrological contexts, is a useful tool to guide the

  12. Biomonitors of urban air pollution: Magnetic studies and SEM observations of corticolous foliose and microfoliose lichens and their suitability for magnetic monitoring

    International Nuclear Information System (INIS)

    Chaparro, Marcos A.E.; Lavornia, Juan M.; Chaparro, Mauro A.E.; Sinito, Ana M.

    2013-01-01

    This study explored the suitability of available lichen species as air pollution biomonitors and assessed their potential for magnetic monitoring in cities. Several lichens on tree bark were collected in urban and industrial sites from Tandil city, as well as control sites. The results showed that magnetite-like minerals were the main magnetic carriers in all sites and samples. However, the concentration varied between clean and polluted sites. In addition, magnetic-grain size-distribution showed clear differences between sites. Observations by scanning electron microscopy showed different particles in a variety of shapes and grain sizes; moreover, the presence of iron oxides and several toxic elements was detected by energy dispersive spectroscopy analysis. Although eleven lichen species were identified that appeared suitable for use as air-pollution monitors, three of them, Parmotrema pilosum, Punctelia hipoleucites and Dirinaria picta, occurred more frequently in the area, thus constituting appropriate species for future monitoring in the study area. - Highlights: ► Magnetite-like minerals are the main carriers in lichen samples. ► Magnetic concentration and grain sizes vary between polluted and control sites. ► Different pollution loads were classified from pcoorda and K-means clustering analysis. ► Parmotrema pilosum, Punctelia hipoleucites and Dirinaria picta appear to be suitable air pollution monitors. - Lichen species are airborne pollutant collectors that are well-distributed in some urban areas and allow effective magnetic monitoring at low cost in cities.

  13. Additional media studies for site suitability criteria

    International Nuclear Information System (INIS)

    Donich, T.R.; Kaufman, A.M.; Sauter, G.D.; Steinborn, T.L.; Towse, D.F.

    1978-01-01

    Site suitability studies have been made previously at LLL on bedded salt and shale. In the present study domed salt, basalt, and crystalline rock are compared with bedded salt and shale and with each other as possible repositories. The level of effort required to develop models for these media that are similar in quality to those available for bedded salt and shale is evaluated. The effort necessary to develop data bases on the physical and chemical properties comparable to that available for bedded salt and shale is also estimated. Each medium is evaluated as a suitable repository environment. The funding necessary for model and data base development is estimated

  14. From Suitable Weak Solutions to Entropy Viscosity

    KAUST Repository

    Guermond, Jean-Luc

    2010-12-16

    This paper focuses on the notion of suitable weak solutions for the three-dimensional incompressible Navier-Stokes equations and discusses the relevance of this notion to Computational Fluid Dynamics. The purpose of the paper is twofold (i) to recall basic mathematical properties of the three-dimensional incompressible Navier-Stokes equations and to show how they might relate to LES (ii) to introduce an entropy viscosity technique based on the notion of suitable weak solution and to illustrate numerically this concept. © 2010 Springer Science+Business Media, LLC.

  15. Suitability of obstetric ultrasonographic parameters in determining ...

    African Journals Online (AJOL)

    Objective: A prospective study aimed at assessing the suitability of Biparietal Diameter (BPD), Femoral Length (FL), Transverse abdominal Diameter (TAD) and Composite value by ultrasonography, in determining foetal or gestational age derived by last menstrual period (LMP) in our environment was undertaken.

  16. SUITABILITY OF CARAMBOLA ( AVERRHOA CARAMBOLA ) FRUIT ...

    African Journals Online (AJOL)

    SUITABILITY OF CARAMBOLA ( AVERRHOA CARAMBOLA ) FRUIT JUICE AS A SUBSTRATE FOR WINE FERMENTATION. ... The analysis of the sugars showed glucose, fructose and sucrose as the predominant sugars present. Vitamin C content was substantially high (35 mg/100 g), but fat content was low (0.25%).

  17. Readability, complexity, and suitability analysis of online lymphedema resources.

    Science.gov (United States)

    Tran, Bao Ngoc N; Singh, Mansher; Lee, Bernard T; Rudd, Rima; Singhal, Dhruv

    2017-06-01

    Over 72% of Americans use online health information to assist in health care decision-making. Previous studies of lymphedema literature have focused only on reading level of patient-oriented materials online. Findings indicate they are too advanced for most patients to comprehend. This, more comprehensive study, expands the previous analysis to include critical elements of health materials beyond readability using assessment tools to report on the complexity and density of data as well as text design, vocabulary, and organization. The top 10 highest ranked websites on lymphedema were identified using the most popular search engine (Google). Website content was analyzed for readability, complexity, and suitability using Simple Measure of Gobbledygook, PMOSE/iKIRSCH, and Suitability Assessment of Materials (SAM), respectively. PMOSE/iKIRSCH and SAM were performed by two independent raters. Fleiss' kappa score was calculated to ensure inter-rater reliability. Online lymphedema literature had a reading grade level of 14.0 (SMOG). Overall complexity score was 6.7 (PMOSE/iKIRSCH) corresponding to "low" complexity and requiring a 8th-12th grade education. Fleiss' kappa score was 80% (P = 0.04, "substantial" agreement). Overall suitability score was 45% (SAM) correlating to the lowest level of "adequate" suitability. Fleiss' kappa score was 76% (P = 0.06, "substantial" agreement). Online resources for lymphedema are above the recommended levels for readability and complexity. The suitability level is barely adequate for the intended audience. Overall, these materials are too sophisticated for the average American adult, whose literacy skills are well documented. Further efforts to revise these materials are needed to improve patient comprehension and understanding. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Land Suitability and Insurance Premiums: A GIS-based Multicriteria Analysis Approach for Sustainable Rice Production

    Directory of Open Access Journals (Sweden)

    Md Monjurul Islam

    2018-05-01

    Full Text Available The purpose of this research is to develop a land suitability model for rice production based on suitability levels and to propose insurance premiums to obtain maximum returns based on the harvest index and subsidy dependence factor for the marginal and moderately suitable lands in the northern part of Bangladesh. A multicriteria analysis was undertaken and a rice land suitability map was developed using geographical information system and analytical hierarchy process. The analysis identified that 22.74% of the area was highly suitable, while 14.86% was marginally suitable, and 28.54% was moderately suitable for rice production. However, 32.67% of the area, which was occupied by water bodies, rivers, forests, and settlements, is permanently not suitable; 1.19% is presently not suitable. To motivate low-quality land owners to produce rice, there is no alternative but to provide protection through crop insurance. We suggest producing rice up to marginally suitable lands to obtain support from insurance. The minimum coverage is marginal coverage (70% to cover the production costs, while the maximum coverage is high coverage (90% to enable a maximum return. This new crop insurance model, based on land suitability can be a rational support for owners of different quality land to increase production.

  19. Suitability of commercial transport for a shift to electric mobility

    DEFF Research Database (Denmark)

    Christensen, Linda; Kveiborg, Ole; Klauenberg, Jens

    2016-01-01

    the travel range of large vans is an important barrier for electrification due to the battery weight and the limitation of 3.5 tonnes gross vehicle weight for driving with a normal driving licence. The rule needs amendments for electric vehicles, as has been done in Germany. The paper recommends EU countries......This paper identifies commercial sectors suitable for a shift to electric mobility. The paper concludes that the construction and the health care service sectors are the most suitable for electric mobility because many vehicles are registered in these sectors and daily mileage is reasonably low....... They should be primary target groups of specific policy measures to promote the use of electric vehicles. Denmark has only had a few incentives to promote the use of commercial electric vehicles. Until now electric vehicles do generally not show economic benefits unless travel distance is high. However, today...

  20. Land use suitability screening for power plant sites in Maryland

    International Nuclear Information System (INIS)

    Dobson, J.E.

    1975-01-01

    Since 1974 Oak Ridge National Laboratory (ORNL) has been engaged in developing an automated procedure for land use suitability screening. The Nuclear Regulatory Commission has funded the project to aid in the selection of power plant sites in Maryland. Its purpose is to identify candidate areas from which specific candidate sites can be chosen for detailed analyses. The ORNL approach assures that certain key variables are examined empirically for every cell in the study region before candidate sites are selected. Each variable is assigned an importance weight and compatibility score based upon its effect on the economic, social, or ecologic costs associated with construction in a given cell. The weighted scores for each variable are aggregated and output as a suitability score for each cell

  1. Projective synchronization based on suitable separation

    International Nuclear Information System (INIS)

    Li Guohui; Xiong Chuan; Sun Xiaonan

    2007-01-01

    A new approach for constructing a projective-synchronized chaotic slave system is proposed in this paper. This method is based on suitable separation by decomposing the system as the linear part and the nonlinear one. From matrix measure theory, some simple but efficient criteria are derived for projective synchronization of chaotic system. Numerical simulations for the Lorenz system show that this control method works very well

  2. Identification of suitable areas for the occurrence of Rift Valley fever outbreaks in Spain using a multiple criteria decision framework.

    Science.gov (United States)

    Sánchez-Vizcaíno, Fernando; Martínez-López, Beatriz; Sánchez-Vizcaíno, José Manuel

    2013-07-26

    Rift Valley fever (RVF) is a mosquito-borne viral disease that may produce a considerable impact on the economy in affected countries. In the last decades, the geographic distribution of RVF virus has increased including most of the countries in Africa, Arabia Saudi and Yemen. This situation has raised the concerns regarding its potential introduction in the European Union (EU) countries where the high number of susceptible species and competent vectors may contribute to the spread of the disease and challenge its rapid control. Thus, the identification of the areas and time periods with highest suitability for RVF outbreak occurrence would be useful for improving the early detection and rapid response of the disease into free countries. The objective of this study was to identify suitable areas for the occurrence of RVF outbreaks in Spain using a multiple criteria decision making model based on weighted linear combination of factors in geographical information systems (GIS). To the best of the author's knowledge this is the first comprehensive GIS-based framework that provides risk maps for RVF suitability in an EU country. Spanish zones with the highest suitability for RVF were concentrated in the regions of Extremadura, south-western Castile and Leon, eastern Galicia, Asturias, Cantabria, Basque Country, northern-central and southern region of Andalusia and in the Balearic Islands. October and May were the most suitable months for RVF outbreak occurrence. Methods and results presented here may be useful to target risk-based surveillance strategies and to more cost-effectively control potential RVFV incursions into Spain. Copyright © 2013 Elsevier B.V. All rights reserved.

  3. Present habitat suitability for Anopheles atroparvus (Diptera, Culicidae and its coincidence with former malaria areas in mainland Portugal

    Directory of Open Access Journals (Sweden)

    César Capinha

    2009-05-01

    Full Text Available Malaria was a major health problem in the first half of the 20th Century in mainland Portugal. Nowadays, although the disease is no longer endemic, there is still the risk of future endemic infections due to the continuous occurrence of imported cases and the possibility of transmission in the country by Anopheles atroparvus Van Thiel, 1927. Since vector abundance constitute one of the foremost factors in malaria transmission, we have created several habitat suitability models to describe this vector species’ current distribution. Three different correlative models; namely (i a multilayer perceptron artificial neural network (MLP-ANN; (ii binary logistic regression (BLR; and (iii Mahalanobis distance were used to combine the species records with a set of five environmental predictors. Kappa coefficient values from k-fold cross-validation records showed that binary logistic regression produced the best predictions, while the other two models also produced acceptable results. Therefore, in order to reduce uncertainty, the three suitability models were combined. The resulting model identified high suitability for An. atroparvus in the majority of the country with exception of the northern and central coastal areas. Malaria distribution during the last endemic period in the country was also compared with the combined suitability model, and a high degree of spatial agreement was obtained (kappa = 0.62. It was concluded that habitat suitability for malaria vectors can constitute valuable information on the assessment of several spatial attributes of the disease. In addition, the results suggest that the spatial distribution of An. atroparvus in the country remains very similar to the one known about seven decades ago.

  4. Deep-Sea Soft Coral Habitat Suitability

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Deep-sea corals, also known as cold water corals, create complex communities that provide habitat for a variety of invertebrate and fish species, such as grouper,...

  5. Deep-Sea Stony Coral Habitat Suitability

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — Deep-sea corals, also known as cold water corals, create complex communities that provide habitat for a variety of invertebrate and fish species, such as grouper,...

  6. Habitat suitability models of mountain ungulates: identifying potential areas for conservation

    Czech Academy of Sciences Publication Activity Database

    Paudel, Prakash K.; Hais, M.; Kindlmann, Pavel

    2015-01-01

    Roč. 54, apr (2015), s. 37 ISSN 1021-5506 R&D Projects: GA MŠk(CZ) LO1415; GA MŠk LC06073; GA ČR GB14-36098G Institutional support: RVO:67179843 Keywords : capricornis thar * habitat model * Midhills * Muntiacus muntjak * Naemorhedus goral * Nepal Subject RIV: EH - Ecology, Behaviour Impact factor: 0.885, year: 2015

  7. Tree-growth analyses to estimate tree species' drought tolerance.

    Science.gov (United States)

    Eilmann, Britta; Rigling, Andreas

    2012-02-01

    Climate change is challenging forestry management and practices. Among other things, tree species with the ability to cope with more extreme climate conditions have to be identified. However, while environmental factors may severely limit tree growth or even cause tree death, assessing a tree species' potential for surviving future aggravated environmental conditions is rather demanding. The aim of this study was to find a tree-ring-based method suitable for identifying very drought-tolerant species, particularly potential substitute species for Scots pine (Pinus sylvestris L.) in Valais. In this inner-Alpine valley, Scots pine used to be the dominating species for dry forests, but today it suffers from high drought-induced mortality. We investigate the growth response of two native tree species, Scots pine and European larch (Larix decidua Mill.), and two non-native species, black pine (Pinus nigra Arnold) and Douglas fir (Pseudotsuga menziesii Mirb. var. menziesii), to drought. This involved analysing how the radial increment of these species responded to increasing water shortage (abandonment of irrigation) and to increasingly frequent drought years. Black pine and Douglas fir are able to cope with drought better than Scots pine and larch, as they show relatively high radial growth even after irrigation has been stopped and a plastic growth response to drought years. European larch does not seem to be able to cope with these dry conditions as it lacks the ability to recover from drought years. The analysis of trees' short-term response to extreme climate events seems to be the most promising and suitable method for detecting how tolerant a tree species is towards drought. However, combining all the methods used in this study provides a complete picture of how water shortage could limit species.

  8. Bounding species distribution models

    Directory of Open Access Journals (Sweden)

    Thomas J. STOHLGREN, Catherine S. JARNEVICH, Wayne E. ESAIAS,Jeffrey T. MORISETTE

    2011-10-01

    Full Text Available Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for “clamping” model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART and maximum entropy (Maxent models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5: 642–647, 2011].

  9. Bounding Species Distribution Models

    Science.gov (United States)

    Stohlgren, Thomas J.; Jarnevich, Cahterine S.; Morisette, Jeffrey T.; Esaias, Wayne E.

    2011-01-01

    Species distribution models are increasing in popularity for mapping suitable habitat for species of management concern. Many investigators now recognize that extrapolations of these models with geographic information systems (GIS) might be sensitive to the environmental bounds of the data used in their development, yet there is no recommended best practice for "clamping" model extrapolations. We relied on two commonly used modeling approaches: classification and regression tree (CART) and maximum entropy (Maxent) models, and we tested a simple alteration of the model extrapolations, bounding extrapolations to the maximum and minimum values of primary environmental predictors, to provide a more realistic map of suitable habitat of hybridized Africanized honey bees in the southwestern United States. Findings suggest that multiple models of bounding, and the most conservative bounding of species distribution models, like those presented here, should probably replace the unbounded or loosely bounded techniques currently used [Current Zoology 57 (5): 642-647, 2011].

  10. Modeling habitat suitability of the invasive clam Corbicula fluminea in a Neotropical shallow lagoon, southern Brazil

    Directory of Open Access Journals (Sweden)

    T. C. L. Silveira

    Full Text Available Abstract This study aimed to model the habitat suitability for an invasive clam Corbicula fluminea in a coastal shallow lagoon in the southern Neotropical region (–30.22, –50.55. The lagoon (19km2, maximum deep 2.5m was sampled with an Ekman dredge in an orthogonal matrix comprising 84 points. At each sampling point, were obtained environmental descriptors as depth, organic matter content (OMC, average granulometry (Avgran, and the percentage of sand (Pcsand. Prediction performance of Generalized Linear Models (GLM, Generalized Additive Models (GAM and Boosted Regression Tree (BRT were compared. Also, niche overlapping with other native clam species (Castalia martensi, Neocorbicula limosa and Anodontites trapesialis was examined. A BRT model with 1400 trees was selected as the best model, with cross-validated correlation of 0.82. The relative contributions of predictors were Pcsand-42.6%, OMC-35.8%, Avgran-10.9% and Depth-10.8%. Were identified that C. fluminea occur mainly in sandy sediments with few organic matter, in shallow areas nor by the shore. The PCA showed a wide niche overlap with the native clam species C. martensi, N. limosa and A. trapesialis.

  11. Endangered Species

    Science.gov (United States)

    EPA's Endangered Species Protection Program helps promote recovery of listed species. The ESPP determines if pesticide use in a geographic area may affect any listed species. Find needed limits on pesticide use in Endangered Species Protection Bulletins.

  12. Hydrologic and water-quality rehabilitation of environments for suitable fish habitat

    Science.gov (United States)

    Zhao, C. S.; Yang, S. T.; Xiang, H.; Liu, C. M.; Zhang, H. T.; Yang, Z. L.; Zhang, Y.; Sun, Y.; Mitrovic, S. M.; Yu, Q.; Lim, R. P.

    2015-11-01

    Aquatic ecological rehabilitation is attracting increasing public and research attention, but without knowledge of the responses of aquatic species to their habitats the success of habitat restoration is uncertain. Thus efficient study of species response to habitat, through which to prioritize the habitat factors influencing aquatic ecosystems, is highly important. However many current models have too high requirement for assemblage information and have great bias in results due to consideration of only the species' attribute of presence/absence, abundance or biomass, thus hindering the wider utility of these models. This paper, using fish as a case, presents a framework for identification of high-priority habitat factors based on the responses of aquatic species to their habitats, using presence/absence, abundance and biomass data. This framework consists of four newly developed sub-models aiming to determine weightings for the evaluation of species' contributions to their communities, to quantitatively calculate an integrated habitat suitability index for multi-species based on habitat factors, to assess the suitable probability of habitat factors and to assess the rehabilitation priority of habitat factors. The framework closely links hydrologic, physical and chemical habitat factors to fish assemblage attributes drawn from monitoring datasets on hydrology, water quality and fish assemblages at a total of 144 sites, where 5084 fish were sampled and tested. Breakpoint identification techniques based on curvature in cumulated dominance along with a newly developed weighting calculation model based on theory of mass systems were used to help identify the dominant fish, based on which the presence and abundance of multiple fish were normalized to estimate the integrated habitat suitability index along gradients of various factors, based on their variation with principal habitat factors. Then, the appropriate probability of every principal habitat factor was

  13. A habitat suitability model for Chinese sturgeon determined using the generalized additive method

    Science.gov (United States)

    Yi, Yujun; Sun, Jie; Zhang, Shanghong

    2016-03-01

    The Chinese sturgeon is a type of large anadromous fish that migrates between the ocean and rivers. Because of the construction of dams, this sturgeon's migration path has been cut off, and this species currently is on the verge of extinction. Simulating suitable environmental conditions for spawning followed by repairing or rebuilding its spawning grounds are effective ways to protect this species. Various habitat suitability models based on expert knowledge have been used to evaluate the suitability of spawning habitat. In this study, a two-dimensional hydraulic simulation is used to inform a habitat suitability model based on the generalized additive method (GAM). The GAM is based on real data. The values of water depth and velocity are calculated first via the hydrodynamic model and later applied in the GAM. The final habitat suitability model is validated using the catch per unit effort (CPUEd) data of 1999 and 2003. The model results show that a velocity of 1.06-1.56 m/s and a depth of 13.33-20.33 m are highly suitable ranges for the Chinese sturgeon to spawn. The hydraulic habitat suitability indexes (HHSI) for seven discharges (4000; 9000; 12,000; 16,000; 20,000; 30,000; and 40,000 m3/s) are calculated to evaluate integrated habitat suitability. The results show that the integrated habitat suitability reaches its highest value at a discharge of 16,000 m3/s. This study is the first to apply a GAM to evaluate the suitability of spawning grounds for the Chinese sturgeon. The study provides a reference for the identification of potential spawning grounds in the entire basin.

  14. Proceedings of a workshop on fish habitat suitability index models

    Science.gov (United States)

    Terrell, James W.

    1984-01-01

    One of the habitat-based methodologies for impact assessment currently in use by the U.S. Fish and Wildlife Service is the Habitat Evaluation Procedures (HEP) (U.S. Fish and Wildlife Service 1980). HEP is based on the assumption that the quality of an area as wildlife habitat at a specified target year can be described by a single number, called a Habitat Suitability Index (HSI). An HSI of 1.0 represents optimum habitat: an HSI of 0.0 represents unsuitable habitat. The verbal or mathematical rules by which an HSI is assigned to an area are called an HSI model. A series of Habitat Suitability Index (HSI) models, described by Schamberger et al. (1982), have been published to assist users in applying HEP. HSI model building approaches are described in U.S. Fish and Wildlife Service (1981). One type of HSI model described in detail requires the development of Suitability Index (SI) graphs for habitat variables believed to be important for the growth, survival, standing crop, or other measure of well-being for a species. Suitability indices range from 0 to 1.0, with 1.0 representing optimum conditions for the variable. When HSI models based on suitability indices are used, habitat variable values are measured, or estimated, and converted to SI's through the use of a Suitability Index graph for each variable. Individual SI's are aggregated into an HSI. Standard methods for testing this type of HSI model did not exist at the time the studies reported in this document were performed. A workshop was held in Fort Collins, Colorado, February 14-15, 1983, that brought together biologists experienced in the use, development, and testing of aquatic HSI models, in an effort to address the following objectives: (1) review the needs of HSI model users; (2) discuss and document the results of aquatic HSI model tests; and (3) provide recommendations for the future development, testing, modification, and use of HSI models. Individual presentations, group discussions, and group

  15. BLM Colorado Wild and Scenic Rivers Line Features (Suitable/Eligible)

    Data.gov (United States)

    Department of the Interior — KMZ File Format –- This line feature class represents the segments identified as eligible or suitable for Wild and Scenic River designation. These segments are part...

  16. The suitability of quality-of-life questionnaires for psoriasis research - A systematic literature review

    NARCIS (Netherlands)

    de Korte, John; Mombers, Femke M. C.; Sprangers, Mirjam A. G.; Bos, Jan D.

    2002-01-01

    Objective: To critically appraise the suitability of current quality-of-life (QOL) questionnaires for psoriasis research. Data Sources: Computerized searches of 5 bibliographic databases. Questionnaire Selection: Predefined criteria were used to identify QOL questionnaires in dermatologic studies.

  17. Are current psychometric tools suitable for measuring outcomes of diabetes education?

    DEFF Research Database (Denmark)

    Eigenmann, C. A.; Colagiuri, R.; Skinner, T. C.

    2009-01-01

    Aims To critically appraise the suitability, validity, reliability, feasibility and sensitivity to change of available psychometric tools for measuring the education outcomes identified in the (Australian) National Consensus on Outcomes and Indicators for Diabetes Patient Education. Methods Poten...

  18. 76 FR 82201 - General Site Suitability Criteria for Nuclear Power Stations

    Science.gov (United States)

    2011-12-30

    ... guidelines in identifying suitable candidate sites for nuclear power stations. The decision that a station... combination and a cost-benefit analysis comparing it with alternative site-plant combinations, as discussed in...

  19. The suitability of several aquatic snails as intermediate hosts for Angiostrongylus cantonensis.

    Science.gov (United States)

    Yousif, F; Lämmler, G

    1975-10-16

    Sixteen species of aquatic snails of four families were tested by quantitative technique under standardized conditions for their suitability as intermediate hosts for Angiostrongylus cantonensis. These species were the planorbid snails Biomphalaria glabrata, Biomphalaria alexandrina, Planorbis planorbis, Planorbis intermixtus, Bulinus truncatus, Bulinus contortus, Bulinus africanus, Bulinus tropicus and Helisoma sp.; the lymnaeid snails Lymnaea natalensis, Lymnaea tomentosa, Lymnaea stagnalis, and Stagnicola elodes; the physid snail Physa acuta (an Egyptian and a German strain) and the ampullariid snails Marisa cornuarietis and Lanistes carinatus. All these snail species proved to be susceptible to infection with A. cantonensis, and first stage larvae reached the infective third stage in all of them. However, the rate and intensity of infection varied with different species. B. glabrata was the most susceptible snail species with a 100% infection rate and an average percentage recovery of third stage larvae of 26.1. This was followed by S. elodes and B. africanus, with a 100% infection rate and an average percentage recovery of third stage larvae of 15.6 and 14.6 respectively. The rest of snail species proved to be less susceptible. For comparative evaluation of the suitability of the various snail species as intermediate hosts of A. cantonensis a "Capacity Index" was determined. This index should provide a useful method for the evaluation of the suitability of various snails as intermediate hosts of nematode parasites under standardized conditions in the laboratory.

  20. Risk assessment for invasive species produces net bioeconomic benefits.

    Science.gov (United States)

    Keller, Reuben P; Lodge, David M; Finnoff, David C

    2007-01-02

    International commerce in live organisms presents a policy challenge for trade globalization; sales of live organisms create wealth, but some nonindigenous species cause harm. To reduce damage, some countries have implemented species screening to limit the introduction of damaging species. Adoption of new risk assessment (RA) technologies has been slowed, however, by concerns that RA accuracy remains insufficient to produce positive net economic benefits. This concern arises because only a small proportion of all introduced species escape, spread, and cause harm (i.e., become invasive), so a RA will exclude many noninvasive species (which provide a net economic benefit) for every invasive species correctly identified. Here, we develop a simple cost:benefit bioeconomic framework to quantify the net benefits from applying species prescreening. Because invasive species are rarely eradicated, and their damages must therefore be borne for long periods, we have projected the value of RA over a suitable range of policy time horizons (10-500 years). We apply the model to the Australian plant quarantine program and show that this RA program produces positive net economic benefits over the range of reasonable assumptions. Because we use low estimates of the financial damage caused by invasive species and high estimates of the value of species in the ornamental trade, our results underestimate the net benefit of the Australian plant quarantine program. In addition, because plants have relatively low rates of invasion, applying screening protocols to animals would likely demonstrate even greater benefits.

  1. Genome-wide methylation profiling identifies an essential role of reactive oxygen species in pediatric glioblastoma multiforme and validates a methylome specific for H3 histone family 3A with absence of G-CIMP/isocitrate dehydrogenase 1 mutation.

    Science.gov (United States)

    Jha, Prerana; Pia Patric, Irene Rosita; Shukla, Sudhanshu; Pathak, Pankaj; Pal, Jagriti; Sharma, Vikas; Thinagararanjan, Sivaarumugam; Santosh, Vani; Suri, Vaishali; Sharma, Mehar Chand; Arivazhagan, Arimappamagan; Suri, Ashish; Gupta, Deepak; Somasundaram, Kumaravel; Sarkar, Chitra

    2014-12-01

    Pediatric glioblastoma multiforme (GBM) is rare, and there is a single study, a seminal discovery showing association of histone H3.3 and isocitrate dehydrogenase (IDH)1 mutation with a DNA methylation signature. The present study aims to validate these findings in an independent cohort of pediatric GBM, compare it with adult GBM, and evaluate the involvement of important functionally altered pathways. Genome-wide methylation profiling of 21 pediatric GBM cases was done and compared with adult GBM data (GSE22867). We performed gene mutation analysis of IDH1 and H3 histone family 3A (H3F3A), status evaluation of glioma cytosine-phosphate-guanine island methylator phenotype (G-CIMP), and Gene Ontology analysis. Experimental evaluation of reactive oxygen species (ROS) association was also done. Distinct differences were noted between methylomes of pediatric and adult GBM. Pediatric GBM was characterized by 94 hypermethylated and 1206 hypomethylated cytosine-phosphate-guanine (CpG) islands, with 3 distinct clusters, having a trend to prognostic correlation. Interestingly, none of the pediatric GBM cases showed G-CIMP/IDH1 mutation. Gene Ontology analysis identified ROS association in pediatric GBM, which was experimentally validated. H3F3A mutants (36.4%; all K27M) harbored distinct methylomes and showed enrichment of processes related to neuronal development, differentiation, and cell-fate commitment. Our study confirms that pediatric GBM has a distinct methylome compared with that of adults. Presence of distinct clusters and an H3F3A mutation-specific methylome indicate existence of epigenetic subgroups within pediatric GBM. Absence of IDH1/G-CIMP status further indicates that findings in adult GBM cannot be simply extrapolated to pediatric GBM and that there is a strong need for identification of separate prognostic markers. A possible role of ROS in pediatric GBM pathogenesis is demonstrated for the first time and needs further evaluation. © The Author(s) 2014

  2. Monazite as a suitable actinide waste form

    Energy Technology Data Exchange (ETDEWEB)

    Schlenz, Hartmut; Heuser, Julia; Schmitz, Stephan; Bosbach, Dirk [Forschungszentrum Juelich GmbH (Germany). Inst. fuer Energie und Klimaforschung (IEK), Nukleare Entsorgung und Reaktorsicherheit (IEK-6); Neumann, Andreas [Forschungszentrum Juelich GmbH (Germany). Inst. fuer Energie und Klimaforschung (IEK), Nukleare Entsorgung und Reaktorsicherheit (IEK-6); RWTH Aachen Univ. (Germany). Inst. for Crystallography

    2013-03-01

    The conditioning of radioactive waste from nuclear power plants and in some countries even of weapons plutonium is an important issue for science and society. Therefore the research on appropriate matrices for the immobilization of fission products and actinides is of great interest. Beyond the widely used borosilicate glasses, ceramics are promising materials for the conditioning of actinides like U, Np, Pu, Am, and Cm. Monazite-type ceramics with general composition LnPO{sub 4} (Ln = La to Gd) and solid solutions of monazite with cheralite or huttonite represent important materials in this field. Monazite appears to be a promising candidate material, especially because of its outstanding properties regarding radiation resistance and chemical durability. This article summarizes the most recent results concerning the characterization of monazite and respective solid solutions and the study of their chemical, thermal, physical and structural properties. The aim is to demonstrate the suitability of monazite as a secure and reliable waste form for actinides. (orig.)

  3. The suitability of internal versus external successors

    DEFF Research Database (Denmark)

    Boyd, Britta; Royer, Susanne

    2012-01-01

    Understanding knowledge transfer in family firm succession is important for the survival of family firms. Previous research has begun to explore the suitability of internal versus external successor in family firms with regard to relevant knowledge types. This paper builds on the contingency model...... of family business succession in order to understand when family successors are preferred because of their family-specific experiential knowledge. A case study analysis from the German-Danish border region explores how a family firm has used internal successors for the last 12 successions. We argue...... that in industries where tacit knowledge forms the basis for competitive advantage, the use of internal successors can help family firms excel after a transition of power has occurred. Theoretical and practical implications are discussed to enhance the long-term perspective for family businesses....

  4. Species distribution modeling in regions of high need and limited data: waterfowl of China

    Science.gov (United States)

    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

  5. Land Suitability Assessment And Precision Farming Prospects For ...

    African Journals Online (AJOL)

    The soils on the farm were sampled and profiles classified using South African Binomial system of soil classification. The farm was divided into suitability classes of highly suitable (S1), suitable (S2), and unsuitable (N1), and permanently unsuitable (N2) classes. Maize-soybean suitability maps were produced based on soil ...

  6. Habitat suitability models for cavity-nesting birds in a postfire landscape

    Science.gov (United States)

    Robin E. Russell; Victoria A. Saab; Jonathan G. Dudley

    2007-01-01

    Models of habitat suitability in postfire landscapes are needed by land managers to make timely decisions regarding postfire timber harvest and other management activities. Many species of cavity-nesting birds are dependent on postfire landscapes for breeding and other aspects of their life history and are responsive to postfire management activities (e.g., timber...

  7. A test of the habitat suitability model for Merriam's wild turkeys

    Science.gov (United States)

    Mark A. Rumble; Stanley H. Anderson

    1996-01-01

    An important research area regarding the wild turkey (Meleagris gallopavo) is development of sound habitat models. Habitat models provide standardized methods to quantify wild turkey habitat and stimulate new research hypotheses. Habitat suitability index (HSI) models show species-habitat relationships on a scale of O-l, with 1 being optimum. A...

  8. A methodology for evaluating land suitability for medicinal plants at a regional level

    Directory of Open Access Journals (Sweden)

    Marco Barbaro

    2011-12-01

    Full Text Available Before introducing a new crop in an area, such as medicinal plant species, crop-land suitability analysis is a prerequisite to achieve an optimum exploitation of the available land resources for a sustainable agricultural production. To evaluate the land suitability it is important to take into account the habitats of the plant species. Moreover, agronomic, logistic and product quality aspects have to be considered. The importance of these aspects changes according to the stakeholders: the local government is more involved in supporting environmental suitability and production sustainability, farmers need areas which satisfy agronomic and logistic requirements, while industry is interested in the quality of production. A methodology was developed and implemented to create suitability maps for medicinal plants. Because of the generally limited information about medicinal plant adaptation, a simple methodology, based on a priori information has been developed, based on three different criteria: i environmental suitability (point of view of local government; ii agronomic, productivity and logistic suitability (point of view of the farmer; iii quality suitability (point of view of industry. For each of the three criteria, a specific macro-indicator, based on land characteristics, was calculated using membership functions. Here, a methodology to create maps for the introduction of such species was developed and implemented. This methodology can be repeated by command scripts in an easy-to-use freeware GIS. The structure of the evaluation model can be easily adapted to consider more detailed land information like climate and soil. The methodology (implemented by scripts in a freeware GIS, can be easily repeated and adapted for other situations.

  9. Evaluation of Limiting Climatic Factors and Simulation of a Climatically Suitable Habitat for Chinese Sea Buckthorn.

    Directory of Open Access Journals (Sweden)

    Guoqing Li

    Full Text Available Chinese sea buckthorn (Hippophae rhamnoides subsp. sinensis has considerable economic potential and plays an important role in reclamation and soil and water conservation. For scientific cultivation of this species across China, we identified the key climatic factors and explored climatically suitable habitat in order to maximize survival of Chinese sea buckthorn using MaxEnt and GIS tools, based on 98 occurrence records from herbarium and publications and 13 climatic factors from Bioclim, Holdridge life zone and Kria' index variables. Our simulation showed that the MaxEnt model performance was significantly better than random, with an average test AUC value of 0.93 with 10-fold cross validation. A jackknife test and the regularized gain change, which were applied to the training algorithm, showed that precipitation of the driest month (PDM, annual precipitation (AP, coldness index (CI and annual range of temperature (ART were the most influential climatic factors in limiting the distribution of Chinese sea buckthorn, which explained 70.1% of the variation. The predicted map showed that the core of climatically suitable habitat was distributed from the southwest to northwest of Gansu, Ningxia, Shaanxi and Shanxi provinces, where the most influential climate variables were PDM of 1.0-7.0 mm, AP of 344.0-1089.0 mm, CI of -47.7-0.0°C, and ART of 26.1-45.0°C. We conclude that the distribution patterns of Chinese sea buckthorn are related to the northwest winter monsoon, the southwest summer monsoon and the southeast summer monsoon systems in China.

  10. Selecting suitable enclosures for digitally printed materials

    International Nuclear Information System (INIS)

    Burge, D; Rima, L

    2010-01-01

    It cannot be assumed that storage enclosures considered safe for traditionally printed images and documents are suitable for modern, digitally printed materials. In this project, a large variety of digital print types were tested using a modified version of the ISO 18916 Imaging materials-Processed imaging materials-Photographic activity test for enclosure materials standard to assess the risk to digital prints by paper enclosures known to be inert or reactive with traditional photographic prints. The types of enclosures tested included buffered and non-buffered cotton papers, and groundwood paper. In addition, qualitative filter paper that had been wetted and dried with either an acidic or basic solution was also tested to determine the effects of enclosure pH on digitally printed materials. It was determined that, in general, digital prints tended to be less reactive with various enclosure types than traditional prints. Digital prints were most sensitive to paper that contained groundwood. The enclosure reactivity test results were then integrated with previous published work on the tendencies of various enclosure types to abrade, ferrotype, or block to digital prints in order to create a comprehensive set of recommendations for digital print storage enclosures.

  11. Perspective in site-suitability modelling

    International Nuclear Information System (INIS)

    Chartier, M.

    1989-01-01

    The Steering Committee for Nuclear Energy of the OECD-Nuclear Energy Agency decided in April 1981 to set up a Co-ordinated Research and Environmental Surveillance Programme relevant to sea disposal of radioactive waste (CRESP) with the objective of reinforcing the scientific basis of future assessments of the continued suitability of the North-East Atlantic site to be made under the NEA Multilateral Consultation and Surveillance Mechanism. A major component of the initial CRESP plan was the development of a site-specific model to predict radionuclide transfer rates and patterns in the marine environment. A new general approach to the design of such a site-specific model is discussed.Although this approach originates partly from methodologies presented in GESAMP partly from an approach put forward within the NEA Seabed Working Group/Geochemical and Physical Oceanography Task Group and partly from methods previously agreed by the CRESP Modelling Task Group, the modelling philosophy developed in the text expressed the personal viewpoint of the author. This text aims to state the present methods of modelling the marine transfer of radionuclides and to anticipate modelling strategies which may be adopted in the future (in France for example), but it does not necessarily meet present NEA viewpoints and the philosophy of other CRESP participating countries

  12. Suitability of amphibians and reptiles for translocation.

    Science.gov (United States)

    Germano, Jennifer M; Bishop, Phillip J

    2009-02-01

    Translocations are important tools in the field of conservation. Despite increased use over the last few decades, the appropriateness of translocations for amphibians and reptiles has been debated widely over the past 20 years. To provide a comprehensive evaluation of the suitability of amphibians and reptiles for translocation, we reviewed the results of amphibian and reptile translocation projects published between 1991 and 2006. The success rate of amphibian and reptile translocations reported over this period was twice that reported in an earlier review in 1991. Success and failure rates were independent of the taxonomic class (Amphibia or Reptilia) released. Reptile translocations driven by human-wildlife conflict mitigation had a higher failure rate than those motivated by conservation, and more recent projects of reptile translocations had unknown outcomes. The outcomes of amphibian translocations were significantly related to the number of animals released, with projects releasing over 1000 individuals being most successful. The most common reported causes of translocation failure were homing and migration of introduced individuals out of release sites and poor habitat. The increased success of amphibian and reptile translocations reviewed in this study compared with the 1991 review is encouraging for future conservation projects. Nevertheless, more preparation, monitoring, reporting of results, and experimental testing of techniques and reintroduction questions need to occur to improve translocations of amphibians and reptiles as a whole.

  13. Midyear FY 1983 Richton Dome screening and suitability review

    International Nuclear Information System (INIS)

    1983-08-01

    The NWTS screening of Gulf Coast salt domes for suitable nuclear waste repository sites identified three candidate domes. These are, in order of preference, Richton Dome, Mississippi; Vacherie Dome, Louisiana; and Cypress Creek Dome, Mississippi. A qualitative review of information obtained since this initial ranking gives no basis for revising this ranking. A review of unresolved siting issues at Richton Dome shows siting concerns presently center on the geologic stability and hydrology suitability of Richton Dome and vicinity. Tectonic concerns of regional uplift and faulting are examined, as are salt tectonic concerns related to salt dome movement and dissolution. Both geologic and geodetic data suggest the Mississippi Salt Basin is experiencing uplift. However, uplift rates estimated from geologic evidence are an order of magnitude less than rates estimated from releveling data. Faults are present throughout much of the basin, and most are the result of horizontal and vertical movements of the Louann Salt during the Cretaceous and Early Tertiary. Several faults are present in the sediments surrounding Richton Dome, but current evidence suggests no movements have occurred since the Miocene. Richton Dome's hydrologic suitability is considered in analysis of the regional ground-water flow system. A three-dimensional, ground-water flow model has been utilized to calculate travel paths and travel times for releases of contaminants from various points on the dome. Based on model analyses, a release at repository level would take nearly 39,000 years to reach the upper aquifer and would eventually discharge into the Leaf River or upper reaches of the Pascagoula River over 50 km from the dome. This estimate of travel time greatly exceeds the minimum 1000 year travel time required by proposed Department of Energy (DOE) guidelines. 76 references

  14. Environmental suitability for Lutzomyia (Nyssomyia) whitmani (Diptera: Psychodidae: Phlebotominae) and the occurrence of American cutaneous leishmaniasis in Brazil.

    Science.gov (United States)

    da Costa, Simone Miranda; Cordeiro, José Luís Passos; Rangel, Elizabeth Ferreira

    2018-03-07

    Leishmaniasis represents an important public health problem in Brazil. The continuous process of urbanization and expansion of human activities in forest areas impacts natural habitats, modifying the ecology of some species of Leishmania, as well as its vectors and reservoirs and, consequently, changes the epidemiological pattern that contributes to the expansion of American cutaneous leishmaniasis in Brazil. Here, we discuss Lutzomyia (Nyssomyia) whitmani, the main vector of ACL, transmitting two dermotropic Leishmania species including Leishmania (Viannia) braziliensis and Leishmania (V.) shawi. We used the maximum entropy niche modelling approach (MaxEnt) to evaluate the environmental suitability of L. (N.) whitmani and the transmission of ACL in Brazil, in addition to designing models for a future scenario of climate change. MaxEnt was used under the "auto-features" mode and the default settings, with 100-fold repetition (bootstrap). The logistic output was used with higher values in the habitat suitability map, representing more favourable conditions for the occurrence of L. (N.) whitmani and human cases of ACL. Two models were developed: the Lutzomyia (N.) whitmani model (LWM) and the American cutaneous leishmaniasis model (ACLM). LWM identified the species "preferential habitat" included regions with moderate annual precipitation (AP) between 1000-1600 mm, intermediate vegetation density (NDVI) values, mean temperature of the coldest quarter (MTCQ), between 15-21 °C, and annual mean temperature (AMT), between 19-24 °C. ACLM indicates that ACL is strongly associated with areas of intermediate density vegetation, areas with AP between 800-1200 mm, MTCQ above 16 °C and AMT below 23 °C. The models generated for L. (N.) whitmani and ACL indicated a satisfactory predictive capacity. Future projections of LWM indicate an expansion of climatic suitability for L. (N.) whitmani for the northern and southern regions of Brazil. Future projections of ACL indicate the

  15. Modeling mountain pine beetle habitat suitability within Sequoia National Park

    Science.gov (United States)

    Nguyen, Andrew

    Understanding significant changes in climate and their effects on timber resources can help forest managers make better decisions regarding the preservation of natural resources and land management. These changes may to alter natural ecosystems dependent on historical and current climate conditions. Increasing mountain pine beetle (MBP) outbreaks within the southern Sierra Nevada are the result of these alterations. This study better understands MPB behavior within Sequoia National Park (SNP) and model its current and future habitat distribution. Variables contributing to MPB spread are vegetation stress, soil moisture, temperature, precipitation, disturbance, and presence of Ponderosa (Pinus ponderosa) and Lodgepole (Pinus contorta) pine trees. These variables were obtained using various modeled, insitu, and remotely sensed sources. The generalized additive model (GAM) was used to calculate the statistical significance of each variable contributing to MPB spread and also created maps identifying habitat suitability. Results indicate vegetation stress and forest disturbance to be variables most indicative of MPB spread. Additionally, the model was able to detect habitat suitability of MPB with a 45% accuracy concluding that a geospatial driven modeling approach can be used to delineate potential MPB spread within SNP.

  16. The Protein Identifier Cross-Referencing (PICR service: reconciling protein identifiers across multiple source databases

    Directory of Open Access Journals (Sweden)

    Leinonen Rasko

    2007-10-01

    Full Text Available Abstract Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR service, a web application that provides interactive and programmatic (SOAP and REST access to a mapping algorithm that uses the UniProt Archive (UniParc as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV or Microsoft Excel (XLS files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR

  17. Pastoral suitability driven by future climate change along the Apennines

    Directory of Open Access Journals (Sweden)

    Camilla Dibari

    2015-09-01

    Full Text Available This work aims at evaluating the impacts of climate change on pastoral resources located along the Apennines chain. To this end, random forest machine learning model was first calibrated for the present period and then applied to future conditions, as projected by HadCM3 general circulation model, in order to simulate possible spatial variation/shift of pastoral areas in two time slices (centred on 2050 and 2080 under A2 and B2 SRES scenarios. Pre-existent spatial database, namely Corine land cover map and WorldClim, were integrated and harmonised in a GIS environment in order to extract climate variables (mean seasonal precipitation, mean maximum temperature of the warmest month and minimum temperature of the coldest month and response variables (presence/absence of pastures to be used as model predictors. Random forest model resulted robust and coherent to simulate pastureland suitability under current climatology (classification accuracy error=19%. Accordingly, results indicated that increases in temperatures coupled with decreases in precipitation, as simulated by HadCM3 in the future, would have impacts of great concern on potential pasture distribution. In the specific, an overall decline of pasturelands suitability is predicted by the middle of the century in both A2 (–46% and B2 (–41% along the entire chain. However, despite alarming reductions in pastures suitability along the northern (–69% and –71% under A2 and B2 scenarios, respectively and central Apennines (–90% under both scenarios by the end of the century, expansions are predicted along the southern areas of the chain (+96% and +105% under A2 and B2 scenarios, respectively. This may be probably due to expansions in pastures dominated by xeric and thermophiles species, which will likely benefit from warmer and drier future conditions predicted in the southern zone of the chain by the HadCM3. Hence, the expected climate, coupled with an increasing abandonment of the

  18. Microsites Matter: Improving the Success of Rare Species Reintroductions.

    Directory of Open Access Journals (Sweden)

    Peter W Dunwiddie

    Full Text Available Our study was undertaken to better understand how to increase the success rates of recovery plantings of a rare hemiparasite, golden paintbrush (Castilleja levisecta-Orobanchaceae. This species is endemic to western Washington and Oregon, USA, and southwestern British Columbia, Canada. Over 5000 golden paintbrush plants were outplanted as plugs in 2007 at six different native prairie sites that were considered to be suitable habitat, based on general evaluations of vegetation and soil conditions. Outplantings were installed at regular intervals along transects up to 1 km long to include a range of conditions occurring at each site. All plantings were re-examined five years later. The patchy distribution of surviving plugs and new recruits within each reintroduction site suggested success is strongly influenced by microsite characteristics. Indicator species analysis of taxa growing in microsites around outplanted golden paintbrush identified species that were positively or negatively associated with paintbrush survival. Species such as Festuca roemeri, Eriophyllum lanatum, and Viola adunca were strong indicators at some sites; non-natives such as Hypochaeris radicata and Teesdalia nudicaulis tended to be frequent negative indicators. Overall, higher richness of native perennial forbs was strongly correlated with both survival and flowering of golden paintbrush, a pattern that may reflect interactions of this hemiparasite with the immediately surrounding plant community. Topographic position also influenced outcomes, with greater survival occurring on mounds and in swales, where soils generally were deeper. Our findings suggest that assessments of site suitability based on vegetation alone, and coarser, site-level assessments that do not characterize heterogeneity at the microsite scale, may not be strong predictors of restoration success over the longer term and in sites with variability in vegetation and soils. By identifying suitable

  19. Delineating probabilistic species pools in ecology and biogeography

    OpenAIRE

    Karger, Dirk Nikolaus; Cord, Anna F; Kessler, Michael; Kreft, Holger; Kühn, Ingolf; Pompe, Sven; Sandel, Brody; Sarmento Cabral, Juliano; Smith, Adam B; Svenning, Jens-Christian; Tuomisto, Hanna; Weigelt, Patrick; Wesche, Karsten

    2016-01-01

    Aim To provide a mechanistic and probabilistic framework for defining the species pool based on species-specific probabilities of dispersal, environmental suitability and biotic interactions within a specific temporal extent, and to show how probabilistic species pools can help disentangle the geographical structure of different community assembly processes. Innovation Probabilistic species pools provide an improved species pool definition based on probabilities in conjuncti...

  20. Confronting species distribution model predictions with species functional traits.

    Science.gov (United States)

    Wittmann, Marion E; Barnes, Matthew A; Jerde, Christopher L; Jones, Lisa A; Lodge, David M

    2016-02-01

    Species distribution models are valuable tools in studies of biogeography, ecology, and climate change and have been used to inform conservation and ecosystem management. However, species distribution models typically incorporate only climatic variables and species presence data. Model development or validation rarely considers functional components of species traits or other types of biological data. We implemented a species distribution model (Maxent) to predict global climate habitat suitability for Grass Carp (Ctenopharyngodon idella). We then tested the relationship between the degree of climate habitat suitability predicted by Maxent and the individual growth rates of both wild (N = 17) and stocked (N = 51) Grass Carp populations using correlation analysis. The Grass Carp Maxent model accurately reflected the global occurrence data (AUC = 0.904). Observations of Grass Carp growth rate covered six continents and ranged from 0.19 to 20.1 g day(-1). Species distribution model predictions were correlated (r = 0.5, 95% CI (0.03, 0.79)) with observed growth rates for wild Grass Carp populations but were not correlated (r = -0.26, 95% CI (-0.5, 0.012)) with stocked populations. Further, a review of the literature indicates that the few studies for other species that have previously assessed the relationship between the degree of predicted climate habitat suitability and species functional traits have also discovered significant relationships. Thus, species distribution models may provide inferences beyond just where a species may occur, providing a useful tool to understand the linkage between species distributions and underlying biological mechanisms.

  1. Mapping grasslands suitable for cellulosic biofuels in the Greater Platte River Basin, United States

    Science.gov (United States)

    Wylie, Bruce K.; Gu, Yingxin

    2012-01-01

    Biofuels are an important component in the development of alternative energy supplies, which is needed to achieve national energy independence and security in the United States. The most common biofuel product today in the United States is corn-based ethanol; however, its development is limited because of concerns about global food shortages, livestock and food price increases, and water demand increases for irrigation and ethanol production. Corn-based ethanol also potentially contributes to soil erosion, and pesticides and fertilizers affect water quality. Studies indicate that future potential production of cellulosic ethanol is likely to be much greater than grain- or starch-based ethanol. As a result, economics and policy incentives could, in the near future, encourage expansion of cellulosic biofuels production from grasses, forest woody biomass, and agricultural and municipal wastes. If production expands, cultivation of cellulosic feedstock crops, such as switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus species), is expected to increase dramatically. The main objective of this study is to identify grasslands in the Great Plains that are potentially suitable for cellulosic feedstock (such as switchgrass) production. Producing ethanol from noncropland holdings (such as grassland) will minimize the effects of biofuel developments on global food supplies. Our pilot study area is the Greater Platte River Basin, which includes a broad range of plant productivity from semiarid grasslands in the west to the fertile corn belt in the east. The Greater Platte River Basin was the subject of related U.S. Geological Survey (USGS) integrated research projects.

  2. Modeling Habitat Suitability of Migratory Birds from Remote Sensing Images Using Convolutional Neural Networks.

    Science.gov (United States)

    Su, Jin-He; Piao, Ying-Chao; Luo, Ze; Yan, Bao-Ping

    2018-04-26

    With the application of various data acquisition devices, a large number of animal movement data can be used to label presence data in remote sensing images and predict species distribution. In this paper, a two-stage classification approach for combining movement data and moderate-resolution remote sensing images was proposed. First, we introduced a new density-based clustering method to identify stopovers from migratory birds’ movement data and generated classification samples based on the clustering result. We split the remote sensing images into 16 × 16 patches and labeled them as positive samples if they have overlap with stopovers. Second, a multi-convolution neural network model is proposed for extracting the features from temperature data and remote sensing images, respectively. Then a Support Vector Machines (SVM) model was used to combine the features together and predict classification results eventually. The experimental analysis was carried out on public Landsat 5 TM images and a GPS dataset was collected on 29 birds over three years. The results indicated that our proposed method outperforms the existing baseline methods and was able to achieve good performance in habitat suitability prediction.

  3. Northern protected areas will become important refuges for biodiversity tracking suitable climates.

    Science.gov (United States)

    Berteaux, Dominique; Ricard, Marylène; St-Laurent, Martin-Hugues; Casajus, Nicolas; Périé, Catherine; Beauregard, Frieda; de Blois, Sylvie

    2018-03-15

    The Northern Biodiversity Paradox predicts that, despite its globally negative effects on biodiversity, climate change will increase biodiversity in northern regions where many species are limited by low temperatures. We assessed the potential impacts of climate change on the biodiversity of a northern network of 1,749 protected areas spread over >600,000 km 2 in Quebec, Canada. Using ecological niche modeling, we calculated potential changes in the probability of occurrence of 529 species to evaluate the potential impacts of climate change on (1) species gain, loss, turnover, and richness in protected areas, (2) representativity of protected areas, and (3) extent of species ranges located in protected areas. We predict a major species turnover over time, with 49% of total protected land area potentially experiencing a species turnover >80%. We also predict increases in regional species richness, representativity of protected areas, and species protection provided by protected areas. Although we did not model the likelihood of species colonising habitats that become suitable as a result of climate change, northern protected areas should ultimately become important refuges for species tracking climate northward. This is the first study to examine in such details the potential effects of climate change on a northern protected area network.

  4. The complete genome sequencing of Prevotella intermedia strain OMA14 and a subsequent fine-scale, intra-species genomic comparison reveal an unusual amplification of conjugative and mobile transposons and identify a novel Prevotella-lineage-specific repeat.

    Science.gov (United States)

    Naito, Mariko; Ogura, Yoshitoshi; Itoh, Takehiko; Shoji, Mikio; Okamoto, Masaaki; Hayashi, Tetsuya; Nakayama, Koji

    2016-02-01

    Prevotella intermedia is a pathogenic bacterium involved in periodontal diseases. Here, we present the complete genome sequence of a clinical strain, OMA14, of this bacterium along with the results of comparative genome analysis with strain 17 of the same species whose genome has also been sequenced, but not fully analysed yet. The genomes of both strains consist of two circular chromosomes: the larger chromosomes are similar in size and exhibit a high overall linearity of gene organizations, whereas the smaller chromosomes show a significant size variation and have undergone remarkable genome rearrangements. Unique features of the Pre. intermedia genomes are the presence of a remarkable number of essential genes on the second chromosomes and the abundance of conjugative and mobilizable transposons (CTns and MTns). The CTns/MTns are particularly abundant in the second chromosomes, involved in its extensive genome rearrangement, and have introduced a number of strain-specific genes into each strain. We also found a novel 188-bp repeat sequence that has been highly amplified in Pre. intermedia and are specifically distributed among the Pre. intermedia-related species. These findings expand our understanding of the genetic features of Pre. intermedia and the roles of CTns and MTns in the evolution of bacteria. © The Author 2015. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

  5. Predicting the impact of climate change on threatened species in UK waters.

    Directory of Open Access Journals (Sweden)

    Miranda C Jones

    Full Text Available Global climate change is affecting the distribution of marine species and is thought to represent a threat to biodiversity. Previous studies project expansion of species range for some species and local extinction elsewhere under climate change. Such range shifts raise concern for species whose long-term persistence is already threatened by other human disturbances such as fishing. However, few studies have attempted to assess the effects of future climate change on threatened vertebrate marine species using a multi-model approach. There has also been a recent surge of interest in climate change impacts on protected areas. This study applies three species distribution models and two sets of climate model projections to explore the potential impacts of climate change on marine species by 2050. A set of species in the North Sea, including seven threatened and ten major commercial species were used as a case study. Changes in habitat suitability in selected candidate protected areas around the UK under future climatic scenarios were assessed for these species. Moreover, change in the degree of overlap between commercial and threatened species ranges was calculated as a proxy of the potential threat posed by overfishing through bycatch. The ensemble projections suggest northward shifts in species at an average rate of 27 km per decade, resulting in small average changes in range overlap between threatened and commercially exploited species. Furthermore, the adverse consequences of climate change on the habitat suitability of protected areas were projected to be small. Although the models show large variation in the predicted consequences of climate change, the multi-model approach helps identify the potential risk of increased exposure to human stressors of critically endangered species such as common skate (Dipturus batis and angelshark (Squatina squatina.

  6. Using Species Distribution Models to Predict Potential Landscape Restoration Effects on Puma Conservation.

    Science.gov (United States)

    Angelieri, Cintia Camila Silva; Adams-Hosking, Christine; Ferraz, Katia Maria Paschoaletto Micchi de Barros; de Souza, Marcelo Pereira; McAlpine, Clive Alexander

    2016-01-01

    A mosaic of intact native and human-modified vegetation use can provide important habitat for top predators such as the puma (Puma concolor), avoiding negative effects on other species and ecological processes due to cascade trophic interactions. This study investigates the effects of restoration scenarios on the puma's habitat suitability in the most developed Brazilian region (São Paulo State). Species Distribution Models incorporating restoration scenarios were developed using the species' occurrence information to (1) map habitat suitability of pumas in São Paulo State, Southeast, Brazil; (2) test the relative contribution of environmental variables ecologically relevant to the species habitat suitability and (3) project the predicted habitat suitability to future native vegetation restoration scenarios. The Maximum Entropy algorithm was used (Test AUC of 0.84 ± 0.0228) based on seven environmental non-correlated variables and non-autocorrelated presence-only records (n = 342). The percentage of native vegetation (positive influence), elevation (positive influence) and density of roads (negative influence) were considered the most important environmental variables to the model. Model projections to restoration scenarios reflected the high positive relationship between pumas and native vegetation. These projections identified new high suitability areas for pumas (probability of presence >0.5) in highly deforested regions. High suitability areas were increased from 5.3% to 8.5% of the total State extension when the landscapes were restored for ≥ the minimum native vegetation cover rule (20%) established by the Brazilian Forest Code in private lands. This study highlights the importance of a landscape planning approach to improve the conservation outlook for pumas and other species, including not only the establishment and management of protected areas, but also the habitat restoration on private lands. Importantly, the results may inform environmental

  7. Selection of suitable sites for NPP in Slovenia (stage 3)

    International Nuclear Information System (INIS)

    Grgic, M.; Fabjan, L.; Premru, U.

    1977-01-01

    Selection of suitable sites for nuclear power plants in Slovenia is considered. This includes the studies of available data on regional and local characteristics specified in general site suitability criteria for NPP. The most suitable selected sites will be included into land use urbanistic planning of Slovenia

  8. Suitable level of suppression in Pinus sylvestris

    Energy Technology Data Exchange (ETDEWEB)

    Hagner, Mats

    1999-10-01

    It is `well known` among Swedish foresters that pine trees need light and cannot grow suppressed. It is also `well known` that old trees that have grown slowly are unable to react with good growth. However, these facts can be questioned in the light of new research as it has been found that thinning reaction is not correlated with age. It is also well known that the commercial value of a pine is closely related to the growth at young age. If the first 20 annual rings close to pith are wide (>3 mm) the log cannot be accepted as first class. This is related to number and size of branches on the young tree and to the features of the juvenile wood. This is to say that a pine must not grow fast when it is small and if this has happened it cannot be cured by artificial debranching or by growing the tree slowly at higher age. Accordingly, young pines should be grown under bigger trees that in their young age were grown under big trees, and so on. Today, when clear cutting is the dominating forest management system, the only way to obtain high quality pine trees is to start the rotation age with stands of very high density. This is of course a very expensive way as dense planting, followed by intensive thinning requires a lot of input. However, if pine is a pioneer species and cannot be grown in multistoried stands, then the economic solution is not present. This was the reason why the annual increment of three pines was measured. They were selected because their different growth pattern showed that old `well known facts` should be revised Working papers 139. 3 refs, 7 figs, 1 tab

  9. A Bayesian spawning habitat suitability model for American shad in southeastern United States rivers

    Science.gov (United States)

    Hightower, Joseph E.; Harris, Julianne E.; Raabe, Joshua K.; Brownell, Prescott; Drew, C. Ashton

    2012-01-01

    Habitat suitability index models for American shad Alosa sapidissima were developed by Stier and Crance in 1985. These models, which were based on a combination of published information and expert opinion, are often used to make decisions about hydropower dam operations and fish passage. The purpose of this study was to develop updated habitat suitability index models for spawning American shad in the southeastern United States, building on the many field and laboratory studies completed since 1985. We surveyed biologists who had knowledge about American shad spawning grounds, assembled a panel of experts to discuss important habitat variables, and used raw data from published and unpublished studies to develop new habitat suitability curves. The updated curves are based on resource selection functions, which can model habitat selectivity based on use and availability of particular habitats. Using field data collected in eight rivers from Virginia to Florida (Mattaponi, Pamunkey, Roanoke, Tar, Neuse, Cape Fear, Pee Dee, St. Johns), we obtained new curves for temperature, current velocity, and depth that were generally similar to the original models. Our new suitability function for substrate was also similar to the original pattern, except that sand (optimal in the original model) has a very low estimated suitability. The Bayesian approach that we used to develop habitat suitability curves provides an objective framework for updating the model as new studies are completed and for testing the model's applicability in other parts of the species' range.

  10. Guidelines for using the Delphi Technique to develop habitat suitability index curves

    Science.gov (United States)

    Crance, Johnie H.

    1987-01-01

    Habitat Suitability Index (SI) curves are one method of presenting species habitat suitability criteria. The curves are often used with the Habitat Evaluation Procedures (HEP) and are necessary components of the Instream Flow Incremental Methodology (IFIM) (Armour et al. 1984). Bovee (1986) described three categories of SI curves or habitat suitability criteria based on the procedures and data used to develop the criteria. Category I curves are based on professional judgment, with 1ittle or no empirical data. Both Category II (utilization criteria) and Category III (preference criteria) curves have as their source data collected at locations where target species are observed or collected. Having Category II and Category III curves for all species of concern would be ideal. In reality, no SI curves are available for many species, and SI curves that require intensive field sampling often cannot be developed under prevailing constraints on time and costs. One alternative under these circumstances is the development and interim use of SI curves based on expert opinion. The Delphi technique (Pill 1971; Delbecq et al. 1975; Linstone and Turoff 1975) is one method used for combining the knowledge and opinions of a group of experts. The purpose of this report is to describe how the Delphi technique may be used to develop expert-opinion-based SI curves.

  11. Neuroprotection by Radical Avoidance: Search for Suitable Agents

    Directory of Open Access Journals (Sweden)

    Rüdiger Hardeland

    2009-12-01

    Full Text Available Neurodegeneration is frequently associated with damage by free radicals. However, increases in reactive oxygen and nitrogen species, which may ultimately lead to neuronal cell death, do not necessarily reflect its primary cause, but can be a consequence of otherwise induced cellular dysfunction. Detrimental processes which promote free radical formation are initiated, e.g., by disturbances in calcium homeostasis, mitochondrial malfunction, and an age-related decline in the circadian oscillator system. Free radicals generated at high rates under pathophysiological conditions are insufficiently detoxified by scavengers. Interventions at the primary causes of dysfunction, which avoid secondary rises in radical formation, may be more efficient. The aim of such approaches should be to prevent calcium overload, to reduce mitochondrial electron dissipation, to support electron transport capacity, and to avoid circadian perturbations. l-Theanine and several amphiphilic nitrones are capable of counteracting excitotoxicity and/or mitochondrial radical formation. Resveratrol seems to promote mitochondrial biogenesis. Mitochondrial effects of leptin include attenuation of electron leakage. Melatonin combines all the requirements mentioned, additionally regulates anti- and pro-oxidant enzymes and is, with few exceptions, very well tolerated. In this review, the perspectives, problems and limits of drugs are compared which may be suitable for reducing the formation of free radicals.

  12. On the identity of the adventive species of Eufriesea Cockerell in the USA: systematics and potential distribution of the coerulescens species group (Hymenoptera, Apidae

    Directory of Open Access Journals (Sweden)

    Victor H. Gonzalez

    2017-04-01

    Full Text Available In the summer of 2010, two male specimens of the neotropical orchid bee genus Eufriesea Cockerell were collected in the Guadalupe Mountains of western Texas and southeastern New Mexico, USA. We tentatively identified them as E. coerulescens (Lepeletier de Saint Fargeau because of the uncertainty surrounding the limits of this taxon and hypothesized that they were members of a persistent bee population, rather than long-distance transient vagrants. The goals of this paper are to clarify the identity of these specimens, assess the species limits of E. coerulescens, and to evaluate suitability of habitats in the USA for this adventive species. Herein, we revise the species in the coerulescens group using morphological features of both sexes and confirm that the specimens of Eufriesea from the USA are E. coerulescens. We recognize the following six species in the coerulescens group: E. coerulescens, E. micheneri Ayala & Engel, E. simillima (Moure & Michener, which is reinstated from synonym with E. coerulescens, and three new species from Mexico (E. barthelli Gonzalez & Griswold, sp. n., E. engeli Gonzalez & Griswold, sp. n., and E. oliveri Gonzalez & Griswold, sp. n.. To facilitate the identification of these taxa, we present a fully illustrated account of the species, comparative diagnoses, descriptions, and an updated key to all Mexican species of Eufriesea. Our analyses using species distribution modelling show an absence of suitable habitat for E. coerulescens in western Texas and southeastern New Mexico, thus favoring the long-distance dispersal hypothesis. The analyses also suggest high suitability of habitats across the Caribbean and some areas in Florida, as well as in other regions in Mexico and Central America. We discuss the implications of these results and compare them with the predicted distribution available for the other two known adventive orchid bee species in the USA.

  13. Meta-analysis of the relative sensitivity of semi-natural vegetation species to ozone

    International Nuclear Information System (INIS)

    Hayes, F.; Jones, M.L.M.; Mills, G.; Ashmore, M.

    2007-01-01

    This study identified 83 species from existing publications suitable for inclusion in a database of sensitivity of species to ozone (OZOVEG database). An index, the relative sensitivity to ozone, was calculated for each species based on changes in biomass in order to test for species traits associated with ozone sensitivity. Meta-analysis of the ozone sensitivity data showed a wide inter-specific range in response to ozone. Some relationships in comparison to plant physiological and ecological characteristics were identified. Plants of the therophyte lifeform were particularly sensitive to ozone. Species with higher mature leaf N concentration were more sensitive to ozone than those with lower leaf N concentration. Some relationships between relative sensitivity to ozone and Ellenberg habitat requirements were also identified. In contrast, no relationships between relative sensitivity to ozone and mature leaf P concentration, Grime's CSR strategy, leaf longevity, flowering season, stomatal density and maximum altitude were found. The relative sensitivity of species and relationships with plant characteristics identified in this study could be used to predict sensitivity to ozone of untested species and communities. - Meta-analysis of the relative sensitivity of semi-natural vegetation species to ozone showed some relationships with physiological and ecological characteristics

  14. Radiograph identifying means

    International Nuclear Information System (INIS)

    Sheldon, A.D.

    1983-01-01

    A flexible character-indentable plastics embossing tape is backed by and bonded to a lead strip, not more than 0.025 inches thick, to form a tape suitable for identifying radiographs. The lead strip is itself backed by a relatively thin and flimsy plastics or fabric strip which, when removed, allows the lead plastic tape to be pressure-bonded to the surface to be radiographed. A conventional tape-embossing gun is used to indent the desired characters in succession into the lead-backed tape, without necessarily severing the lead; and then the backing strip is peeled away to expose the layer of adhesive which pressure-bonds the indented tape to the object to be radiographed. X-rays incident on the embossed tape will cause the raised characters to show up dark on the subsequently-developed film, whilst the raised side areas will show up white. Each character will thus stand out on the developed film. (author)

  15. Climate change likely to reduce orchid bee abundance even in climatic suitable sites.

    Science.gov (United States)

    Faleiro, Frederico Valtuille; Nemésio, André; Loyola, Rafael

    2018-06-01

    Studies have tested whether model predictions based on species' occurrence can predict the spatial pattern of population abundance. The relationship between predicted environmental suitability and population abundance varies in shape, strength and predictive power. However, little attention has been paid to the congruence in predictions of different models fed with occurrence or abundance data, in particular when comparing metrics of climate change impact. Here, we used the ecological niche modeling fit with presence-absence and abundance data of orchid bees to predict the effect of climate change on species and assembly level distribution patterns. In addition, we assessed whether predictions of presence-absence models can be used as a proxy to abundance patterns. We obtained georeferenced abundance data of orchid bees (Hymenoptera: Apidae: Euglossina) in the Brazilian Atlantic Forest. Sampling method consisted in attracting male orchid bees to baits of at least five different aromatic compounds and collecting the individuals with entomological nets or bait traps. We limited abundance data to those obtained by similar standard sampling protocol to avoid bias in abundance estimation. We used boosted regression trees to model ecological niches and project them into six climate models and two Representative Concentration Pathways. We found that models based on species occurrences worked as a proxy for changes in population abundance when the output of the models were continuous; results were very different when outputs were discretized to binary predictions. We found an overall trend of diminishing abundance in the future, but a clear retention of climatically suitable sites too. Furthermore, geographic distance to gained climatic suitable areas can be very short, although it embraces great variation. Changes in species richness and turnover would be concentrated in western and southern Atlantic Forest. Our findings offer support to the ongoing debate of suitability

  16. Identification of suitable sites for mountain ginseng cultivation using GIS and geo-temperature.

    Science.gov (United States)

    Kang, Hag Mo; Choi, Soo Im; Kim, Hyun

    2016-01-01

    This study was conducted to explore an accurate site identification technique using a geographic information system (GIS) and geo-temperature (gT) for locating suitable sites for growing cultivated mountain ginseng (CMG; Panax ginseng), which is highly sensitive to the environmental conditions in which it grows. The study site was Jinan-gun, South Korea. The spatial resolution for geographic data was set at 10 m × 10 m, and the temperatures for various climatic factors influencing CMG growth were calculated by averaging the 3-year temperatures obtained from the automatic weather stations of the Korea Meteorological Administration. Identification of suitable sites for CMG cultivation was undertaken using both a conventional method and a new method, in which the gT was added as one of the most important factors for crop cultivation. The results yielded by the 2 methods were then compared. When the gT was added as an additional factor (new method), the proportion of suitable sites identified decreased by 0.4 % compared with the conventional method. However, the proportion matching real CMG cultivation sites increased by 3.5 %. Moreover, only 68.2 % corresponded with suitable sites identified using the conventional factors; i.e., 31.8 % were newly detected suitable sites. The accuracy of GIS-based identification of suitable CMG cultivation sites improved by applying the temperature factor (i.e., gT) in addition to the conventionally used factors.

  17. Agronomic Suitability of Bioenergy Crops in Mississippi

    Energy Technology Data Exchange (ETDEWEB)

    Lemus, Rocky; Baldwin, Brian; Lang, David

    2011-10-01

    In Mississippi, some questions need to be answered about bioenergy crops: how much suitable land is available? How much material can that land produce? Which production systems work best in which scenarios? What levels of inputs will be required for productivity and longterm sustainability? How will the crops reach the market? What kinds of infrastructure will be necessary to make that happen? This publication helps answer these questions: • Which areas in the state are best for bioenergy crop production? • How much could these areas produce sustainably? • How can bioenergy crops impact carbon sequestration and carbon credits? âÂÃÃÂ

  18. Eggs as a Suitable Tool for Species Diagnosis of Causative Agents of Human Diphyllobothriosis (Cestoda)

    Czech Academy of Sciences Publication Activity Database

    Leštinová, Kateřina; Soldánová, Miroslava; Scholz, Tomáš; Kuchta, Roman

    2016-01-01

    Roč. 10, č. 5 (2016), č. článku e0004721. ISSN 1935-2735 R&D Projects: GA ČR GAP506/12/1632 Institutional support: RVO:60077344 Keywords : Adenocephalus pacificus * helminth fauna * infection Subject RIV: EG - Zoology Impact factor: 3.834, year: 2016

  19. Projections of suitable habitat for rare species under global warming scenarios

    Science.gov (United States)

    F. Thomas Ledig; Gerald E. Rehfeldt; Cuauhtemoc Saenz-Romero; Flores-Lopez Celestino

    2010-01-01

    Premise of the study: Modeling the contemporary and future climate niche for rare plants is a major hurdle in conservation, yet such projections are necessary to prevent extinctions that may result from climate change. Methods: We used recently developed spline climatic models and modifi ed Random Forests...

  20. Invasive species research to meet the needs of resource management and planning.

    Science.gov (United States)

    Papeş, M; Sällström, M; Asplund, T R; Vander Zanden, M J

    2011-10-01

    As zebra mussels (Dreissena polymorpha) continue to spread among inland lakes of the United States and Canada, there is growing interest from professionals, citizens, and other stakeholders to know which lakes are likely to be colonized by zebra mussels. Thus, we developed a classification of lake suitability for zebra mussels on the basis of measured or estimated concentrations of dissolved calcium in lake water and applied the classification to >11,500 lakes in Wisconsin and the Upper Peninsula of Michigan. The majority of lakes (58%) were classified as unsuitable (zebra mussels, 27% were identified as suitable (≥21 mg/L Ca), and 15% were classified as borderline suitable (≥10 and zebra mussel records for which data on dissolved calcium were available, our method classified 74 as suitable and 3 as borderline suitable. To communicate this lake-specific suitability information and to help prioritize regional efforts to monitor and prevent the expansion of zebra mussels and other invasive species, we developed a web-based interface (available from http://www.aissmartprevention.wisc.edu/). Although we are still uncertain of how access to suitability information ultimately affects decision making, we believe this is a useful case study of building communication channels among researchers, practitioners, and the public. ©2011 Society for Conservation Biology.

  1. Detection of cryptic species

    International Nuclear Information System (INIS)

    Cockburn, A.F.; Jensen, T.; Seawright, J.A.

    1998-01-01

    Morphologically similar cryptic species are common in insects. In Anopheles mosquitoes morphologically described species are complexes of cryptic species. Cryptic species are of great practical importance for two reasons: first, one or more species of the complex might not be a pest and control efforts directed at the complex as a whole would therefore be partly wasted; and second, genetic (and perhaps biological) control strategies directed against one species of the complex would not affect other species of the complex. At least one SIT effort has failed because the released sterile insect were of a different species and therefore did not mate with the wild insects being targeted. We use a multidisciplinary approach for detection of cryptic species complexes, focusing first on identifying variability in wild populations using RFLPs of mitochondrial and ribosomal RNA genes (mtDNA and rDNA); followed by confirmation using a variety of other techniques. For rapid identification of wild individuals of field collections, we use a DNA dot blot assay. DNA probes can be isolated by differential screening, however we are currently focusing on the sequencing of the rDNA extragenic spacers. These regions are repeated several hundred times per genome in mosquitoes and evolve rapidly. Molecular drive tends to keen the individual genes homogeneous within a species. (author)

  2. Detection of cryptic species

    Energy Technology Data Exchange (ETDEWEB)

    Cockburn, A F; Jensen, T; Seawright, J A [United States Dept. of Agriculture, Agricultural Research Service, Medical and Veterinary Entomology Research Lab., Gainesville, FL (United States)

    1998-01-01

    Morphologically similar cryptic species are common in insects. In Anopheles mosquitoes morphologically described species are complexes of cryptic species. Cryptic species are of great practical importance for two reasons: first, one or more species of the complex might not be a pest and control efforts directed at the complex as a whole would therefore be partly wasted; and second, genetic (and perhaps biological) control strategies directed against one species of the complex would not affect other species of the complex. At least one SIT effort has failed because the released sterile insect were of a different species and therefore did not mate with the wild insects being targeted. We use a multidisciplinary approach for detection of cryptic species complexes, focusing first on identifying variability in wild populations using RFLPs of mitochondrial and ribosomal RNA genes (mtDNA and rDNA); followed by confirmation using a variety of other techniques. For rapid identification of wild individuals of field collections, we use a DNA dot blot assay. DNA probes can be isolated by differential screening, however we are currently focusing on the sequencing of the rDNA extragenic spacers. These regions are repeated several hundred times per genome in mosquitoes and evolve rapidly. Molecular drive tends to keen the individual genes homogeneous within a species. (author). 11 refs, 2 figs, 2 tabs.

  3. Reevaluating Suitability Estimates Based on Dynamics of Cropland Expansion in the Brazilian Amazon

    Science.gov (United States)

    Morton, Douglas C.; Noojipady, Praveen; Macedo, Marcia M.; Victoria, Daniel C.; Bolfe, Edson L.

    2016-01-01

    Agricultural suitability maps are a key input for land use zoning and projections of cropland expansion. Suitability assessments typically consider edaphic conditions, climate, crop characteristics, and sometimes incorporate accessibility to transportation and market infrastructure. However, correct weighting among these disparate factors is challenging, given rapid development of new crop varieties, irrigation, and road networks, as well as changing global demand for agricultural commodities. Here, we compared three independent assessments of cropland suitability to spatial and temporal dynamics of agricultural expansion in the Brazilian state of Mato Grosso during 2001 2012. We found that areas of recent cropland expansion identified using satellite data were generally designated as low to moderate suitability for rainfed crop production. Our analysis highlighted the abrupt nature of suitability boundaries, rather than smooth gradients of agricultural potential, with little additional cropland expansion beyond the extent of the flattest areas (0-2% slope). Satellite-based estimates of the interannual variability in the use of existing crop areas also provided an alternate means to assess suitability. On average, cropland areas in the Cerrado biome had higher utilization (84%) than croplands in the Amazon region of northern Mato Grosso (74%). Areas of more recent expansion had lower utilization than croplands established before 2002, providing empirical evidence for lower suitability or alternative management strategies (e.g., pasture soya rotations) for lands undergoing more recent land use transitions. This unplanted reserve constitutes a large area of potentially available cropland (PAC)without further expansion, within the management limits imposed for pest management and fallow cycles. Using two key constraints on future cropland expansion, slope and restrictions on further deforestation of Amazon or Cerrado vegetation, we found little available flat land for

  4. Land Suitability Assessment for Camelina (Camelina sativa L. Development in Chile

    Directory of Open Access Journals (Sweden)

    Celián Román-Figueroa

    2017-01-01

    Full Text Available Camelina (Camelina sativa L. is an oilseed with potential for use as a raw material in second-generation biofuels. Camelina has a seed yield of up to 2380 kg·ha−1 and contains around 45% fatty acids. Selection of a suitable site is critical for production optimization. The objective of this study was to determine Chilean agro-climatic suitability for establishing camelina as a productive alternative. Climate and soil requirements and geographical restraints were evaluated for the species, considering the climatological characteristics of its regions of origin, as well as regions where camelina is successfully grown in the rest of the world. The variables considered included factors (maximum temperatures of the warmest month, water deficits, and degree days and limitations (altitude, geomorphology, and current land use, which permitted the evaluation of the national territory for a certain level of suitability. It was determined that 1.3% of the national territory (960,664 ha has some degree of suitability for camelina adoption. Between the Biobío and Los Lagos regions, 49.0% of the land (471,203 ha is in the category of no thermic restrictions, with mild water restrictions, and mild soil restrictions or without information, which can be used for camelina production. The Los Ríos region has 21.4% surface area (321,176 ha with some level of suitability for camelina, the most suitable region to establish this crop in Chile. This research has provided valuable information applicable to new species and geographic areas which facilitate the adaptation of agricultural and forestry production to global changes.

  5. Suitability of asthma education materials for school-age children: Implications for health literacy.

    Science.gov (United States)

    Tzeng, Yu-Fen; Gau, Bih-Shya

    2018-03-01

    To investigate the suitability of asthma education materials for school-age children with asthma and elucidate how these children used their health-literacy abilities to identify whether the materials can be accepted, comprehended and applied. Effective asthma self-management education is influenced by the suitability of materials and an individual's health literacy. A mixed-method research design was developed using quantitative and qualitative surveys. The suitability of the materials was assessed on the basis of the Chinese version of the Suitability Assessment of Materials by five experts. In addition, five school-age children (age: 8-12 years) were recruited and interviewed. In total, 25 pieces of asthma education material for children were collected. On the basis of their type, the materials were categorised as nine brochures, 11 leaflets and five videos. Of the 25 materials, 17 were rated as superior materials, whereas eight were rated as adequate materials. The suitability scores of the video-based materials were significantly higher than those of the brochures and leaflets (p = .006). One print material was considered to have a reading level suitable for fifth-grade or younger children, whereas the remaining materials were considered suitable for sixth-grade or older children. The following six health-literacy domains were identified: recognising asthma through body knowledge, posing reflective questions, identifying self-care difficulties, receiving adult guidance, learning with enjoyment and addressing learning requirements. The video-based materials had integrated content and were appealing to children. Cartoon animations, interactive computer games, and skill demonstrations may enhance learning stimulation and motivation and increase learning effects in children. The present results may help healthcare providers to understand children's capacities to manage their disease, effectively address children's requirements and function as a key resource for

  6. Assessing range-wide habitat suitability for the Lesser Prairie-Chicken

    Science.gov (United States)

    Jarnevich, Catherine S.; Holcombe, Tracy R.; Grisham, Blake A.; Timmer, Jennifer M.; Boal, Clint W.; Butler, Matthew; Pitman, James C.; Kyle, Sean; Klute, David; Beauprez, Grant M.; Janus, Allan; Van Pelt, William E.

    2016-01-01

    Population declines of many wildlife species have been linked to habitat loss incurred through land-use change. Incorporation of conservation planning into development planning may mitigate these impacts. The threatened Lesser Prairie-Chicken (Tympanuchus pallidicinctus) is experiencing loss of native habitat and high levels of energy development across its multijurisdictional range. Our goal was to explore relationships of the species occurrence with landscape characteristics and anthropogenic effects influencing its distribution through evaluation of habitat suitability associated with one particular habitat usage, lekking. Lekking has been relatively well-surveyed, though not consistently, in all jurisdictions. All five states in which Lesser Prairie-Chickens occur cooperated in development of a Maxent habitat suitability model. We created two models, one with state as a factor and one without state. When state was included it was the most important predictor, followed by percent of land cover consisting of known or suspected used vegetation classes within a 5000 m area around a lek. Without state, land cover was the most important predictor of relative habitat suitability for leks. Among the anthropogenic predictors, landscape condition, a measure of human impact integrated across several factors, was most important, ranking third in importance without state. These results quantify the relative suitability of the landscape within the current occupied range of Lesser Prairie-Chickens. These models, combined with other landscape information, form the basis of a habitat assessment tool that can be used to guide siting of development projects and targeting of areas for conservation.

  7. Climate and air pollution impacts on habitat suitability of Austrian forest ecosystems.

    Science.gov (United States)

    Dirnböck, Thomas; Djukic, Ika; Kitzler, Barbara; Kobler, Johannes; Mol-Dijkstra, Janet P; Posch, Max; Reinds, Gert Jan; Schlutow, Angela; Starlinger, Franz; Wamelink, Wieger G W

    2017-01-01

    Climate change and excess deposition of airborne nitrogen (N) are among the main stressors to floristic biodiversity. One particular concern is the deterioration of valuable habitats such as those protected under the European Habitat Directive. In future, climate-driven shifts (and losses) in the species potential distribution, but also N driven nutrient enrichment may threaten these habitats. We applied a dynamic geochemical soil model (VSD+) together with a novel niche-based plant response model (PROPS) to 5 forest habitat types (18 forest sites) protected under the EU Directive in Austria. We assessed how future climate change and N deposition might affect habitat suitability, defined as the capacity of a site to host its typical plant species. Our evaluation indicates that climate change will be the main driver of a decrease in habitat suitability in the future in Austria. The expected climate change will increase the occurrence of thermophilic plant species while decreasing cold-tolerant species. In addition to these direct impacts, climate change scenarios caused an increase of the occurrence probability of oligotrophic species due to a higher N immobilisation in woody biomass leading to soil N depletion. As a consequence, climate change did offset eutrophication from N deposition, even when no further reduction in N emissions was assumed. Our results show that climate change may have positive side-effects in forest habitats when multiple drivers of change are considered.

  8. Climate and air pollution impacts on habitat suitability of Austrian forest ecosystems

    Science.gov (United States)

    Djukic, Ika; Kitzler, Barbara; Kobler, Johannes; Mol-Dijkstra, Janet P.; Posch, Max; Reinds, Gert Jan; Schlutow, Angela; Starlinger, Franz; Wamelink, Wieger G. W.

    2017-01-01

    Climate change and excess deposition of airborne nitrogen (N) are among the main stressors to floristic biodiversity. One particular concern is the deterioration of valuable habitats such as those protected under the European Habitat Directive. In future, climate-driven shifts (and losses) in the species potential distribution, but also N driven nutrient enrichment may threaten these habitats. We applied a dynamic geochemical soil model (VSD+) together with a novel niche-based plant response model (PROPS) to 5 forest habitat types (18 forest sites) protected under the EU Directive in Austria. We assessed how future climate change and N deposition might affect habitat suitability, defined as the capacity of a site to host its typical plant species. Our evaluation indicates that climate change will be the main driver of a decrease in habitat suitability in the future in Austria. The expected climate change will increase the occurrence of thermophilic plant species while decreasing cold-tolerant species. In addition to these direct impacts, climate change scenarios caused an increase of the occurrence probability of oligotrophic species due to a higher N immobilisation in woody biomass leading to soil N depletion. As a consequence, climate change did offset eutrophication from N deposition, even when no further reduction in N emissions was assumed. Our results show that climate change may have positive side-effects in forest habitats when multiple drivers of change are considered. PMID:28898262

  9. Climate and air pollution impacts on habitat suitability of Austrian forest ecosystems.

    Directory of Open Access Journals (Sweden)

    Thomas Dirnböck

    Full Text Available Climate change and excess deposition of airborne nitrogen (N are among the main stressors to floristic biodiversity. One particular concern is the deterioration of valuable habitats such as those protected under the European Habitat Directive. In future, climate-driven shifts (and losses in the species potential distribution, but also N driven nutrient enrichment may threaten these habitats. We applied a dynamic geochemical soil model (VSD+ together with a novel niche-based plant response model (PROPS to 5 forest habitat types (18 forest sites protected under the EU Directive in Austria. We assessed how future climate change and N deposition might affect habitat suitability, defined as the capacity of a site to host its typical plant species. Our evaluation indicates that climate change will be the main driver of a decrease in habitat suitability in the future in Austria. The expected climate change will increase the occurrence of thermophilic plant species while decreasing cold-tolerant species. In addition to these direct impacts, climate change scenarios caused an increase of the occurrence probability of oligotrophic species due to a higher N immobilisation in woody biomass leading to soil N depletion. As a consequence, climate change did offset eutrophication from N deposition, even when no further reduction in N emissions was assumed. Our results show that climate change may have positive side-effects in forest habitats when multiple drivers of change are considered.

  10. Modelling Fish Habitat Suitability in the Eastern English Channel. Application to community habitat level

    OpenAIRE

    Vaz, Sandrine; Carpentier, Andre; Loots, Christophe; Koubbi, Philippe

    2004-01-01

    Valuable marine habitats and living resources can be found in the Eastern English Channel and in 2003, a Franco-British Interreg IIIA project, ‘Eastern Channel Habitat Atlas for Marine Resource Management’ (CHARM), was initiated to support decision-making for management of essential fish habitats. Fish habitat corresponds to geographic areas within which ranges of environmental factors define the presence of a particular species. Habitat Suitability index (HSI) modelling was used to relate fi...

  11. Phylogenetic climatic niche conservatism and evolution of climatic suitability in Neotropical Angraecinae (Vandeae, Orchidaceae) and their closest African relatives.

    Science.gov (United States)

    Kolanowska, Marta; Grochocka, Elżbieta; Konowalik, Kamil

    2017-01-01

    In the present study we investigate the concept of phylogenetic niche conservatism (PNC) within the American species of angraecoid orchids ( Campylocentrum and Dendrophylax ) and their closest relatives in the Old World ( Angraecum ) using ecological niche modelling (ENM). The predicted niche occupancy profiles were matched with the outcomes of previous phylogenetic studies to reconstruct the evolution of climatic suitability within the orchid group studied and evaluate the role of niche differentiation in the speciation of Angraecinae. No correlation between preferred niches and taxonomic relationships within the orchid group studied was revealed. The climatic suitability of the majority of the species overlapped each other, either fully or partially. This pattern is also present in the species of other orchid genera. Our research confirms a significant level of PNC in Orchidaceae, even within taxa exhibiting a transatlantic disjunction. The analysis of the evolution of climatic suitability indicated that the adaptation to various climatic conditions is not a factor that has driven speciation within orchids studied.

  12. Use of geographic information systems (GIS to identify adequate sites for cultivation of the seaweed Gracilaria birdiae in Rio Grande do Norte, Northeastern Brazil

    Directory of Open Access Journals (Sweden)

    Flavo E. S. de Sousa

    2012-06-01

    Full Text Available This study was designed to select potential areas for cultivation of the seaweed Gracilaria birdiae Plastino & E.C. Oliveira (Gracilariales, Rhodophyta on the coast of Rio Grande do Norte state, Brazil. The Geographic Information System (GIS and multi-criteria evaluation (MCE were used to identify the most suitable areas. The Analytical Hierarchical Process (AHP was applied to establish MCE weights, thereby generating viable areas for species cultivation. From a total of 3316.82 ha, around 53.67% (1780.06 ha were indicated as highly suitable areas, 40.93% (1357.58 ha as moderately suitable and 5.40% (179.18 ha as scarcely suitable for seaweed cultivation. Seven areas (1084.62 ha are located on the northern coast and 20 (2232.20 ha on the eastern coast. The results show that GIS can be used as an effective instrument for selecting seaweed cultivation areas.

  13. Geographical information system (GIS) suitability analysis of radioactive waste repository site in Pahang, Malaysia

    International Nuclear Information System (INIS)

    Faizal Azrin Abd Razalim; Noraini Surip; Ahmad Hasnulhadi; Nazran Harun; Nurul Nadia Abd Malek; Roziah Che Musa

    2010-01-01

    The aim of this project is to identify a suitable site for radioactive waste repository in Pahang using remote sensing and geographical information system (GIS) technologies. There are ten parameters considered in the analysis, which divided into Selection Criteria and Exclusion Criteria. The Selection Criteria parameters consists of land use, rainfall, lineament, slope, groundwater potential and elevation while Exclusion Criteria parameters consist of urban, protected land and island. Furthermore, all parameters were integrated, given weight age and ranked for site selection evaluation in GIS environment. At the first place, about twelve sites have been identified as suitable sites for radioactive waste repository throughout the study area. These sites were further analysed by ground checking on the physical setting including geological, drainage, and population density in order to finalise three most suitable sites for radioactive waste repository. (author)

  14. Hydro-power production and fish habitat suitability: Assessing impact and effectiveness of ecological flows at regional scale

    Science.gov (United States)

    Ceola, Serena; Pugliese, Alessio; Ventura, Matteo; Galeati, Giorgio; Montanari, Alberto; Castellarin, Attilio

    2018-06-01

    Anthropogenic activities along streams and rivers may be of major concern for fluvial ecosystems, e.g. abstraction and impoundment of surface water resources may profoundly alter natural streamflow regimes. An established approach aimed at preserving the behavior and distribution of fluvial species relies on the definition of ecological flows (e-flows) downstream of dams and diversion structures. E-flow prescriptions are usually set by basin authorities at regional scale, often without a proper assessment of their impact and effectiveness. On the contrary, we argue that e-flows should be identified on the basis of (i) regional and (ii) quantitative assessments. We focus on central Italy and evaluate the effects on habitat suitability of two near-threatened fish species (i.e. Barbel and Chub) and an existing hydro-power network when shifting from the current time-invariant e-flow policy to a tighter and seasonally-varying soon-to-be-enforced one. Our example clearly shows that: (a) quantitative regional scale assessments are viable even when streamflow observations are entirely missing at study sites; (b) aprioristic e-flows policies may impose releases that exceed natural streamflows for significantly long time intervals (weeks, or months); (c) unduly tightening e-flow policies may heavily impact regional hydro-power productivity (15% and 42% losses on annual and seasonal basis, respectively), yet resulting in either marginal or negligible improvements of fluvial ecosystem.

  15. LC-MS/MS Identification of Species-Specific Muscle Peptides in Processed Animal Proteins.

    Science.gov (United States)

    Marchis, Daniela; Altomare, Alessandra; Gili, Marilena; Ostorero, Federica; Khadjavi, Amina; Corona, Cristiano; Ru, Giuseppe; Cappelletti, Benedetta; Gianelli, Silvia; Amadeo, Francesca; Rumio, Cristiano; Carini, Marina; Aldini, Giancarlo; Casalone, Cristina

    2017-12-06

    An innovative analytical strategy has been applied to identify signature peptides able to distinguish among processed animal proteins (PAPs) derived from bovine, pig, fish, and milk products. Proteomics was first used to elucidate the proteome of each source. Starting from the identified proteins and using a funnel based approach, a set of abundant and well characterized peptides with suitable physical-chemical properties (signature peptides) and specific for each source was selected. An on-target LC-ESI-MS/MS method (MRM mode) was set up using standard peptides and was then applied to selectively identify the PAP source and also to distinguish proteins from bovine carcass and milk proteins. We believe that the method described meets the request of the European Commission which has developed a strategy for gradually lifting the "total ban" toward "species to species ban", therefore requiring official methods for species-specific discrimination in feed.

  16. Expansion of Protected Areas under Climate Change: An Example of Mountainous Tree Species in Taiwan

    Directory of Open Access Journals (Sweden)

    Wei-Chih Lin

    2014-11-01

    Full Text Available Tree species in mountainous areas are expected to shift their distribution upward in elevation in response to climate change, calling for a potential redesign of existing protected areas. This study aims to predict whether or not the distributions of two high-mountain tree species, Abies (Abies kawakamii and Tsuga (Tsuga chinensis var. formosana, will significantly shift upward due to temperature change, and whether current protected areas will be suitable for conserving these species. Future temperature change was projected for 15 different future scenarios produced from five global climate models. Shifts in Abies and Tsuga distributions were then predicted through the use of species distribution models (SDMs which included occurrence data of Abies and Tsuga, as well as seasonal temperature, and elevation. The 25 km × 25 km downscaled General Circulation Model (GCMs data for 2020–2039 produced by the Taiwan Climate Change Projection and Information Platform was adopted in this study. Habitat suitability in the study area was calculated using maximum entropy model under different climatic scenarios. A bootstrap method was applied to assess the parameter uncertainty of the maximum entropy model. In comparison to the baseline projection, we found that there are significant differences in suitable habitat distributions for Abies and Tsuga under seven of the 15 scenarios. The results suggest that mountainous ecosystems will be substantially impacted by climate change. We also found that the uncertainty originating from GCMs and the parameters of the SDM contribute most to the overall level of variability in species distributions. Finally, based on the uncertainty analysis and the shift in habitat suitability, we applied systematic conservation planning approaches to identify suitable areas to add to Taiwan’s protected area network.

  17. Tolerability and suitability of brief group mindfulness-oriented interventions in psychiatric inpatients: a pilot study.

    Science.gov (United States)

    Nikolitch, Katerina; Laliberté, Vincent; Yu, Ching; Strychowsky, Natalie; Segal, Marilyn; Looper, Karl J; Rej, Soham

    2016-09-01

    Mindfulness-oriented therapies have a positive impact on patients' overall well-being and alleviate many psychiatric conditions. However, little is known about their use in people with severe mental illness. We aimed to identify which clinical and sociodemographic factors are associated with suitability/tolerability of a brief group mindfulness-oriented therapy. This retrospective study examines pre-/post-data from 40 psychiatric inpatients who underwent one session of a 10-min mindfulness-oriented group intervention between January and March 2014. The main outcome was 'suitability for and tolerating the brief mindfulness-oriented group intervention'. We assessed potential correlates of the main outcome, including female gender, shorter hospitalisation, the absence of psychosis and good pre-morbid functioning. The intervention was well tolerated (92.5%) and 50% of patients met both of our relatively stringent suitability and tolerability criteria. Sociodemographic and clinical variables were not associated with suitability/tolerability. Tai chi was the most suitable/tolerable compared to body scan and mindful eating (76.5% vs. 35.7% vs. 22.2%, Fisher's exact p = 0.01, Bonferroni p mindfulness therapy interventions are very well tolerated and often suitable for acutely hospitalised psychiatric inpatients, including those with acute psychosis. Mindfulness-oriented intervention with an active component (e.g., tai chi, mindful walking) may potentially be best suited for this population.

  18. An Expert-Based Assessment Model for Evaluating Habitat Suitability of Pond-Breeding Amphibians

    Directory of Open Access Journals (Sweden)

    Shin-Ruoh Juang

    2017-02-01

    Full Text Available Farm ponds are important habitats for amphibians, birds, and other wildlife. In Taiwan, artificial ponds were originally created on farmlands for irrigation purposes and the needs of the domestic water supply. Although pond creation is a typical farming practice, it also provides habitats for pond-breeding amphibians. Thus, it is essential to understand the current status of habitats and their vulnerability regarding urgent conservation needs for target species. Günther’s frog (Hylarana guentheri, a pond-breeding amphibian, has a high sensitivity towards surrounding environmental changes, and can be used as an indicator species to assess habitat suitability. The purpose of this study is to establish a systematic framework to assess the habitat suitability of pond-breeding amphibians by using Günther’s frog as a pilot-study species. First, we collected frog survey data from Chiayi, Taiwan, from winter 2013 to spring 2015, and investigated the present status of the environmental conditions around the ponds. Next, expert questionnaires and the fuzzy Delphi method were applied to establish the hierarchical evaluation criteria regarding the habitat suitability assessment. Four indicators: the aquatic environments of farm ponds; the terrestrial environments around ponds; landscape connectivity; and the conservation perceptions of the residents, were determined as first-layer factors in the assessment criteria, while ten other indicators were defined as second-layer factors. Based on the established assessment criteria, we performed in situ habitat suitability evaluations on 69 selected sites and surveyed the perceptions of the residents using questionnaires. Results revealed that 19% of locations were rich in frog species with a high habitat suitability. However, 67% of locations showed signs of habitat degradation, which may imply a higher need in practicing habitat improvement or restoration. The Kappa value was 0.6061, which indicated a high

  19. Barcoding the Dendrobium (Orchidaceae Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2

    Directory of Open Access Journals (Sweden)

    Xiaoyue Wang

    2017-01-01

    Full Text Available Many species belonging to the genus Dendrobium are of great commercial value. However, their difficult growth conditions and high demand have caused many of these species to become endangered. Indeed, counterfeit Dendrobium products are common, especially in medicinal markets. This study aims to assess the suitability of the internal transcribed spacer 2 (ITS2 region as a marker for identifying Dendrobium and to evaluate its intragenomic variation in Dendrobium species. In total, 29,624 ITS2 copies from 18 species were obtained using 454 pyrosequencing to evaluate intragenomic variation. In addition, 513 ITS2 sequences from 26 Dendrobium species were used to assess its identification suitability. The highest intragenomic genetic distance was observed in Dendrobium chrysotoxum (0.081. The average intraspecific genetic distances of each species ranged from 0 to 0.032. Phylogenetic trees based on ITS2 sequences showed that most Dendrobium species are monophyletic. The intragenomic and intraspecies divergence analysis showed that greater intragenomic divergence is mostly correlated with larger intraspecific variation. As a major ITS2 variant becomes more common in genome, there are fewer intraspecific variable sites in ITS2 sequences at the species level. The results demonstrated that the intragenomic multiple copies of ITS2 did not affect species identification.

  20. Barcoding the Dendrobium (Orchidaceae) Species and Analysis of the Intragenomic Variation Based on the Internal Transcribed Spacer 2.

    Science.gov (United States)

    Wang, Xiaoyue; Chen, Xiaochen; Yang, Pei; Wang, Lili; Han, Jianping

    2017-01-01

    Many species belonging to the genus Dendrobium are of great commercial value. However, their difficult growth conditions and high demand have caused many of these species to become endangered. Indeed, counterfeit Dendrobium products are common, especially in medicinal markets. This study aims to assess the suitability of the internal transcribed spacer 2 (ITS2) region as a marker for identifying Dendrobium and to evaluate its intragenomic variation in Dendrobium species. In total, 29,624 ITS2 copies from 18 species were obtained using 454 pyrosequencing to evaluate intragenomic variation. In addition, 513 ITS2 sequences from 26 Dendrobium species were used to assess its identification suitability. The highest intragenomic genetic distance was observed in Dendrobium chrysotoxum (0.081). The average intraspecific genetic distances of each species ranged from 0 to 0.032. Phylogenetic trees based on ITS2 sequences showed that most Dendrobium species are monophyletic. The intragenomic and intraspecies divergence analysis showed that greater intragenomic divergence is mostly correlated with larger intraspecific variation. As a major ITS2 variant becomes more common in genome, there are fewer intraspecific variable sites in ITS2 sequences at the species level. The results demonstrated that the intragenomic multiple copies of ITS2 did not affect species identification.

  1. Suitability of technical materials for machinery subsoilers for soil tillage

    Directory of Open Access Journals (Sweden)

    Radek Bednář

    2013-01-01

    Full Text Available Agricultural soil processing belongs to the basic elements in the process of crop production. Currently classic tillage method is decreasing and the only trend has stated as a shallow plowing. Suitable post harvest soil tillage greatly affects yields in the next cycle. The aim of the study is the analysis of abrasive wear of selected construction materials and their subsequent use for DXRV-HD cultivator. The performed tests are focused on monitoring the mechanical properties of the materials and their use for variable cutting tip of cultivator body. Tested materials are divided into four categories. These materials include tool steel (19436, carbon steel (12050, cast iron with globular graphite and welding material supplied as a functional complex on low carbon steel by the Abraweld company. These materials are tested together with the original part of share cultivator. The present experiment is focused on metallorgraphic, mechanical and abrasive analysis. Structural component of the material is identified by metallographic photos and then compared with the impact strength tested on Charpy hammer. Followed the abrasion resistance according to CSN 01 5084 and the total evaluation of the tested samples are done.

  2. The Edge Detectors Suitable for Retinal OCT Image Segmentation

    Directory of Open Access Journals (Sweden)

    Su Luo

    2017-01-01

    Full Text Available Retinal layer thickness measurement offers important information for reliable diagnosis of retinal diseases and for the evaluation of disease development and medical treatment responses. This task critically depends on the accurate edge detection of the retinal layers in OCT images. Here, we intended to search for the most suitable edge detectors for the retinal OCT image segmentation task. The three most promising edge detection algorithms were identified in the related literature: Canny edge detector, the two-pass method, and the EdgeFlow technique. The quantitative evaluation results show that the two-pass method outperforms consistently the Canny detector and the EdgeFlow technique in delineating the retinal layer boundaries in the OCT images. In addition, the mean localization deviation metrics show that the two-pass method caused the smallest edge shifting problem. These findings suggest that the two-pass method is the best among the three algorithms for detecting retinal layer boundaries. The overall better performance of Canny and two-pass methods over EdgeFlow technique implies that the OCT images contain more intensity gradient information than texture changes along the retinal layer boundaries. The results will guide our future efforts in the quantitative analysis of retinal OCT images for the effective use of OCT technologies in the field of ophthalmology.

  3. Nurses' understandings of suitable footwear for older people.

    Science.gov (United States)

    Borland, Andrea; Martin, Caroline Hollins; Locke, John

    2013-01-01

    The purpose of this paper is to gain insight into nurses' understandings of what constitutes suitable footwear for older people in care homes. An exploratory descriptive qualitative survey was carried out of 20 registered nurses employed in six Scottish care homes for older people. Data were collected using a semi-structured questionnaire that included five open-ended questions. Content analysis was used to theme footwear perceptions. Participants had several views about what encompasses safe footwear; some were erroneous. The link between inappropriate footwear and falls was recognised by 80 per cent of respondents, but some were unclear about the features that effect or inhibit safety. No UK or international standardised guidelines were identified that advise nurses about appropriate footwear for older people. It is unknown whether respondents represent the nurse population because findings are restricted by a small sample size. Nonetheless, the group showed variable understanding of what constitutes safe footwear for older people and links with fall prevention. Improved nurse-education about what comprises safe footwear and the links with falls prevention in older people is required. Structured guidelines to direct nurse educators about what to teach student nurses about appropriate footwear for older people may work towards reducing falls. No guidelines to direct nurses about appropriate footwear for older people in care homes have been written. Key points have been developed.

  4. Maxent modeling for predicting the potential geographical distribution of two peony species under climate change.

    Science.gov (United States)

    Zhang, Keliang; Yao, Linjun; Meng, Jiasong; Tao, Jun

    2018-09-01

    Paeonia (Paeoniaceae), an economically important plant genus, includes many popular ornamentals and medicinal plant species used in traditional Chinese medicine. Little is known about the properties of the habitat distribution and the important eco-environmental factors shaping the suitability. Based on high-resolution environmental data for current and future climate scenarios, we modeled the present and future suitable habitat for P. delavayi and P. rockii by Maxent, evaluated the importance of environmental factors in shaping their distribution, and identified distribution shifts under climate change scenarios. The results showed that the moderate and high suitable areas for P. delavayi and P. rockii encompassed ca. 4.46×10 5 km 2 and 1.89×10 5 km 2 , respectively. Temperature seasonality and isothermality were identified as the most critical factors shaping P. delavayi distribution, and UVB-4 and annual precipitation were identified as the most critical for shaping P. rockii distribution. Under the scenario with a low concentration of greenhouse gas emissions (RCP2.6), the range of both species increased as global warming intensified; however, under the scenario with higher concentrations of emissions (RCP8.5), the suitable habitat range of P. delavayi decreased while P. rockii increased. Overall, our prediction showed that a shift in distribution of suitable habitat to higher elevations would gradually become more significant. The information gained from this study should provide a useful reference for implementing long-term conservation and management strategies for these species. Copyright © 2018. Published by Elsevier B.V.

  5. Utilizing NASA Earth Observations to investigate habitat suitability of the Cape Vulture in the Western Cape Province of South Africa

    Science.gov (United States)

    Gray, D.; Estes, M. G., Jr.; Griffin, R.; Estes, S. M.

    2017-12-01

    As the global urban population rapidly increases, many wild species lose habitat to human development. The Western Cape of South Africa contains one of Earth's 35 biodiversity hotspots, with remarkably high levels of species richness and endemism. Understanding the relationship between anthropogenic changes and key species in this region is crucial for conservation of its threatened ecosystems. The objective of this research was to investigate the effect that climate change and urbanization each have on habitat suitability of the Cape Vulture. This research utilized NASA satellite data and crowdsourced species sightings to model past, current, and future habitat suitability for this key species in the Western Cape. Data used from NASA Earth Observations included: Landsat 8- derived Land Cover, Modis Land Surface Temperature, Digital Elevation Models from the Shuttle Radar Topography Mission, and precipitation data which integrated in-situ stations with Infrared data. Species observations were sourced from the Global Biodiversity Information Facility online database. A geospatial modelling framework was used to generate maps of present, past and future suitable habitats for analysis and comparison. Changes in precipitation and temperature may be a factor in the extreme loss of habitat since 1995, and predict even more drastic loss in the future. This research provides insights on anthropogenic effects on a species' range which may be used to inform discussions of conservation as an element of environmentally sustainable development.

  6. suitability of burnt and crushed cow bones as partial replacement

    African Journals Online (AJOL)

    HOD

    3 mix ratio measuring 150x150x150mm were tested for the compressive strength at 7, 14, 21 and 28 days respectively. ... the suitability of using waste products to produce lightweight ... suitability of machine crushed animal bones as partial or.

  7. Site Suitability For Yam, Rice And Cotton Production In Adamawa ...

    African Journals Online (AJOL)

    This paper demonstrated the potentials of GIS technique for mapping and delineating the suitable sites for Yam, Rice and Cotton production in Adamawa State. Site suitability mapping is necessary to create data bank and to guide the farmers in decision making on sites for crop production in the state. The use of GIS for this ...

  8. Comprehensive environment-suitability evaluation model about Carya cathayensis

    International Nuclear Information System (INIS)

    Da-Sheng, W.; Li-Juan, L.; Qin-Fen, Y.

    2013-01-01

    On the relation between the suitable environment and the distribution areas of Carya cathayensis Sarg., the current studies are mainly committed to qualitative descriptions, but did not consider quantitative models. The objective of this study was to establish a environment-suitability evaluation model which used to predict potential suitable areas of C. cathayensis. Firstly, the 3 factor data of soil type, soil parent material and soil thickness were obtained based on 2-class forest resource survey, and other factor data, which included elevation, slope, aspect, surface curvature, humidity index, and solar radiation index, were extracted from DEM (Digital Elevation Model). Additionally, the key affecting factors were defined by PCA (Principal Component Analysis), the weights of evaluation factors were determined by AHP (Analysis Hierarchy Process) and the quantitative classification of single factor was determined by membership function with fuzzy mathematics. Finally, a comprehensive environment-suitability evaluation model was established and which was also used to predict the potential suitable areas of C. cathayensis in Daoshi Town in the study region. The results showed that 85.6% of actual distribution areas were in the most suitable and more suitable regions and 11.5% in the general suitable regions

  9. Technical suitability mapping of feedstocks for biological hydrogen production

    NARCIS (Netherlands)

    Panagiotopoulos, I.A.; Karaoglanoglou, L.S.; Koullas, D.P.; Bakker, R.R.; Claassen, P.A.M.; Koukios, E.G.

    2015-01-01

    The objective of this work was to map and compare the technical suitability of different raw materials for biological hydrogen production. Our model was based on hydrogen yield potential, sugar mobilization efficiency, fermentability and coproduct yield and value. The suitability of the studied

  10. Land Suitability Assessment for Pineapple Production in the A ...

    African Journals Online (AJOL)

    linking land resources assessment to any land use decision-making process. like elsewhere, land ... managers as decision-support tools, for instance, to outline the most suitable land areas for subsidy ...... increase rational decisions. In this ..... essentially dynamic. it is pertinent that land suitability analysis is framed within an ...

  11. Solid waste dumping site suitability analysis using geographic ...

    African Journals Online (AJOL)

    Solid waste dumping is a serious problem in the urban areas because most solid wastes are not dumped in the suitable areas. Bahir Dar Town has the problem of solid waste dumping site identification. The main objective of this study was to select potential areas for suitable solid waste dumping sites for Bahir Dar Town, ...

  12. Aquatic Nuisance Species Locator

    Science.gov (United States)

    Data in this map has been collected by the United States Geological Survey's Nonindigenous Aquatic Species program located in Gainesville, Florida (http://nas.er.usgs.gov/default.aspx). This dataset may have some inaccuracies and is only current to June 15, 2012. The species identified in this dataset are not inclusive of all aquatic nuisance species, but rather a subset identified to be at risk for transport by recreational activities such as boating and angling. Additionally, the locations where organisims have been identified are also not inclusive and should be treated as a guide. Organisms are limited to the following: American bullfrog, Asian clam, Asian shore crab, Asian tunicate, Australian spotted jellyfish, Chinese mitten crab, New Zealand mudsnail, Colonial sea squirt, Alewife, Bighead carp, Black carp, Flathead catfish, Grass carp, Green crab, Lionfish, Northern snakehead, Quagga mussel, Round Goby, Ruffe, Rusty crayfish, Sea lamprey, Silver carp, Spiny water flea, Veined rapa whelk, Zebra mussel

  13. Spatial modelling of Lutzomyia (Nyssomyia whitmani s.l. (Antunes & Coutinho, 1939 (Diptera: Psychodidae: Phlebotominae habitat suitability in the state of Mato Grosso, Brazil

    Directory of Open Access Journals (Sweden)

    Peter Zeilhofer

    2008-11-01

    Full Text Available Lutzomyia (Nyssomyia whitmani s.l.is the main vector of cutaneous leishmaniasis in state of Mato Grosso, but little is known about environmental determinants of its spatial distribution on a regional scale. Entomologic surveys of this sand fly species, conducted between 1996 and 2001 in 41 state municipalities, were used to investigate the relationships between environmental factors and the presence of the species, and to develop a spatial model of habitat suitability. The relationship between averaged CDC light trap indexes and 15 environmental and socio-economic factors were tested by logistic regression (LR analysis. Spatial layers of deforestation tax and the Brazilian index of gross net production (IGNP were identified as significant explanatory variables for vector presence in the LR model, and these were then overlaid with habitat maps. The highest habitat suitability in 2001 was obtained for the heavily deforested areas in the Central-North, South, East, and Southwest of Mato Grosso, particularly in municipalities with lower IGNP values.

  14. The readability and suitability of sexual health promotion leaflets.

    Science.gov (United States)

    Corcoran, Nova; Ahmad, Fatuma

    2016-02-01

    To investigate the readability and suitability of sexual health promotion leaflets. Application of SMOG, FRY and SAM tests to assess the readability and suitability of a selection of sexual health leaflets. SMOG and FRY scores illustrate an average reading level of grade 9. SAM scores indicate that 59% of leaflets are superior in design and 41% are average in design. Leaflets generally perform well in the categories of content, literacy demand, typography and layout. They perform poorly in use of graphics, learning stimulation/motivation and cultural appropriateness. Sexual health leaflets have a reading level that is too high. Leaflets perform well on the suitability scores indicating they are reasonably suitable. There are a number of areas where sexual health leaflets could improve their design. Numerous practical techniques are suggested for improving the readability and suitability of sexual health leaflets. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  15. Predicted deep-sea coral habitat suitability for the U.S. West coast.

    Directory of Open Access Journals (Sweden)

    John M Guinotte

    Full Text Available Regional scale habitat suitability models provide finer scale resolution and more focused predictions of where organisms may occur. Previous modelling approaches have focused primarily on local and/or global scales, while regional scale models have been relatively few. In this study, regional scale predictive habitat models are presented for deep-sea corals for the U.S. West Coast (California, Oregon and Washington. Model results are intended to aid in future research or mapping efforts and to assess potential coral habitat suitability both within and outside existing bottom trawl closures (i.e. Essential Fish Habitat (EFH and identify suitable habitat within U.S. National Marine Sanctuaries (NMS. Deep-sea coral habitat suitability was modelled at 500 m×500 m spatial resolution using a range of physical, chemical and environmental variables known or thought to influence the distribution of deep-sea corals. Using a spatial partitioning cross-validation approach, maximum entropy models identified slope, temperature, salinity and depth as important predictors for most deep-sea coral taxa. Large areas of highly suitable deep-sea coral habitat were predicted both within and outside of existing bottom trawl closures and NMS boundaries. Predicted habitat suitability over regional scales are not currently able to identify coral areas with pin point accuracy and probably overpredict actual coral distribution due to model limitations and unincorporated variables (i.e. data on distribution of hard substrate that are known to limit their distribution. Predicted habitat results should be used in conjunction with multibeam bathymetry, geological mapping and other tools to guide future research efforts to areas with the highest probability of harboring deep-sea corals. Field validation of predicted habitat is needed to quantify model accuracy, particularly in areas that have not been sampled.

  16. Global decline in suitable habitat for Angiostrongylus ( = Parastrongylus cantonensis: the role of climate change.

    Directory of Open Access Journals (Sweden)

    Emily M York

    Full Text Available Climate change is implicated in the alteration of the ranges of species worldwide. Such shifts in species distributions may introduce parasites/pathogens, hosts, and vectors associated with disease to new areas. The parasite Angiostrongylus ( = Parastrongylus cantonensis is an invasive species that causes eosinophilic meningitis in humans and neurological abnormalities in domestic/wild animals. Although native to southeastern Asia, A. cantonensis has now been reported from more than 30 countries worldwide. Given the health risks, it is important to describe areas with potentially favorable climate for the establishment of A. cantonensis, as well as areas where this pathogen might become established in the future. We used the program Maxent to develop an ecological niche model for A. cantonensis based on 86 localities obtained from published literature. We then modeled areas of potential A. cantonensis distribution as well as areas projected to have suitable climatic conditions under four Representative Concentration Pathways (RCP scenarios by the 2050s and the 2070s. The best model contained three bioclimatic variables: mean diurnal temperature range, minimum temperature of coldest month and precipitation of warmest quarter. Potentially suitable habitat for A. cantonensis was located worldwide in tropical and subtropical regions. Under all climate change RCP scenarios, the center of the projected distribution shifted away from the equator at a rate of 68-152 km per decade. However, the extent of areas with highly suitable habitat (>50% declined by 10.66-15.66% by the 2050s and 13.11-16.11% by the 2070s. These results conflict with previous studies, which have generally found that the prevalence of tropical pathogens will increase during the 21st century. Moreover, it is likely that A. cantonensis will continue to expand its current range in the near future due to introductions and host expansion, whereas climate change will reduce the total

  17. Global decline in suitable habitat for Angiostrongylus ( = Parastrongylus) cantonensis: the role of climate change.

    Science.gov (United States)

    York, Emily M; Butler, Christopher J; Lord, Wayne D

    2014-01-01

    Climate change is implicated in the alteration of the ranges of species worldwide. Such shifts in species distributions may introduce parasites/pathogens, hosts, and vectors associated with disease to new areas. The parasite Angiostrongylus ( = Parastrongylus) cantonensis is an invasive species that causes eosinophilic meningitis in humans and neurological abnormalities in domestic/wild animals. Although native to southeastern Asia, A. cantonensis has now been reported from more than 30 countries worldwide. Given the health risks, it is important to describe areas with potentially favorable climate for the establishment of A. cantonensis, as well as areas where this pathogen might become established in the future. We used the program Maxent to develop an ecological niche model for A. cantonensis based on 86 localities obtained from published literature. We then modeled areas of potential A. cantonensis distribution as well as areas projected to have suitable climatic conditions under four Representative Concentration Pathways (RCP) scenarios by the 2050s and the 2070s. The best model contained three bioclimatic variables: mean diurnal temperature range, minimum temperature of coldest month and precipitation of warmest quarter. Potentially suitable habitat for A. cantonensis was located worldwide in tropical and subtropical regions. Under all climate change RCP scenarios, the center of the projected distribution shifted away from the equator at a rate of 68-152 km per decade. However, the extent of areas with highly suitable habitat (>50%) declined by 10.66-15.66% by the 2050s and 13.11-16.11% by the 2070s. These results conflict with previous studies, which have generally found that the prevalence of tropical pathogens will increase during the 21st century. Moreover, it is likely that A. cantonensis will continue to expand its current range in the near future due to introductions and host expansion, whereas climate change will reduce the total geographic area of

  18. Monitoring of fish species in the Lamone river: distribution and morphometric measures of the populations

    Directory of Open Access Journals (Sweden)

    Riccardo Bozzi

    2010-01-01

    Full Text Available Fish samplings were carried out monthly from spring to autumn during 2008, on the Lamone river and the Campigno stream by an electrofishing, in order to verify the presence of fish populations and the most common species represented. Barb, Barbus plebejus, Blageon, Leuciscus muticellus, Chub, Leuciscus cephalus, South European Nase, Chondrostoma genei were identified. A small population of Brown trout, Salmo trutta fario was also recognized. Barb is the most represented species in all the sites. The samplings highlight that Lamone river presented conditions suitable to fully guarantee the life of the fish populations.

  19. Suitability of voltage stability study methods for real-time assessment

    DEFF Research Database (Denmark)

    Perez, Angel; Jóhannsson, Hjörtur; Vancraeyveld, Pieter

    2013-01-01

    This paper analyzes the suitability of existing methods for long-term voltage stability assessment for real-time operation. An overview of the relevant methods is followed with a comparison that takes into account the accuracy, computational efficiency and characteristics when used for security...... assessment. The results enable an evaluation of the run time of each method with respect to the number of inputs. Furthermore, the results assist in identifying which of the methods is most suitable for realtime operation in future power system with production based on fluctuating energy sources....

  20. Fast identification of folded human protein domains expressed in E. coli suitable for structural analysis

    Directory of Open Access Journals (Sweden)

    Schlegel Brigitte

    2004-03-01

    Full Text Available Abstract Background High-throughput protein structure analysis of individual protein domains requires analysis of large numbers of expression clones to identify suitable constructs for structure determination. For this purpose, methods need to be implemented for fast and reliable screening of the expressed proteins as early as possible in the overall process from cloning to structure determination. Results 88 different E. coli expression constructs for 17 human protein domains were analysed using high-throughput cloning, purification and folding analysis to obtain candidates suitable for structural analysis. After 96 deep-well microplate expression and automated protein purification, protein domains were directly analysed using 1D 1H-NMR spectroscopy. In addition, analytical hydrophobic interaction chromatography (HIC was used to detect natively folded protein. With these two analytical methods, six constructs (representing two domains were quickly identified as being well folded and suitable for structural analysis. Conclusion The described approach facilitates high-throughput structural analysis. Clones expressing natively folded proteins suitable for NMR structure determination were quickly identified upon small scale expression screening using 1D 1H-NMR and/or analytical HIC. This procedure is especially effective as a fast and inexpensive screen for the 'low hanging fruits' in structural genomics.

  1. Evaluation of Suitable Reference Genes for Normalization of qPCR Gene Expression Studies in Brinjal (Solanum melongena L.) During Fruit Developmental Stages.

    Science.gov (United States)

    Kanakachari, Mogilicherla; Solanke, Amolkumar U; Prabhakaran, Narayanasamy; Ahmad, Israr; Dhandapani, Gurusamy; Jayabalan, Narayanasamy; Kumar, Polumetla Ananda

    2016-02-01

    Brinjal/eggplant/aubergine is one of the major solanaceous vegetable crops. Recent availability of genome information greatly facilitates the fundamental research on brinjal. Gene expression patterns during different stages of fruit development can provide clues towards the understanding of its biological functions. Quantitative real-time PCR (qPCR) has become one of the most widely used methods for rapid and accurate quantification of gene expression. However, its success depends on the use of a suitable reference gene for data normalization. For qPCR analysis, a single reference gene is not universally suitable for all experiments. Therefore, reference gene validation is a crucial step. Suitable reference genes for qPCR analysis of brinjal fruit development have not been investigated so far. In this study, we have selected 21 candidate reference genes from the Brinjal (Solanum melongena) Plant Gene Indices database (compbio.dfci.harvard.edu/tgi/plant.html) and studied their expression profiles by qPCR during six different fruit developmental stages (0, 5, 10, 20, 30, and 50 days post anthesis) along with leaf samples of the Pusa Purple Long (PPL) variety. To evaluate the stability of gene expression, geNorm and NormFinder analytical softwares were used. geNorm identified SAND (SAND family protein) and TBP (TATA binding protein) as the best pairs of reference genes in brinjal fruit development. The results showed that for brinjal fruit development, individual or a combination of reference genes should be selected for data normalization. NormFinder identified Expressed gene (expressed sequence) as the best single reference gene in brinjal fruit development. In this study, we have identified and validated for the first time reference genes to provide accurate transcript normalization and quantification at various fruit developmental stages of brinjal which can also be useful for gene expression studies in other Solanaceae plant species.

  2. SALMONELLA SPECIES

    African Journals Online (AJOL)

    DR. AMINU

    ... of Salmonella species serotypes in relation to age and sex among children, ..... However, most antimicrobials show sufficient selective toxicity to be of value in ... salmonellosis should be given good attention (Barrow et al., 2007). To reduce ...

  3. Creating a Ruggedness Layer for Use in Habitat Suitability Modeling for Ikh Nart Nature Reserve, Mongolia

    Directory of Open Access Journals (Sweden)

    Nanette Bragin

    2013-12-01

    Full Text Available Spatially-explicit wildlife habitat models are increasingly used to study optimal habitat for species of conservation focus. A ruggedness layer, that summarizes aspect and slope, provides a useful tool for analyses conducted in a Geographic Information System (GIS, such as developing a habitat suitability index model to measure species habitat use. Ruggedness layers prove especially useful in areas where topography represents a key habitat component. We created a ruggedness layer for the Ikh Nart Nature Reserve and surrounding areas in northern Dornogobi Aimag (province, Mongolia. Using a 90 m Shuttle Radar Topography Mission (SRTM digital elevation model (DEM and ArcGIS 10 spatial analyst, we created 9 categories for ruggedness. When combined with other thematic layers such as vegetation, the ruggedness layer becomes a powerful tool for analyzing habitat use by individual animals. The results of such analyses may inform decision makers in protected area planning and conservation of endangered species.

  4. Ability of Slovakian Pupils to Identify Birds

    Science.gov (United States)

    Prokop, Pavol; Rodak, Rastislav

    2009-01-01

    A pupil's ability to identify common organisms is necessary for acquiring further knowledge of biology. We investigated how pupils were able to identify 25 bird species following their song, growth habits, or both features presented simultaneously. Just about 19% of birds were successfully identified by song, about 39% by growth habit, and 45% of…

  5. Assessing the suitability of stream water for five different uses and its aquatic environment.

    Science.gov (United States)

    Fulazzaky, Mohamad Ali

    2013-01-01

    Surface water is one of the essential resources for supporting sustainable development. The suitability of such water for a given use depends both on the available quantity and tolerable quality. Temporary status for a surface water quality has been identified extensively. Still the suitability of the water for different purposes needs to be verified. This study proposes a water quality evaluation system to assess the aptitude of the Selangor River water for aquatic biota, drinking water production, leisure and aquatic sport, irrigation use, livestock watering, and aquaculture use. Aptitude of the water has been classified in many parts of the river segment as unsuitable for aquatic biota, drinking water production, leisure and aquatic sport as well as aquaculture use. The water quality aptitude classes of the stream water for nine locations along the river are evaluated to contribute to decision support system. The suitability of the water for five different uses and its aquatic ecosystem are verified.

  6. Selection of suitable e-learning approach using TOPSIS technique with best ranked criteria weights

    Science.gov (United States)

    Mohammed, Husam Jasim; Kasim, Maznah Mat; Shaharanee, Izwan Nizal Mohd

    2017-11-01

    This paper compares the performances of four rank-based weighting assessment techniques, Rank Sum (RS), Rank Reciprocal (RR), Rank Exponent (RE), and Rank Order Centroid (ROC) on five identified e-learning criteria to select the best weights method. A total of 35 experts in a public university in Malaysia were asked to rank the criteria and to evaluate five e-learning approaches which include blended learning, flipped classroom, ICT supported face to face learning, synchronous learning, and asynchronous learning. The best ranked criteria weights are defined as weights that have the least total absolute differences with the geometric mean of all weights, were then used to select the most suitable e-learning approach by using TOPSIS method. The results show that RR weights are the best, while flipped classroom approach implementation is the most suitable approach. This paper has developed a decision framework to aid decision makers (DMs) in choosing the most suitable weighting method for solving MCDM problems.

  7. Projected changes in climatic suitability for Kinosternon turtles by 2050 and 2070.

    Science.gov (United States)

    Butler, Christopher J; Stanila, Brian D; Iverson, John B; Stone, Paul A; Bryson, Matthew

    2016-11-01

    Chelonians are expected to be negatively impacted by climate change due to limited vagility and temperature-dependent sex determination. However, few studies have examined how freshwater turtle distributions may shift under different climate change scenarios. We used a maximum entropy approach to model the distribution of five widespread North American Kinosternon species ( K. baurii , K. flavescens , K. hirtipes , K. sonoriense , and K. subrubrum ) under four climate change scenarios. We found that areas with suitable climatic conditions for K. baurii and K. hirtipes are expected to decline substantially during the 21st century. In contrast, the area with suitable climate for K. sonoriense will remain essentially unchanged, while areas suitable for K. flavescens and K. subrubrum are expected to substantially increase. The centroid for the distribution of four of the five species shifted northward, while the centroid for K. sonoriense shifted slightly southward. Overall, centroids shifted at a median rate of 37.5 km per decade across all scenarios. Given the limited dispersal ability of turtles, it appears unlikely that range shifts will occur rapidly enough to keep pace with climate change during the 21st century. The ability of chelonians to modify behavioral and physiological responses in response to unfavorable conditions may allow turtles to persist for a time in areas that have become increasingly unsuitable, but this plasticity will likely only delay local extinctions.

  8. Alien species recorded in the United Arab Emirates: an initial list of terrestrial and freshwater species

    Directory of Open Access Journals (Sweden)

    Pritpal Soorae

    2015-10-01

    Full Text Available Little is documented on the alien terrestrial and freshwater species in the United Arab Emirates. To address this, an assessment of terrestrial and freshwater alien species was conducted using various techniques such as a questionnaire, fieldwork data, networking with relevant people, and a detailed literature review. The results of the initial assessment show that there are 146 alien species recorded in the following seven major taxonomic groups: invertebrates 49 species, freshwater fish five species, amphibian one species, reptiles six species, birds 71 species, mammals six species and plants eight species. To inform decision makers a full list of the 146 species identified in this assessment is presented. 

  9. Novel hantavirus identified in European bat species Nyctalus noctula

    Czech Academy of Sciences Publication Activity Database

    Straková, Petra; Dufková, L.; Širmarová, J.; Salát, J.; Bartonička, T.; Klempa, B.; Pfaff, F.; Höper, D.; Hoffmann, B.; Ulrich, R. G.; Růžek, Daniel

    2017-01-01

    Roč. 48, March (2017), s. 127-130 ISSN 1567-1348 Institutional support: RVO:68081766 ; RVO:60077344 Keywords : Hantavirus * Bat * Phylogenetic analysis * Emerging virus * Bat-borne virus Subject RIV: FN - Epidemiology, Contagious Diseases ; Clinical Immunology; EE - Microbiology, Virology (BC-A) OBOR OECD: Infectious Diseases; Virology (BC-A) Impact factor: 2.885, year: 2016

  10. Suitability of European climate for the Asian tiger mosquito Aedes albopictus: recent trends and future scenarios

    Science.gov (United States)

    Caminade, Cyril; Medlock, Jolyon M.; Ducheyne, Els; McIntyre, K. Marie; Leach, Steve; Baylis, Matthew; Morse, Andrew P.

    2012-01-01

    The Asian tiger mosquito (Aedes albopictus) is an invasive species that has the potential to transmit infectious diseases such as dengue and chikungunya fever. Using high-resolution observations and regional climate model scenarios for the future, we investigated the suitability of Europe for A. albopictus using both recent climate and future climate conditions. The results show that southern France, northern Italy, the northern coast of Spain, the eastern coast of the Adriatic Sea and western Turkey were climatically suitable areas for the establishment of the mosquito during the 1960–1980s. Over the last two decades, climate conditions have become more suitable for the mosquito over central northwestern Europe (Benelux, western Germany) and the Balkans, while they have become less suitable over southern Spain. Similar trends are likely in the future, with an increased risk simulated over northern Europe and slightly decreased risk over southern Europe. These distribution shifts are related to wetter and warmer conditions favouring the overwintering of A. albopictus in the north, and drier and warmer summers that might limit its southward expansion. PMID:22535696

  11. Predicted effects of future climate warming on thermal habitat suitability for Lake Sturgeon (Acipenser fulvescens, Rafinesque, 1817) in rivers in Wisconsin, USA

    Science.gov (United States)

    Lyons, John D.; Stewart, Jana S.

    2015-01-01

    The Lake Sturgeon (Acipenser fulvescens, Rafinesque, 1817) may be threatened by future climate warming. The purpose of this study was to identify river reaches in Wisconsin, USA, where they might be vulnerable to warming water temperatures. In Wisconsin, A. fulvescens is known from 2291 km of large-river habitat that has been fragmented into 48 discrete river-lake networks isolated by impassable dams. Although the exact temperature tolerances are uncertain, water temperatures above 28–30°C are potentially less suitable for this coolwater species. Predictions from 13 downscaled global climate models were input to a lotic water temperature model to estimate amounts of potential thermally less-suitable habitat at present and for 2046–2065. Currently, 341 km (14.9%) of the known habitat are estimated to regularly exceed 28°C for an entire day, but only 6 km (0.3%) to exceed 30°C. In 2046–2065, 685–2164 km (29.9–94.5%) are projected to exceed 28°C and 33–1056 km (1.4–46.1%) to exceed 30°C. Most river-lake networks have cooler segments, large tributaries, or lakes that might provide temporary escape from potentially less suitable temperatures, but 12 short networks in the Lower Fox and Middle Wisconsin rivers totaling 93.6 km are projected to have no potential thermal refugia. One possible adaptation to climate change could be to provide fish passage or translocation so that riverine Lake Sturgeon might have access to more thermally suitable habitats.

  12. Predicting Greater Prairie-Chicken Lek Site Suitability to Inform Conservation Actions.

    Directory of Open Access Journals (Sweden)

    Torre J Hovick

    Full Text Available The demands of a growing human population dictates that expansion of energy infrastructure, roads, and other development frequently takes place in native rangelands. Particularly, transmission lines and roads commonly divide rural landscapes and increase fragmentation. This has direct and indirect consequences on native wildlife that can be mitigated through thoughtful planning and proactive approaches to identifying areas of high conservation priority. We used nine years (2003-2011 of Greater Prairie-Chicken (Tympanuchus cupido lek locations totaling 870 unique leks sites in Kansas and seven geographic information system (GIS layers describing land cover, topography, and anthropogenic structures to model habitat suitability across the state. The models obtained had low omission rates (0.81, indicating high model performance and reliability of predicted habitat suitability for Greater Prairie-Chickens. We found that elevation was the most influential in predicting lek locations, contributing three times more predictive power than any other variable. However, models were improved by the addition of land cover and anthropogenic features (transmission lines, roads, and oil and gas structures. Overall, our analysis provides a hierarchal understanding of Greater Prairie-Chicken habitat suitability that is broadly based on geomorphological features followed by land cover suitability. We found that when land features and vegetation cover are suitable for Greater Prairie-Chickens, fragmentation by anthropogenic sources such as roadways and transmission lines are a concern. Therefore, it is our recommendation that future human development in Kansas avoid areas that our models identified as highly suitable for Greater Prairie-Chickens and focus development on land cover types that are of lower conservation concern.

  13. Development of a seaweed species-selection index for successful culture in a seaweed-based integrated aquaculture system

    Science.gov (United States)

    Kang, Yun Hee; Hwang, Jae Ran; Chung, Ik Kyo; Park, Sang Rul

    2013-03-01

    Integrated multi-trophic aquaculture (IMTA) has been proposed as a concept that combines the cultivation of fed aquaculture species ( e.g., finfish/shrimp) with extractive aquaculture species ( e.g., shellfish/seaweed). In seaweed-based integrated aquaculture, seaweeds have the capacity to reduce the environmental impact of nitrogen-rich effluents on coastal ecosystems. Thus, selection of optimal species for such aquaculture is of great importance. The present study aimed to develop a seaweed species-selection index for selecting suitable species in seaweed-based integrated aquaculture system. The index was synthesized using available literature-based information, reference data, and physiological seaweed experiments to identify and prioritize the desired species. Undaria pinnatifida, Porphyra yezoensis and Ulva compressa scored the highest according to a seaweed-based integrated aquaculture suitability index (SASI). Seaweed species with the highest scores were adjudged to fit the integrated aquaculture systems. Despite the application of this model limited by local aquaculture environment, it is considered to be a useful tool for selecting seaweed species in IMTA.

  14. Different localization patterns of anthocyanin species in the pericarp of black rice revealed by imaging mass spectrometry.

    Directory of Open Access Journals (Sweden)

    Yukihiro Yoshimura

    Full Text Available Black rice (Oryza sativa L. Japonica contains high levels of anthocyanins in the pericarp and is considered an effective health-promoting food. Several studies have identified the molecular species of anthocyanins in black rice, but information about the localization of each anthocyanin species is limited because methodologies for investigating the localization such as determining specific antibodies to anthocyanin, have not yet been developed Matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS is a suitable tool for investigating the localization of metabolites. In this study, we identified 7 species of anthocyanin monoglycosides and 2 species of anthocyanin diglycosides in crude extracts from black rice by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS analysis. We also analyzed black rice sections by MALDI-IMS and found 2 additional species of anthocyanin pentosides and revealed different localization patterns of anthocyanin species composed of different sugar moieties. Anthocyanin species composed of a pentose moiety (cyanidin-3-O-pentoside and petunidin-3-O-pentoside were localized in the entire pericarp, whereas anthocyanin species composed of a hexose moiety (cyanidin-3-O-hexoside and peonidin-3-O-hexoside were focally localized in the dorsal pericarp. These results indicate that anthocyanin species composed of different sugar moieties exhibit different localization patterns in the pericarp of black rice. This is the first detailed investigation into the localization of molecular species of anthocyanins by MALDI-IMS.

  15. Suitability of macrophytes for nutrient removal from surface flow constructed wetlands receiving secondary treated sewage effluent in Queensland, Australia.

    Science.gov (United States)

    Greenway, M

    2003-01-01

    From a botanical perspective the major difference between waste stabilisation ponds and wetlands is the dominance of algae or floating plants in the former and emergent plants in the latter. Algae, floating and submerged plants remove nutrients directly from the water column whereas emergent species remove nutrients from the sediment. Water depth is a crucial factor in determining which plant types will become established. Surface flow constructed wetlands offer the greatest potential to grow a wide variety of different types of macrophytes. In assessing the suitability of plant species for nutrient removal, consideration must be given not only to nutrient uptake for growth but also storage of nutrients as plant biomass. A survey of macrophytes in 15 surface flow constructed wetlands treating secondary effluent was conducted in Queensland; 63 native species and 14 introduced species were found. Emergent species have been able to tolerate deeper water than in their natural environment and permanent waterlogging. All species grew well in the higher nutrient enriched wastewater. Submerged, floating leaved-attached and free floating species had the highest tissue nutrient content, followed by aquatic creepers. All these species remove nutrients from the water column. Emergent species had lower nutrient content but a greater biomass and were therefore able to store more nutrients per unit area of wetland. In order to maximise the efficiency of constructed wetlands for nutrient removal, a range of species should be used. Native species should be selected in preference to introduced/exotic species.

  16. Investigation into the suitability of capillary tubes for microcrystalline testing.

    Science.gov (United States)

    Elie, Leonie E; Baron, Mark G; Croxton, Ruth S; Elie, Mathieu P

    2013-07-01

    A comparison between microcrystalline tests performed on microscope slides and flat capillary tubes with inner diameters ranging from 0.1 to 0.7 mm was carried out to explore the appropriateness of tubes for rapid testing of suspected drugs of abuse in the laboratory as well as in the field. Tests for mephedrone, cocaine, and phencyclidine were chosen as examples to investigate the handling of the capillary tubes, the influence on crystal habit, size, and the effects on the limit of detection. Image stacking software was used to increase the depth of field of micrographs taken from developed microcrystals greatly enhancing the interpretability even months after carrying out the microcrystalline test. Additionally, the potential of seeding capillary tubes with a reagent was studied. Pre-treatment of tubes would allow microcrystalline tests to be carried out quicker and anywhere without the necessity of taking along expensive and hazardous reagents. The sealing of capillary tubes containing developed microcrystalline tests in order to preserve results for a long period of time was successfully done by applying paraffin wax to the open ends. Finally, it was concluded that capillary tubes are suitable vessels for performing microcrystalline tests. The increased portability of the improved set-up allows tests to be safely executed outside laboratories without impairing the quality of the result. Findings were applied to six legal high samples purchased online between May and August 2011. The active ingredients like MDAI as well as cutting agents like caffeine were successfully identified using the microcrystalline test technique in capillary tubes. Copyright © 2012 John Wiley & Sons, Ltd.

  17. Evaluation of the suitability of the WIPP site

    International Nuclear Information System (INIS)

    Neill, R.H.; Channell, J.K.; Chaturvedi, L.; Little, M.S.; Rehfeldt, K.; Spiegler, P.

    1983-05-01

    Determination of the suitability of the site for WIPP is only the first major phase in the evaluation of the radiological impact of the repository on the public health and safety. The Environmental Evaluation Group (EEG) will continue to independently review the design of the facility, the operational procedures, the criteria for packaging and shipment of the waste, the plans, procedures and results of the WIPP experiments, emergency preparedness, adherence to EPA and pertinent NRC regulations, and other important features of the project. EEG has concluded from existing evidence that the Los Medanos site for the WIPP project has been characterized in sufficient detail to warrant confidence in the validation of the site for the permanent emplacement of approximately 6 million cubic feet of defense transuranic waste. This conclusion is based on the assumption that the maximum surface dose rate for the unshielded remote-handled transuranic waste canisters will be 100 rem/hr with a maximum radionuclide concentration of 23 Ci/liter. The Site and Preliminary Design Validation program, through the drilling of two shafts to the selected repository level at 2160 ft below the surface and excavation of about 9000 ft of tunnels, has confirmed the interpretations made about the subsurface geological conditions at the site. For an assessment of the potential radiation effects of the nuclear waste repository on the public health and safety, it is necessary to understand the regional geological and hydrological setting. Much work has been done to understand these conditions and to address several specific issues which have arisen as a result of such studies. However, it is almost inevitable that some questions remain unanswered at a given time in the decision-making process. EEG has identified work which still needs to be done at the Los Medanos site in order to improve confidence in the worst case scenario models of possible breaches of the repository

  18. FORMS OF SUSTAINABLE TOURISM SUITABLE TO APUSENI MOUNTAINS, ROMANIA

    Directory of Open Access Journals (Sweden)

    Bac Dorin Paul

    2015-07-01

    Full Text Available Sustainable tourism is the result of the melange between tourism and sustainable tourism. The concept has evolved during the last decades of the twentieth century, in international conferences, summits etc. organized by the World Tourism Organization, the United Nations and other international organizations where it was defined, characterized and criticized. Unfortunately, the concept was not able to overcome its theoretical conceptualization and it did not reach practitioners of the tourism industry. Sustainable tourism has several forms which are actually practiced by tourists all over the world: ecotourism, backpacking, rural tourism, nature-based tourism, pro-poor tourism, volunteer tourism etc. In the present paper, we have focused on an area in Apuseni Mountains, Romania. We tried to identify the forms of sustainable tourism most suitable for this area considering: natural resources, socio-economical development, protected areas, gastronomic traditions etc. After considering all these we have selected three forms: ecotourism, volunteer tourism and slow tourism, which could have the highest impact in promoting this area, and actually all the Apuseni Mountains as an important destination for sustainable tourism. The arguments for ecotourism are based on the numerous natural tourism resources> caves, gorges, forests and wildlife. Volunteers are needed especially in conservation and English language course. For slow tourism, there are numerous trails for walking and biking. Also there are several foods, mainly based on milk and wild berries that should be promoted and sold under the slow food brand. The shortcomings of the research are the lack of quantitative and qualitative results, as there is no information regarding the number of tourists which visit the area during each year. Also, it is hard to compare the benefits of sustainable tourism with those of mass tourism, due to the lack of references. So it is harder to argue for sustainable

  19. Report of early site suitability evaluation of the potential repository site at Yucca Mountain, Nevada

    International Nuclear Information System (INIS)

    Younker, J.L.; Andrews, W.B.; Fasano, G.A.; Herrington, C.C.; Mattson, S.R.; Murray, R.C.; Ballou, L.B.; Revelli, M.A.; Ducharme, A.R.; Shephard, L.E.; Dudley, W.W.; Hoxie, D.T.; Herbst, R.J.; Patera, E.A.; Judd, B.R.; Docka, J.A.; Rickertsen, L.D.

    1992-01-01

    This study evaluated the technical suitability of Yucca Mountain, Nevada, as a potential site for a mined geologic repository for the permanent disposal of radioactive waste. The evaluation was conducted primarily to determine early in the site characterization program if there are any features or conditions at the site that indicate it is unsuitable for repository development. A secondary purpose was to determine the status of knowledge in the major technical areas that affect the suitability of the site. This early site suitability evaluation (ESSE) was conducted by a team of technical personnel at the request of the Associate Director of the US Department of Energy (DOE) Office of Geologic Disposal, a unit within the DOE's Office of Civilian Radioactive Waste Management. The Yucca Mountain site has been the subject of such evaluations for over a decade. In 1983, the site was evaluated as part of a screening process to identify potentially acceptable sites. The site was evaluated in greater detail and found suitable for site characterization as part of the Environmental Assessment (EA) (DOE, 1986) required by the Nuclear Waste Policy Act of 1982 (NWPA). Additional site data were compiled during the preparation of the Site Characterization Plan (SCP) (DOE, 1988a). This early site suitability evaluation has considered information that was used in preparing both-documents, along with recent information obtained since the EA and SCP were published. This body of information is referred to in this report as ''current information'' or ''available evidence.''

  20. Hearing aid user guides: suitability for older adults.

    Science.gov (United States)

    Caposecco, Andrea; Hickson, Louise; Meyer, Carly

    2014-02-01

    The aim of this study was to analyse the content, design, and readability of printed hearing aid user guides to determine their suitability for older adults, who are the main users of hearing aids. Hearing aid user guides were assessed using four readability formulae and a standardized tool to assess content and design (SAM - Suitability Assessment of Materials). A sample of 36 hearing aid user guides (four user guides from nine different hearing aid manufacturers) were analysed. Sixty nine percent of user guides were rated 'not suitable' and 31% were rated 'adequate' for their suitability. Many scored poorly for scope, vocabulary, aspects of layout and typography, and learning stimulation and motivation. The mean reading grade level for all user guides was grade 9.6 which is too high for older adults. The content, design, and readability of hearing aid user guides are not optimal for older adults and thus may serve as a barrier to successful hearing aid outcomes for this population.

  1. The Importance of Selecting Suitable Components and Apparatus in ...

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 15; Issue 1. The Importance of Selecting Suitable Components and Apparatus in Physics Laboratories. Vijay H Raybagkar. Classroom Volume 15 Issue 1 January 2010 pp 76-82 ...

  2. Suitability of integrated protection diodes from diverse semiconductor technologies

    NARCIS (Netherlands)

    van Wanum, Maurice; Lebouille, Tom; Visser, Guido; van Vliet, Frank Edward

    2009-01-01

    Abstract In this article diodes from three different semiconductor technologies are compared based on their suitability to protect a receiver. The semiconductor materials involved are silicon, gallium arsenide and gallium nitride. The diodes in the diverse semiconductor technologies themselves are

  3. Selecting Suitable Sites for Wind Energy Development in Ghana ...

    African Journals Online (AJOL)

    Selecting Suitable Sites for Wind Energy Development in Ghana. ... In the event of shortages in petroleum products, these power plants will have ... Layers of these criteria setting were combined using the overlay function in a GIS environment.

  4. A RECURSIVE ALGORITHM SUITABLE FOR REAL-TIME MEASUREMENT

    Directory of Open Access Journals (Sweden)

    Giovanni Bucci

    1995-12-01

    Full Text Available This paper deals with a recursive algorithm suitable for realtime measurement applications, based on an indirect technique, useful in those applications where the required quantities cannot be measured in a straightforward way. To cope with time constraints a parallel formulation of it, suitable to be implemented on multiprocessor systems, is presented. The adopted concurrent implementation is based on factorization techniques. Some experimental results related to the application of the system for carrying out measurements on synchronous motors are included.

  5. Isolation and identification of oedogonium species and strains for biomass applications.

    Directory of Open Access Journals (Sweden)

    Rebecca J Lawton

    Full Text Available Freshwater macroalgae from the genus Oedogonium have recently been targeted for biomass applications; however, strains of Oedogonium for domestication have not yet been identified. Therefore, the objective of this study was to compare the performance of isolates of Oedogonium collected from multiple geographic locations under varying environmental conditions. We collected and identified wild-type isolates of Oedogonium from three geographic locations in Eastern Australia, then measured the growth of these isolates under a range of temperature treatments corresponding to ambient conditions in each geographic location. Our sampling identified 11 isolates of Oedogonium that could be successfully maintained under culture conditions. It was not possible to identify most isolates to species level using DNA barcoding techniques or taxonomic keys. However, there were considerable genetic and morphological differences between isolates, strongly supporting each being an identifiable species. Specific growth rates of species were high (>26% day-1 under 7 of the 9 temperature treatments (average tested temperature range: 20.9-27.7°C. However, the variable growth rates of species under lower temperature treatments demonstrated that some were better able to tolerate lower temperatures. There was evidence for local adaptation under lower temperature treatments (winter conditions, but not under higher temperature treatments (summer conditions. The high growth rates we recorded across multiple temperature treatments for the majority of species confirm the suitability of this diverse genus for biomass applications and the domestication of Oedogonium.

  6. Regional prediction of basin-scale brown trout habitat suitability

    Directory of Open Access Journals (Sweden)

    S. Ceola

    2014-09-01

    Full Text Available In this study we propose a novel method for the estimation of ecological indices describing the habitat suitability of brown trout (Salmo trutta. Traditional hydrological tools are coupled with an innovative regional geostatistical technique, aiming at the prediction of the brown trout habitat suitability index where partial or totally ungauged conditions occur. Several methods for the assessment of ecological indices are already proposed in the scientific literature, but the possibility of exploiting a geostatistical prediction model, such as Topological Kriging, has never been investigated before. In order to develop a regional habitat suitability model we use the habitat suitability curve, obtained from measured data of brown trout adult individuals collected in several river basins across the USA. The Top-kriging prediction model is then employed to assess the spatial correlation between upstream and downstream habitat suitability indices. The study area is the Metauro River basin, located in the central part of Italy (Marche