Science.gov

Sample records for linking biomarker community

  1. Community Links

    ERIC Educational Resources Information Center

    Nelson, Mary

    1975-01-01

    At Moraine Valley Community College (Illinois), a chain of events, programs, activities, and services has linked the college and community in such areas as fine arts, ethnic groups, public services, community action, community service, and community education. (Author/NHM)

  2. Linking Archaeal Molecular Diversity and Lipid Biomarker Composition in a Hypersaline Microbial Mat Community

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda; Orphan, Victoria; Turk, Kendra; Embaye, Tsegereda; Kubo, Mike; Summons, Roger

    2005-01-01

    Lipid biomarkers for discrete microbial groups are a valuable tool for establishing links to ancient microbial ecosystems. Lipid biomarkers can establish organism source and function in contemporary microbial ecosystems (membrane lipids) and by analogy, potential relevance to the fossilized carbon skeletons (geolipids) extracted from ancient sedimentary rock. The Mars Exploration Rovers have provided clear evidence for an early wet Mars and the presence of hypersaline evaporitic basins. Ongoing work on an early Earth analog, the hypersaline benthic mats in Guerrero Negro, Baja California Sur, may provide clues to what may have evolved and flourished on an early wet Mars, if only for a short period. Cyanobacterial mats are a pertinent early Earth analog for consideration of evolutionary and microbial processes within the aerobic photosynthetic and adjacent anoxic layers. Fluctuations in physio-chemical parameters associated with spatial and temporal scales are expressed through vast microbial metabolic diversity. Our recent work hopes to establish the dynamic of archaeal diversity, particularly as it relates to methane production in this high sulfate environment, through the use of lipid biomarker and phylogenetic analyses. Archaeal 16s rRNA and mcrA gene assemblages, demonstrated distinct spatial separation over the 130 mm core of at least three distinct genera within the order Methanosarcinales, as well as an abundance of uncultured members of the Thermoplasmales and Crenarchaeota. Ether-bound lipid analysis identified abundant 0-alkyl and 0-isopranyl chains throughout the core, and the presence of sn-2 hydroxyarchaeol, a biomarker for methylotrophic methanogens. A unique ether isoprenoid chain, a C30:1 , possibly related to the geolipid squalane, a paleobiomarker associated with hypersaline environments, was most abundant within the oxic-anoxic transition zone.

  3. Relationships between lines of evidence of pollution in estuarine areas: Linking contaminant levels with biomarker responses in mussels and with structure of macroinvertebrate benthic communities.

    PubMed

    De Los Ríos, A; Echavarri-Erasun, B; Lacorte, S; Sánchez-Ávila, J; De Jonge, M; Blust, R; Orbea, A; Juanes, J A; Cajaraville, M P

    2016-10-01

    Data obtained in a pollution survey performed in estuarine areas were integrated using multivariate statistics. The sites selected for the study were areas affected by treated and untreated urban discharges, harbours or industrial activities as well as reference sites. Mussels were transplanted to each site and after different times of exposure, samples of water, sediments and mussels were collected. Biomarkers were analysed on mussels after 3 and 21 days of transplant whereas concentrations of contaminants were measured in water, sediments and mussels after 21 days of transplant. The structure of macroinvertebrate benthic communities was studied in sediment samples. Studied variables were organised into 5 datasets, each one constituting a line of evidence (LOE): contaminants in water, contaminants in sediments, contaminants accumulated by transplanted mussels, biomarkers in transplanted mussels and changes in the structure of macroinvertebrate benthic communities of each sampling site. Principal Component Analysis (PCA) identified the variables of each LOE best explaining variability among sites. In order to know how LOEs relate to each other, Pearson's correlations were performed. Contaminants in sediments were not correlated with the rest of LOEs. Contaminants in water were significantly correlated with contaminants and biomarkers in mussels and with structure of macroinvertebrate benthic communities. Similarly, significant correlations were found between contaminants and biomarkers in mussels and between biomarkers in mussels and structure of macroinvertebrate benthic communities. In conclusion, biomarker responses give relevant information on pollution in estuarine areas and provide a link between chemical and ecological statuses of water bodies in the context of the Water Framework Directive.

  4. Relationships between lines of evidence of pollution in estuarine areas: Linking contaminant levels with biomarker responses in mussels and with structure of macroinvertebrate benthic communities.

    PubMed

    De Los Ríos, A; Echavarri-Erasun, B; Lacorte, S; Sánchez-Ávila, J; De Jonge, M; Blust, R; Orbea, A; Juanes, J A; Cajaraville, M P

    2016-10-01

    Data obtained in a pollution survey performed in estuarine areas were integrated using multivariate statistics. The sites selected for the study were areas affected by treated and untreated urban discharges, harbours or industrial activities as well as reference sites. Mussels were transplanted to each site and after different times of exposure, samples of water, sediments and mussels were collected. Biomarkers were analysed on mussels after 3 and 21 days of transplant whereas concentrations of contaminants were measured in water, sediments and mussels after 21 days of transplant. The structure of macroinvertebrate benthic communities was studied in sediment samples. Studied variables were organised into 5 datasets, each one constituting a line of evidence (LOE): contaminants in water, contaminants in sediments, contaminants accumulated by transplanted mussels, biomarkers in transplanted mussels and changes in the structure of macroinvertebrate benthic communities of each sampling site. Principal Component Analysis (PCA) identified the variables of each LOE best explaining variability among sites. In order to know how LOEs relate to each other, Pearson's correlations were performed. Contaminants in sediments were not correlated with the rest of LOEs. Contaminants in water were significantly correlated with contaminants and biomarkers in mussels and with structure of macroinvertebrate benthic communities. Similarly, significant correlations were found between contaminants and biomarkers in mussels and between biomarkers in mussels and structure of macroinvertebrate benthic communities. In conclusion, biomarker responses give relevant information on pollution in estuarine areas and provide a link between chemical and ecological statuses of water bodies in the context of the Water Framework Directive. PMID:27017466

  5. Developing community friendly appropriate biomarkers

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In this presentation we discuss the statistical methodology used in the development of biomarkers to track disease as an outcome for nutrition or exercise interventions in community settings. Obesity and co-morbidities are of growing concern. Nutrition and physical activity interventions have been d...

  6. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Embaye, Tsege; Turk, Kendra A.

    2003-01-01

    The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments where microorganisms had virtually no competition apart from the harsh conditions of hypersalinity, desiccation and intense light. Today, the modern counterparts of these microbial ecosystems find appropriate niches in only a few places where extremes eliminate eukaryotic grazers. Answers to many outstanding questions about the evolution of microorganisms and their environments on early Earth are best answered through study of these extant analogs. Lipids associated with various groups of bacteria can be valuable biomarkers for identification of specific groups of microorganisms both in ancient organic-rich sedimentary rocks (geolipids) and contemporary microbial communities (membrane lipids). Use of compound specific isotope analysis adds additional refinement to the identification of biomarker source, so that it is possible to take advantage of the 3C-depletions associated with various functional groups of organisms (i.e. autotrophs, heterotrophs, methanotrophs, methanogens) responsible for the cycling of carbon within a microbial community. Our recent work has focused on a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico which support the abundant growth of Microcoleus-dominated microbial mats. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface.

  7. Linking Families, Building Community.

    ERIC Educational Resources Information Center

    Fowler, R. Clarke; Corley, Kathy Klebs

    1996-01-01

    A year-round magnet elementary school in Salem, Massachusetts, has increased its family involvement by borrowing elements from many models. The school has mixed-age groupings, integrated social services, and community outreach strategies such as a parent center, business-sponsored Friday clubs, and celebrations of learning. (MLH)

  8. Teachers' Link to Community Resources.

    ERIC Educational Resources Information Center

    West Virginia Education Fund, Charleston.

    This directory consists of profiles of more than 500 companies and organizations which responded to a West Virginia Education Fund survey during the summer of 1990. The purposes of the directory are: (1) to provide a reference that helps educators locate resources from business, industry and community groups; (2) to initiate and facilitate…

  9. Lipid Biomarkers for a Hypersaline Microbial Mat Community

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda; Orphan, Victoria; Embaye, Tsegereda; Turk, Kendra; Kubo, Mike; Summons, Roger

    2004-01-01

    The use of lipid biomarkers and their carbon isotopic compositions are valuable tools for establishing links to ancient microbial ecosystems. Various lipids associated with specific microbial groups can serve as biomarkers for establishing organism source and function in contemporary microbial ecosystems (membrane lipids), and by analogy, potential relevance to ancient organic-rich sedimentary rocks (geolipids). As witnessed by the stromatolite record, benthic microbial mats grew in shallow water lagoonal environments. Our recent work has focused on lipid biomarker analysis of a potential analogue for such ancient mats growing in a set of hypersaline evaporation ponds at Guerrero Negro, Baja California Sur, Mexico. The aerobic, surface layer of this mat (0 to 1 mm) contained a variety of ester-bound fatty acids (FA) representing a diverse bacterial population including cyanobacteria, sulphate reducers (SRB) and heterotrophs. Biomarkers for microeukaryotes detected in this layer included sterols, C-20 polyunsaturated FA and a highly branched isoprenoid, diagnostic for diatoms. Cyanobacteria were also indicated by the presence of a diagnostic set of mid-chain methylalkanes. C-28, to C-34 wax esters (WXE) present in relatively small amounts in the upper 3 mm of the mat are considered biomarkers for green non-sulphur bacteria. Ether-bound isoprenoids were also identified although in considerably lower abundance than ester-bound FA (approx. 1:l0). These complex ether lipids included archatol, hydroxyarchaeol and a C-40 tetraether, all in small amounts. After ether cleavage with boron tribromide, the major recovered isoprenyl was a C-30:1. This C(sub 30;1) yelded squalane after hydrogenation, a known geobiomarker for hypersaline environments in ancient oils and sediments. In this mat, it represents the dominant Archaeal population. The carbon isotopic composition of biomarker lipids were generally depleted relative to the bulk organic material (delta C-13 TOC -10%). Most

  10. Weighting links based on edge centrality for community detection

    NASA Astrophysics Data System (ADS)

    Sun, Peng Gang

    2014-01-01

    Link weights have the equally important position as links in complex networks, and they are closely associated with each other for the emergence of communities. How to assign link weights to make a clear distinction between internal links of communities and external links connecting communities is of vital importance for community detection. Edge centralities provide a powerful approach for distinguishing internal links from external ones. Here, we first use edge centralities such as betweenness, information centrality and edge clustering coefficient to weight links of networks respectively to transform unweighted networks into weighted ones, and then a weighted function that both considers links and link weights is adopted on the weighted networks for community detection. We evaluate the performance of our approach on random networks as well as real-world networks. Better results are achieved on weighted networks with stronger weights of internal links of communities, and the results on unweighted networks outperform that of weighted networks with weaker weights of internal links of communities. The availability of our findings is also well-supported by the study of Granovetter that the weak links maintain the global integrity of the network while the strong links maintain the communities. Especially in the Karate club network, all the nodes are correctly classified when we weight links by edge betweenness. The results also give us a more comprehensive understanding on the correlation between links and link weights for community detection.

  11. Linking Biomarker and Comparative Omics to Pathogens in Legumes.

    PubMed

    Diapari, Marwan

    2016-01-01

    It is envisioned that a more precise study of the association between the traits and biomarkers will dramatically decrease the time and costs required to bring new improved disease resistance lines to market. The field of omics has an enormous potential to assess diseases more precise, including the identification and understanding of pathogenic mechanisms in legume crops, and have been exemplified by a relatively large number of studies. Recently, molecular genetic studies have accumulated a huge amount of genotypic data, through a more affordable next generation sequencing (NGS) technology, causing the omics approaches to fall behind. In this paper I provide an overview of genomics and proteomics and their use in legume crops, including the use of comparative genomics to identify homologous markers within legume crops. PMID:26364313

  12. Linking Biomarker and Comparative Omics to Pathogens in Legumes.

    PubMed

    Diapari, Marwan

    2016-01-01

    It is envisioned that a more precise study of the association between the traits and biomarkers will dramatically decrease the time and costs required to bring new improved disease resistance lines to market. The field of omics has an enormous potential to assess diseases more precise, including the identification and understanding of pathogenic mechanisms in legume crops, and have been exemplified by a relatively large number of studies. Recently, molecular genetic studies have accumulated a huge amount of genotypic data, through a more affordable next generation sequencing (NGS) technology, causing the omics approaches to fall behind. In this paper I provide an overview of genomics and proteomics and their use in legume crops, including the use of comparative genomics to identify homologous markers within legume crops.

  13. Identification of hybrid node and link communities in complex networks

    NASA Astrophysics Data System (ADS)

    He, Dongxiao; Jin, Di; Chen, Zheng; Zhang, Weixiong

    2015-03-01

    Identifying communities in complex networks is an effective means for analyzing complex systems, with applications in diverse areas such as social science, engineering, biology and medicine. Finding communities of nodes and finding communities of links are two popular schemes for network analysis. These schemes, however, have inherent drawbacks and are inadequate to capture complex organizational structures in real networks. We introduce a new scheme and an effective approach for identifying complex mixture structures of node and link communities, called hybrid node-link communities. A central piece of our approach is a probabilistic model that accommodates node, link and hybrid node-link communities. Our extensive experiments on various real-world networks, including a large protein-protein interaction network and a large network of semantically associated words, illustrated that the scheme for hybrid communities is superior in revealing network characteristics. Moreover, the new approach outperformed the existing methods for finding node or link communities separately.

  14. Ecology and distribution of a new biomarker linked to 1,2-dichloropropane dechlorination in subsurface environments

    NASA Astrophysics Data System (ADS)

    Padilla-Crespo, E.; Loeffler, F. E.

    2011-12-01

    Reductive dechlorination plays a major role in the transformation and detoxification of chlorinated solvents, including chlorinated ethenes. Molecular biological tools are being applied at contaminated sites in order to assess the process-specific biomarkers that impact site performance, and to monitor the progress of bioremediation approaches. The few current biomarker genes in use provide an incomplete picture of the reductively dechlorinating bacterial community; this is a limitation for implementing enhanced bioremediation and monitored natural attenuation as cleanup strategies at chlorinated solvent contaminated sites. Reductively dehalogenating organisms, particularly Dehalococcoides (Dhc) strains, possess multiple reductive dehalogenase (RDase) genes, which are promising targets to specifically monitor dehalogenation processes of interest. Dehalococcoides populations in two highly enriched cultures (RC and KS) have been implicated in the reductive dechlorination of dechlorination of 1,2-dichloropropane (1,2-D), a widespread halogenated organic pollutant, to the non-toxic propene. Using a combined approach of transcription, expression and molecular analysis a new biomarker linked to 1,2-dichloropropane has been identified in Dhc strains RC and KS providing for the first time, convincing evidence of a specific RDase implicated in 1,2-D dechlorination to propene. Further analyses imply that new biomarker is in a "mobile DNA segment", a genomic island (GI) of horizontal gene transfer origin. A valid quantitative PCR approach was designed to detect and enumerate this gene in cultures and environmental samples; this will be a useful to bioremediation practitioners to more efficiently implement reductive dechlorination as a remediation tool. The new biomarker has been identified in fresh water sediment samples from different geographical locations in Europe, North and South America. Further research aims to shed light on RDase gene dissemination and the adaptation

  15. Biomarker as a Research Tool in Linking Exposure to Air Particles and Respiratory Health

    PubMed Central

    2015-01-01

    Some of the environmental toxicants from air pollution include particulate matter (PM10), fine particulate matter (PM2.5), and ultrafine particles (UFP). Both short- and long-term exposure could result in various degrees of respiratory health outcomes among exposed persons, which rely on the individuals' health status. Methods. In this paper, we highlight a review of the studies that have used biomarkers to understand the association between air particles exposure and the development of respiratory problems resulting from the damage in the respiratory system. Data from previous epidemiological studies relevant to the application of biomarkers in respiratory system damage reported from exposure to air particles are also summarized. Results. Based on these analyses, the findings agree with the hypothesis that biomarkers are relevant in linking harmful air particles concentrations to increased respiratory health effects. Biomarkers are used in epidemiological studies to provide an understanding of the mechanisms that follow airborne particles exposure in the airway. However, application of biomarkers in epidemiological studies of health effects caused by air particles in both environmental and occupational health is inchoate. Conclusion. Biomarkers unravel the complexity of the connection between exposure to air particles and respiratory health. PMID:25984536

  16. Immunization Coverage Surveys and Linked Biomarker Serosurveys in Three Regions in Ethiopia

    PubMed Central

    Travassos, Mark A.; Beyene, Berhane; Adam, Zenaw; Campbell, James D.; Mulholland, Nigisti; Diarra, Seydou S.; Kassa, Tassew; Oot, Lisa; Sequeira, Jenny; Reymann, Mardi; Blackwelder, William C.; Wu, Yukun; Ruslanova, Inna; Goswami, Jaya; Sow, Samba O.; Pasetti, Marcela F.; Steinglass, Robert; Kebede, Amha; Levine, Myron M.

    2016-01-01

    Objective Demographic and health surveys, immunization coverage surveys and administrative data often divergently estimate vaccination coverage, which hinders pinpointing districts where immunization services require strengthening. We assayed vaccination coverage in three regions in Ethiopia by coverage surveys and linked serosurveys. Methods Households with children aged 12–23 (N = 300) or 6–8 months (N = 100) in each of three districts (woredas) were randomly selected for immunization coverage surveys (inspection of vaccination cards and immunization clinic records and maternal recall) and linked serosurveys. IgG-ELISA serologic biomarkers included tetanus antitoxin ≥ 0.15 IU/ml in toddlers (receipt of tetanus toxoid) and Haemophilus influenzae type b (Hib) anti-capsular titers ≥ 1.0 mcg/ml in infants (timely receipt of Hib vaccine). Findings Coverage surveys enrolled 1,181 children across three woredas; 1,023 (87%) also enrolled in linked serosurveys. Administrative data over-estimated coverage compared to surveys, while maternal recall was unreliable. Serologic biomarkers documented a hierarchy among the districts. Biomarker measurement in infants provided insight on timeliness of vaccination not deducible from toddler results. Conclusion Neither administrative projections, vaccination card or EPI register inspections, nor parental recall, substitute for objective serological biomarker measurement. Including infants in serosurveys informs on vaccination timeliness. PMID:26934372

  17. Biomarkers Linking PCB Exposure and Obesity£

    PubMed Central

    Ghosh, Somiranjan; Murinova, Lubica; Trnovec, Tomas; Loffredo, Christopher A.; Washington, Kareem; Mitra, Partha S.; Dutta, Sisir K.

    2015-01-01

    Recently the prevalence of obesity has increased dramatically across much of the world. Obesity, as a complex, multifactorial disease, and its health consequences probably result from the interplay of environmental, genetic, and behavioral factors. Several lines of evidence support the theory that obesity is programmed during early development and that environmental exposures can play a key role. We therefore hypothesize that the current epidemic might associated with the influence of chemical exposures upon genetically controlled developmental pathways, leading to metabolic disorders. Some environmental chemicals, such as PCBs and pesticide residues, are widespread in food, drinking water, soil, and they exert multiple effects including estrogenic on cellular processes; some have been shown to affect the development of obesity, insulin resistance, type 2 diabetes, and metabolic syndrome. To bring these lines of evidence together and address an important health problem, this narrative review has been primarily designed to address PCBs exposures that have linked with human disease, obesity in particular, and to assess the effects of PCBs on gene expression in a highly-exposed population. The results strongly suggest that further research into the specific mechanisms of PCBs-associated diseases is warranted. PMID:25420728

  18. Linking biomarkers to reproductive success of caged fathead minnows in streams with increasing urbanization

    USGS Publications Warehouse

    Crago, J.; Corsi, S.R.; Weber, D.; Bannerman, R.; Klaper, R.

    2011-01-01

    Reproductive and oxidative stress biomarkers have been recommended as tools to assess the health of aquatic organisms. Though validated in the laboratory, there are few studies that tie a change in gene expression to adverse reproductive or population outcomes in the field. This paper looked at 17 streams with varying degrees of urbanization to assess the use of biomarkers associated with reproduction or stress in predicting reproductive success of fathead minnows. In addition, the relationship between biomarkers and water quality measures in streams with varying degrees of urbanization was examined. Liver vitellogenin mRNA was correlated with reproduction within a period of 11. d prior to sampling irrespective of habitat, but its correlation with egg output declined at 12. d and beyond indicating its usefulness as a short-term biomarker but its limits as a biomarker of total reproductive output. Stress biomarkers such as glutathione S-transferase may be better correlated with factors affecting reproduction over a longer term. There was a significant correlation between GST mRNA and a variety of anthropogenic pollutants. There was also an inverse correlation between glutathione S-transferase and the amount of the watershed designated as wetland. Egg production over the 21-d was negatively correlated with the amount of urbanization and positively correlated to wetland habitats. This study supports the development of multiple biomarkers linking oxidative stress and other non-reproductive endpoints to changes in aquatic habitats will be useful for predicting the health of fish populations and identifying the environmental factors that may need mitigation for sustainable population management. ?? 2010 Elsevier Ltd.

  19. Virtual Rural Community Development: Human Links That Sustain Web Links.

    ERIC Educational Resources Information Center

    Bright, Larry K.; Evans, Wayne H.; Marmet, Kathy

    Outmigration in the rural Upper Midwest prompted a group of citizens and University of South Dakota faculty to form the Center for the Advancement of Rural Communities (ARC). ARC considers how to stimulate traditionally competitive and isolated South Dakota peoples to collaborate for economic, social, educational, political, and cultural gains. As…

  20. Link community detection using generative model and nonnegative matrix factorization.

    PubMed

    He, Dongxiao; Jin, Di; Baquero, Carlos; Liu, Dayou

    2014-01-01

    Discovery of communities in complex networks is a fundamental data analysis problem with applications in various domains. While most of the existing approaches have focused on discovering communities of nodes, recent studies have shown the advantages and uses of link community discovery in networks. Generative models provide a promising class of techniques for the identification of modular structures in networks, but most generative models mainly focus on the detection of node communities rather than link communities. In this work, we propose a generative model, which is based on the importance of each node when forming links in each community, to describe the structure of link communities. We proceed to fit the model parameters by taking it as an optimization problem, and solve it using nonnegative matrix factorization. Thereafter, in order to automatically determine the number of communities, we extend the above method by introducing a strategy of iterative bipartition. This extended method not only finds the number of communities all by itself, but also obtains high efficiency, and thus it is more suitable to deal with large and unexplored real networks. We test this approach on both synthetic benchmarks and real-world networks including an application on a large biological network, and compare it with two highly related methods. Results demonstrate the superior performance of our approach over competing methods for the detection of link communities.

  1. Linking case management and community development.

    PubMed

    Austin, Carol D; McClelland, Robert W; Gursansky, Di

    2006-01-01

    Case management, in various forms, is now institutionalized as a core part of policy and programs designed to deliver home- and community-based services to older adults. The case management role, in theory, requires attention to both client and system goals, although in practice the system goals that have received most attention have been gatekeeping and resource allocation. While case managers have been admonished to find and develop resources in the community, this has primarily taken the form of including informal services in individual client care plans. What has been missing is focused attention to the potential of the community as a nurturing environment with the capacity to support older adults and their caregivers. Sustainable care for older adults cannot be achieved by formal service and family support alone. This article proposes the creation of linkages between case managers, who build the service arrangements for older people, and community developers, who are responsible for building community capacity and social capital. It is argued that this linkage is essential for establishing the foundations of a caring community with the capacity to support older people.

  2. Biomarkers in community-acquired pneumonia: A state-of-the-art review

    PubMed Central

    Seligman, Renato; Ramos-Lima, Luis Francisco; do Amaral Oliveira, Vivian; Sanvicente, Carina; Pacheco, Elyara F.; Rosa, Karoline Dalla

    2012-01-01

    Community-acquired pneumonia (CAP) exhibits mortality rates, between 20% and 50% in severe cases. Biomarkers are useful tools for searching for antibiotic therapy modifications and for CAP diagnosis, prognosis and follow-up treatment. This non-systematic state-of-the-art review presents the biological and clinical features of biomarkers in CAP patients, including procalcitonin, C-reactive protein, copeptin, pro-ANP (atrial natriuretic peptide), adrenomedullin, cortisol and D-dimers. PMID:23184211

  3. Communities of Coaches: The Missing Link

    ERIC Educational Resources Information Center

    Barnson, Steven C.

    2010-01-01

    Interscholastic coaches have unique needs relative to how they learn their practice and progress toward higher levels of professional comfort and competence. The purpose of this article is to review the professional development needs of interscholastic coaches and suggest the use of social-learning techniques, specifically communities of practice,…

  4. Environmental Justice: A Crucial Link between Environmentalism and Community Development?

    ERIC Educational Resources Information Center

    Hillman, Mick

    2002-01-01

    Environmental justice provides a linking theme with which community development workers and environmental activists can build cross-sectoral coalitions. Examples of Australian environmental problems illustrate constraints that must be overcome. Building vertical and horizontal links between and within nongovernmental organizations is one solution.…

  5. Linking Academic and Community Guidelines for Community-Engaged Scholarship

    ERIC Educational Resources Information Center

    DeLugan, Robin Maria; Roussos, Stergios; Skram, Geneva

    2014-01-01

    Research universities seeking to promote community-engaged scholarship (CES), defined here as research of mutual benefit to community and academic interests, will discover that it requires capacity building and institutional support. At the University of California at Merced, our 7-year experience in building a new public research university that…

  6. Linked Learning Communities. What Works Clearinghouse Intervention Report

    ERIC Educational Resources Information Center

    What Works Clearinghouse, 2014

    2014-01-01

    Linked learning communities in postsecondary education are programs defined by having social and curricular linkages that provide undergraduate students with intentional integration of the themes and concepts that they are learning. The theory behind these programs is that active learning in a community-based setting can improve academic outcomes…

  7. Linking changes in community composition and function under climate change.

    PubMed

    Mokany, Karel; Thomson, Joshua J; Lynch, Jasmyn J; Jordan, Gregory J; Ferrier, Simon

    2015-12-01

    Climate change is expected to directly alter the composition of communities and the functioning of ecosystems across the globe. Improving our understanding of links between biodiversity and ecosystem functioning across large spatial scales and rapid global change is a major priority to help identify management responses that will retain diverse, functioning systems. Here we address this challenge by linking projected changes in plant community composition and functional attributes (height, leaf area, seed mass) under climate change across Tasmania, Australia. Using correlative community-level modeling, we found that projected changes in plant community composition were not consistently related to projected changes in community mean trait values. In contrast, we identified specific mechanisms through which alternative combinations of projected functional and compositional change across Tasmania could be realized, including loss/replacement of functionally similar species (lowland grasslands/grassy woodlands) and loss of a small number of functionally unique species (lowland forests). Importantly, we demonstrate how these linked projections of change in community composition and functional attributes can be utilized to inform specific management actions that may assist in maintaining diverse, functioning ecosystems under climate change.

  8. Community Websites: Linking the Personal to Urban History

    ERIC Educational Resources Information Center

    de Wildt, Annemarie

    2013-01-01

    New technology enables museums and other heritage institutions to establish more personal links with their audience, and hopefully by doing so make history more compelling to them. The author explores some Dutch practices with interactive community websites and other ways of making connections between personal stories and urban history.

  9. Community detection in networks with positive and negative links

    NASA Astrophysics Data System (ADS)

    Traag, V. A.; Bruggeman, Jeroen

    2009-09-01

    Detecting communities in complex networks accurately is a prime challenge, preceding further analyses of network characteristics and dynamics. Until now, community detection took into account only positively valued links, while many actual networks also feature negative links. We extend an existing Potts model to incorporate negative links as well, resulting in a method similar to the clustering of signed graphs, as dealt with in social balance theory, but more general. To illustrate our method, we applied it to a network of international alliances and disputes. Using data from 1993-2001, it turns out that the world can be divided into six power blocs similar to Huntington’s civilizations, with some notable exceptions.

  10. Active link selection for efficient semi-supervised community detection.

    PubMed

    Yang, Liang; Jin, Di; Wang, Xiao; Cao, Xiaochun

    2015-01-01

    Several semi-supervised community detection algorithms have been proposed recently to improve the performance of traditional topology-based methods. However, most of them focus on how to integrate supervised information with topology information; few of them pay attention to which information is critical for performance improvement. This leads to large amounts of demand for supervised information, which is expensive or difficult to obtain in most fields. For this problem we propose an active link selection framework, that is we actively select the most uncertain and informative links for human labeling for the efficient utilization of the supervised information. We also disconnect the most likely inter-community edges to further improve the efficiency. Our main idea is that, by connecting uncertain nodes to their community hubs and disconnecting the inter-community edges, one can sharpen the block structure of adjacency matrix more efficiently than randomly labeling links as the existing methods did. Experiments on both synthetic and real networks demonstrate that our new approach significantly outperforms the existing methods in terms of the efficiency of using supervised information. It needs ~13% of the supervised information to achieve a performance similar to that of the original semi-supervised approaches. PMID:25761385

  11. Linking the levels: network and relational perspectives for community psychology.

    PubMed

    Neal, Jennifer Watling; Christens, Brian D

    2014-06-01

    In this article, we assert that relationships and networks are of paramount importance for understanding and improving settings, neighborhoods, communities, and larger social systems. Despite previous acknowledgements of their relevance, relational and social network perspectives and analyses remain underrepresented in community psychological research and action. Here, we claim that network and relational perspectives can provide conceptual and empirical 'links' between levels of analysis, more fully reflecting a transactional view. We also describe some of the sophisticated methodologies that can be employed in empirical studies drawing on these perspectives. Additionally, we contend that core concepts in community psychology such as health promotion, empowerment, coalition building, and dissemination and implementation can be better understood when employing relational and network perspectives. As an introduction to this special issue of American Journal of Community Psychology, we draw out themes and key points from the articles in the issue, and offer recommendations for future advancement of these perspectives in the field.

  12. Linking community size structure and ecosystem functioning using metabolic theory

    PubMed Central

    Yvon-Durocher, Gabriel; Allen, Andrew P.

    2012-01-01

    Understanding how biogeochemical cycles relate to the structure of ecological communities is a central research question in ecology. Here we approach this problem by focusing on body size, which is an easily measured species trait that has a pervasive influence on multiple aspects of community structure and ecosystem functioning. We test the predictions of a model derived from metabolic theory using data on ecosystem metabolism and community size structure. These data were collected as part of an aquatic mesocosm experiment that was designed to simulate future environmental warming. Our analyses demonstrate significant linkages between community size structure and ecosystem functioning, and the effects of warming on these links. Specifically, we show that carbon fluxes were significantly influenced by seasonal variation in temperature, and yielded activation energies remarkably similar to those predicted based on the temperature dependencies of individual-level photosynthesis and respiration. We also show that community size structure significantly influenced fluxes of ecosystem respiration and gross primary production, particularly at the annual time-scale. Assessing size structure and the factors that control it, both empirically and theoretically, therefore promises to aid in understanding links between individual organisms and biogeochemical cycles, and in predicting the responses of key ecosystem functions to future environmental change. PMID:23007088

  13. Linking sub-cellular biomarkers to embryo aberrations in the benthic amphipod Monoporeia affinis.

    PubMed

    Reutgard, Martin; Furuhagen, Sara

    2016-04-01

    To adequately assess and monitor environmental status in the aquatic environment a broad approach is needed that integrates physical variables, chemical analyses and biological effects at different levels of the biological organization. Embryo aberrations in the Baltic Sea key species Monoporeia affinis can be induced by both metals and organic substances as well as by hypoxia, increasing temperatures and malnutrition. This amphipod has therefore been used for more than three decades as a biological effect indicator in monitoring and assessment of chemical pollution and environmental stress. However, little is known about the sub-cellular mechanisms underlying embryo aberrations. An improved mechanistic understanding may open up the possibility of including sub-cellular alterations as sensitive warning signals of stress-induced embryo aberrations. In the present study, M. affinis was exposed in microcosms to 4 different sediments from the Baltic Sea. After 88-95 days of exposure, survival and fecundity were determined as well as the frequency and type of embryo aberrations. Moreover, oxygen radical absorption capacity (ORAC) was assayed as a proxy for antioxidant defense, thiobarbituric acid reactive substances (TBARS) level as a measure of lipid peroxidation and acetylcholinesterase (AChE) activity as an indicator of neurotoxicity. The results show that AChE and ORAC can be linked to the frequency of malformed embryos and arrested embryo development. The occurrence of dead broods was significantly associated with elevated TBARS levels. It can be concluded that these sub-cellular biomarkers are indicative of effects that could affect Darwinian fitness and that oxidative stress is a likely mechanism in the development of aberrant embryos in M. affinis. PMID:26836507

  14. Linking sub-cellular biomarkers to embryo aberrations in the benthic amphipod Monoporeia affinis.

    PubMed

    Reutgard, Martin; Furuhagen, Sara

    2016-04-01

    To adequately assess and monitor environmental status in the aquatic environment a broad approach is needed that integrates physical variables, chemical analyses and biological effects at different levels of the biological organization. Embryo aberrations in the Baltic Sea key species Monoporeia affinis can be induced by both metals and organic substances as well as by hypoxia, increasing temperatures and malnutrition. This amphipod has therefore been used for more than three decades as a biological effect indicator in monitoring and assessment of chemical pollution and environmental stress. However, little is known about the sub-cellular mechanisms underlying embryo aberrations. An improved mechanistic understanding may open up the possibility of including sub-cellular alterations as sensitive warning signals of stress-induced embryo aberrations. In the present study, M. affinis was exposed in microcosms to 4 different sediments from the Baltic Sea. After 88-95 days of exposure, survival and fecundity were determined as well as the frequency and type of embryo aberrations. Moreover, oxygen radical absorption capacity (ORAC) was assayed as a proxy for antioxidant defense, thiobarbituric acid reactive substances (TBARS) level as a measure of lipid peroxidation and acetylcholinesterase (AChE) activity as an indicator of neurotoxicity. The results show that AChE and ORAC can be linked to the frequency of malformed embryos and arrested embryo development. The occurrence of dead broods was significantly associated with elevated TBARS levels. It can be concluded that these sub-cellular biomarkers are indicative of effects that could affect Darwinian fitness and that oxidative stress is a likely mechanism in the development of aberrant embryos in M. affinis.

  15. Molecular and lipid biomarker analysis of a gypsum-hosted endoevaporitic microbial community.

    PubMed

    Jahnke, L L; Turk-Kubo, K A; N Parenteau, M; Green, S J; Kubo, M D Y; Vogel, M; Summons, R E; Des Marais, D J

    2014-01-01

    Modern evaporitic microbial ecosystems are important analogs for understanding the record of earliest life on Earth. Although mineral-depositing shallow-marine environments were prevalent during the Precambrian, few such environments are now available today for study. We investigated the molecular and lipid biomarker composition of an endoevaporitic gypsarenite microbial mat community in Guerrero Negro, Mexico. The 16S ribosomal RNA gene-based phylogenetic analyses of this mat corroborate prior observations indicating that characteristic layered microbial communities colonize gypsum deposits world-wide despite considerable textural and morphological variability. Membrane fatty acid analysis of the surface tan/orange and lower green mat crust layers indicated cell densities of 1.6 × 10(9) and 4.2 × 10(9)  cells cm(-3) , respectively. Several biomarker fatty acids, ∆7,10-hexadecadienoic, iso-heptadecenoic, 10-methylhexadecanoic, and a ∆12-methyloctadecenoic, correlated well with distributions of Euhalothece, Stenotrophomonas, Desulfohalobium, and Rhodobacterales, respectively, revealed by the phylogenetic analyses. Chlorophyll (Chl) a and cyanobacterial phylotypes were present at all depths in the mat. Bacteriochlorophyl (Bchl) a and Bchl c were first detected in the oxic-anoxic transition zone and increased with depth. A series of monomethylalkanes (MMA), 8-methylhexadecane, 8-methylheptadecane, and 9-methyloctadecane were present in the surface crust but increased in abundance in the lower anoxic layers. The MMA structures are similar to those identified previously in cultures of the marine Chloroflexus-like organism 'Candidatus Chlorothrix halophila' gen. nov., sp. nov., and may represent the Bchl c community. Novel 3-methylhopanoids were identified in cultures of marine purple non-sulfur bacteria and serve as a probable biomarker for this group in the lower anoxic purple and olive-black layers. Together microbial culture and environmental analyses

  16. The role of biomarkers in community-acquired pneumonia: predicting mortality and response to adjunctive therapy

    PubMed Central

    Mira, Jean-Paul; Max, Adeline; Burgel, Pierre-Regis

    2008-01-01

    Patients with community-acquired pneumonia (CAP) in the hospital setting exhibit markedly abnormal levels of various biomarkers of infection, inflammation and coagulation. CAP is a well characterized disease, relatively homogeneous and amenable to management according to defined protocols. Hence, this group of patients represents an opportunity to investigate further these biomarkers as a means of determining disease severity and identifying candidates for new therapies. Changes in biomarker levels during the course of disease may enable physicians to identify those patients who are most at risk for deterioration and progression toward severe CAP and who are in greatest need of early intervention. Subgroup analysis of the placebo-controlled OPTIMIST trial of tifacogin in severe sepsis revealed a trend toward benefit in patients with procalcitonin levels of 2 ng/ml or greater and in those with high baseline markers of activated coagulation. Biomarker studies are being undertaken as part of the ongoing CAPTIVATE study. This study includes patients with severe CAP and will compare the efficacy and safety of recombinant tissue factor pathway inhibitor (tifacogin) versus placebo. In the future it may also be possible to use genomic markers to identify patients at greatest risk for deterioration or complications. PMID:19105798

  17. MetaBoot: a machine learning framework of taxonomical biomarker discovery for different microbial communities based on metagenomic data

    PubMed Central

    Wang, Xiaojun; Su, Xiaoquan

    2015-01-01

    As more than 90% of species in a microbial community could not be isolated and cultivated, the metagenomic methods have become one of the most important methods to analyze microbial community as a whole. With the fast accumulation of metagenomic samples and the advance of next-generation sequencing techniques, it is now possible to qualitatively and quantitatively assess all taxa (features) in a microbial community. A set of taxa with presence/absence or their different abundances could potentially be used as taxonomical biomarkers for identification of the corresponding microbial community’s phenotype. Though there exist some bioinformatics methods for metagenomic biomarker discovery, current methods are not robust, accurate and fast enough at selection of non-redundant biomarkers for prediction of microbial community’s phenotype. In this study, we have proposed a novel method, MetaBoot, that combines the techniques of mRMR (minimal redundancy maximal relevance) and bootstrapping, for discover of non-redundant biomarkers for microbial communities through mining of metagenomic data. MetaBoot has been tested and compared with other methods on well-designed simulated datasets considering normal and gamma distribution as well as publicly available metagenomic datasets. Results have shown that MetaBoot was robust across datasets of varied complexity and taxonomical distribution patterns and could also select discriminative biomarkers with quite high accuracy and biological consistency. Thus, MetaBoot is suitable for robustly and accurately discover taxonomical biomarkers for different microbial communities. PMID:26213658

  18. Linking ‘toxic outliers’ to environmental justice communities

    NASA Astrophysics Data System (ADS)

    Collins, Mary B.; Munoz, Ian; JaJa, Joseph

    2016-01-01

    Several key studies have found that a small minority of producers, polluting at levels far exceeding group averages, generate the majority of overall exposure to industrial toxics. Frequently, such patterns go unnoticed and are understudied outside of the academic community. To our knowledge, no research to date has systematically described the scope and extent of extreme variations in industrially based exposure estimates and sought to link inequities in harm produced to inequities in exposure. In an analysis of all permitted industrial facilities across the United States, we show that there exists a class of hyper-polluters—the worst-of-the-worst—that disproportionately expose communities of color and low income populations to chemical releases. This study hopes to move beyond a traditional environmental justice research frame, bringing new computational methods and perspectives aimed at the empirical study of societal power dynamics. Our findings suggest the possibility that substantial environmental gains may be made through selective environmental enforcement, rather than sweeping initiatives.

  19. Enlarging the Academic Community: Creating Retirement Communities Linked to Academic Institutions

    ERIC Educational Resources Information Center

    Harrison, Andrew; Tsao, Tien-Chien

    2006-01-01

    This article explores a major opportunity that universities have to capitalize on their existing property portfolio to both earn additional revenue and enhance the quality of the student and staff experience: the creation of university-linked retirement communities. We examine this opportunity in the context of demographic and educational trends…

  20. Protein Biomarkers for Insulin Resistance and Type 2 Diabetes Risk in Two Large Community Cohorts.

    PubMed

    Nowak, Christoph; Sundström, Johan; Gustafsson, Stefan; Giedraitis, Vilmantas; Lind, Lars; Ingelsson, Erik; Fall, Tove

    2016-01-01

    Insulin resistance (IR) is a precursor of type 2 diabetes (T2D), and improved risk prediction and understanding of the pathogenesis are needed. We used a novel high-throughput 92-protein assay to identify circulating biomarkers for HOMA of IR in two cohorts of community residents without diabetes (n = 1,367) (mean age 73 ± 3.6 years). Adjusted linear regression identified cathepsin D and confirmed six proteins (leptin, renin, interleukin-1 receptor antagonist [IL-1ra], hepatocyte growth factor, fatty acid-binding protein 4, and tissue plasminogen activator [t-PA]) as IR biomarkers. Mendelian randomization analysis indicated a positive causal effect of IR on t-PA concentrations. Two biomarkers, IL-1ra (hazard ratio [HR] 1.28, 95% CI 1.03-1.59) and t-PA (HR 1.30, 1.02-1.65) were associated with incident T2D, and t-PA predicted 5-year transition to hyperglycemia (odds ratio 1.30, 95% CI 1.02-1.65). Additional adjustment for fasting glucose rendered both coefficients insignificant and revealed an association between renin and T2D (HR 0.79, 0.62-0.99). LASSO regression suggested a risk model including IL-1ra, t-PA, and the Framingham Offspring Study T2D score, but prediction improvement was nonsignificant (difference in C-index 0.02, 95% CI -0.08 to 0.12) over the T2D score only. In conclusion, proteomic blood profiling indicated cathepsin D as a new IR biomarker and suggested a causal effect of IR on t-PA. PMID:26420861

  1. Community-based knowledge transfer and exchange: Helping community-based organizations link research to action

    PubMed Central

    2010-01-01

    Background Community-based organizations (CBOs) are important stakeholders in health systems and are increasingly called upon to use research evidence to inform their advocacy, program planning, and service delivery efforts. CBOs increasingly turn to community-based research (CBR) given its participatory focus and emphasis on linking research to action. In order to further facilitate the use of research evidence by CBOs, we have developed a strategy for community-based knowledge transfer and exchange (KTE) that helps CBOs more effectively link research evidence to action. We developed the strategy by: outlining the primary characteristics of CBOs and why they are important stakeholders in health systems; describing the concepts and methods for CBR and for KTE; comparing the efforts of CBR to link research evidence to action to those discussed in the KTE literature; and using the comparison to develop a framework for community-based KTE that builds on both the strengths of CBR and existing KTE frameworks. Discussion We find that CBR is particularly effective at fostering a climate for using research evidence and producing research evidence relevant to CBOs through community participation. However, CBOs are not always as engaged in activities to link research evidence to action on a larger scale or to evaluate these efforts. Therefore, our strategy for community-based KTE focuses on: an expanded model of 'linkage and exchange' (i.e., producers and users of researchers engaging in a process of asking and answering questions together); a greater emphasis on both producing and disseminating systematic reviews that address topics of interest to CBOs; developing a large-scale evidence service consisting of both 'push' efforts and efforts to facilitate 'pull' that highlight actionable messages from community relevant systematic reviews in a user-friendly way; and rigorous evaluations of efforts for linking research evidence to action. Summary Through this type of strategy

  2. Interpreting Recent Water Quality Changes in Florida Bay in a Paleoecological Context Using Diatoms and Linked Organic Biomarkers

    NASA Astrophysics Data System (ADS)

    Gaiser, E. E.; Wachnicka, A.; Xu, Y.; Jaffe, R.; Fourqurean, J.

    2005-05-01

    Recent alterations in the quality and quantity of freshwater flowing into Florida Bay from the Everglades and surrounding landscape of south Florida has altered the salinity and nutrient regime of the Bay. To interpret these changes with respect to natural variability in this ecosystem we conducted a multiproxy paleoecological investigation at several sites in the Bay. Sediments were cored to bedrock, chronologically calibrated using conventional radiometric methods and sampled at 2 cm intervals for a variety of paleoenvironmental proxies including diatoms, organic biomarkers and nutrient concentrations. Interpretations of paleoenvironmental settings were based on habitat specificities of diatoms and their relationships to biomarkers and nutrients determined by a survey of the modern environment. Signatures in basal peat deposits suggest fresh to brackish-water mangrove-dominated communities existed in central Florida Bay as little as 2000 YBP. Overlying marl contains benthic diatom assemblages indicative of a shallow, seagrass-dominated marine environment that experienced large, decadal-scale fluctuations in salinity. Recent sediments (<100 years) reveal a third zone that contains a flora that is compositionally dissimilar to those occurring in the past. Together with organic biomarkers, phosphorus and nitrogen data, the recent diatom record generally suggests a transition to conditions favoring proliferation of planktonic algae over benthic epiphytes, suggesting displacement of primary production from seagrass beds (which have declined in aerial extent) to the plankton as water-borne nutrients become more available. Several sites show an increase in diatom-inferred salinity after 1990, while the amplitude of fluctuation in salinity has declined.

  3. Monitoring human lymphocytic DNA-protein cross-links as biomarkers of biologically active doses of chromate.

    PubMed

    Costa, M; Zhitkovich, A; Toniolo, P; Taioli, E; Popov, T; Lukanova, A

    1996-10-01

    A simple and sensitive assay for DNA-protein cross-links has been used as a biomarker of chromate exposure and early carcinogenic effects. Pilot studies of DNA-protein cross-links in peripheral blood lymphocytes have been conducted with individuals who had higher exposure to chromate, including welders, and with individuals who had lower levels of exposure such as residents living in a chromium-contaminated area in Jersey City, New Jersey. Studies were also conducted in two Bulgarian cities (Jambol and Burgas) with different levels of air pollution and Cr(VI) exposure and in chrome platers in Bulgaria who had high exposure to chromate. DNA-protein cross-links in U.S. welders and in individuals living in Hudson County, New Jersey around chromium-contaminated areas were significantly higher compared to matched controls. Although blood and urinary levels of chromium were not extensively studied in these populations, we were able to obtain these measurements in the Bulgarian population. Chromium levels in red blood cells of controls living in Burgas were in the order of 1 to 2 ppb chromium, and these individuals had the lowest levels of DNA-protein cross-links. However, the chromium levels in Jambol ranged from about 2 to 7 ppb in red blood cells of city residents to about 22 ppb in chrome platers. DNA-protein cross-links were saturated at about 7 to 8 ppb chromium in the red blood cells, and cross-links correlated well only with chromium levels in red blood cells. Urinary chromium levels did not correlate well with either DNA-protein cross-links or chromium levels in with red blood cells.

  4. Monitoring human lymphocytic DNA-protein cross-links as biomarkers of biologically active doses of chromate.

    PubMed Central

    Costa, M; Zhitkovich, A; Toniolo, P; Taioli, E; Popov, T; Lukanova, A

    1996-01-01

    A simple and sensitive assay for DNA-protein cross-links has been used as a biomarker of chromate exposure and early carcinogenic effects. Pilot studies of DNA-protein cross-links in peripheral blood lymphocytes have been conducted with individuals who had higher exposure to chromate, including welders, and with individuals who had lower levels of exposure such as residents living in a chromium-contaminated area in Jersey City, New Jersey. Studies were also conducted in two Bulgarian cities (Jambol and Burgas) with different levels of air pollution and Cr(VI) exposure and in chrome platers in Bulgaria who had high exposure to chromate. DNA-protein cross-links in U.S. welders and in individuals living in Hudson County, New Jersey around chromium-contaminated areas were significantly higher compared to matched controls. Although blood and urinary levels of chromium were not extensively studied in these populations, we were able to obtain these measurements in the Bulgarian population. Chromium levels in red blood cells of controls living in Burgas were in the order of 1 to 2 ppb chromium, and these individuals had the lowest levels of DNA-protein cross-links. However, the chromium levels in Jambol ranged from about 2 to 7 ppb in red blood cells of city residents to about 22 ppb in chrome platers. DNA-protein cross-links were saturated at about 7 to 8 ppb chromium in the red blood cells, and cross-links correlated well only with chromium levels in red blood cells. Urinary chromium levels did not correlate well with either DNA-protein cross-links or chromium levels in with red blood cells. PMID:8933034

  5. Rheumatoid Arthritis: Notable Biomarkers Linking to Chronic Systemic Conditions and Cancer.

    PubMed

    Olumuyiwa-Akeredolu, Oore-Ofe O; Pretorius, Etheresia

    2016-01-01

    Adult rheumatoid arthritis (RA) is an autoimmune disorder affecting joints and frequently characterised by initial local and later systemic inflammation. Researchers have, for many years, traced its cause to diverse genetic, environmental and especially immunological responses that work against the body's own cells and tissues. Investigation into several of these biomarkers reveals interconnections that exist between multiple factors, which ultimately lead to specific pathologies. The goal of this paper is to highlight connections present between the major biological players long identified by researchers including more recently uncovered biomarkers in the RA repertoire and some of the pathophysiologies typically affiliated with the disease. Biomarkers reviewed, and becoming more clearly defined for RA include genetic, cytokines like tumor-necrosis factor-α (TNF-α), lymphocytes, nuclear antigens, antibodies to citrullinated peptides (anti-CPs), acute-phase proteins (APPs), microRNA, S100 proteins, platelets and erythrocytes. Some of the disease manifestations that have been connected are bone erosion, diabetes, metabolic syndrome, anemia, synovitis, felty's syndrome, extra-articular manifestations (EAMs) such as atherosclerosis, rheumatoid nodules and cardiovascular (CV) events. Several RA markers associated with malignancy have been identified in literature although there is insufficient evidence of cancer in patients. Due to the complex nature of the disease, the appearance of symptoms and markers vary amongst individuals and the connections may manifest only in part. This manuscript addresses defining factors relevant to rapid identification of pathological influences these biomolecules could exert and to the management of the disease. Each of these biological players may have its place in connecting to symptomatic pathologies and help to highlight potential targets for therapy. PMID:26648464

  6. Lipid metabolites as potential diagnostic and prognostic biomarkers for acute community acquired pneumonia.

    PubMed

    To, Kelvin K W; Lee, Kim-Chung; Wong, Samson S Y; Sze, Kong-Hung; Ke, Yi-Hong; Lui, Yin-Ming; Tang, Bone S F; Li, Iris W S; Lau, Susanna K P; Hung, Ivan F N; Law, Chun-Yiu; Lam, Ching-Wan; Yuen, Kwok-Yung

    2016-06-01

    Early diagnosis of acute community-acquired pneumonia (CAP) is important in patient triage and treatment decisions. To identify biomarkers that distinguish patients with CAP from non-CAP controls, we conducted an untargeted global metabolome analysis for plasma samples from 142 patients with CAP (CAP cases) and 97 without CAP (non-CAP controls). Thirteen lipid metabolites could discriminate between CAP cases and non-CAP controls with area-under-the-receiver-operating-characteristic curve of >0.8 (P ≤ 10(-9)). The levels of glycosphingolipids, sphingomyelins, lysophosphatidylcholines and L-palmitoylcarnitine were higher, while the levels of lysophosphatidylethanolamines were lower in the CAP cases than those in non-CAP controls. All 13 metabolites could distinguish CAP cases from the non-infection, extrapulmonary infection and non-CAP respiratory tract infection subgroups. The levels of trihexosylceramide (d18:1/16:0) were higher, while the levels of lysophosphatidylethanolamines were lower, in the fatal than those of non-fatal CAP cases. Our findings suggest that lipid metabolites are potential diagnostic and prognostic biomarkers for CAP.

  7. Novel serologic biomarkers provide accurate estimates of recent Plasmodium falciparum exposure for individuals and communities

    PubMed Central

    Helb, Danica A.; Tetteh, Kevin K. A.; Felgner, Philip L.; Skinner, Jeff; Hubbard, Alan; Arinaitwe, Emmanuel; Mayanja-Kizza, Harriet; Ssewanyana, Isaac; Kamya, Moses R.; Beeson, James G.; Tappero, Jordan; Smith, David L.; Crompton, Peter D.; Rosenthal, Philip J.; Dorsey, Grant; Drakeley, Christopher J.; Greenhouse, Bryan

    2015-01-01

    Tools to reliably measure Plasmodium falciparum (Pf) exposure in individuals and communities are needed to guide and evaluate malaria control interventions. Serologic assays can potentially produce precise exposure estimates at low cost; however, current approaches based on responses to a few characterized antigens are not designed to estimate exposure in individuals. Pf-specific antibody responses differ by antigen, suggesting that selection of antigens with defined kinetic profiles will improve estimates of Pf exposure. To identify novel serologic biomarkers of malaria exposure, we evaluated responses to 856 Pf antigens by protein microarray in 186 Ugandan children, for whom detailed Pf exposure data were available. Using data-adaptive statistical methods, we identified combinations of antibody responses that maximized information on an individual’s recent exposure. Responses to three novel Pf antigens accurately classified whether an individual had been infected within the last 30, 90, or 365 d (cross-validated area under the curve = 0.86–0.93), whereas responses to six antigens accurately estimated an individual’s malaria incidence in the prior year. Cross-validated incidence predictions for individuals in different communities provided accurate stratification of exposure between populations and suggest that precise estimates of community exposure can be obtained from sampling a small subset of that community. In addition, serologic incidence predictions from cross-sectional samples characterized heterogeneity within a community similarly to 1 y of continuous passive surveillance. Development of simple ELISA-based assays derived from the successful selection strategy outlined here offers the potential to generate rich epidemiologic surveillance data that will be widely accessible to malaria control programs. PMID:26216993

  8. Five Cities, One Vision. CORAL: Linking Communities, Children and Learning.

    ERIC Educational Resources Information Center

    James G. Irvine Foundation, San Francisco, CA.

    This booklet describes the CORAL (Communities Organizing Resources To Advance Learning) program within five California communities: Pasadena, Long Beach, San Jose, Fresno, and Sacramento. This initiative, begun in 1999, is committed to a community-based and community-building approach to supporting learning and focuses on improving academic…

  9. Cross-Site Soil Microbial Communities under Tillage Regimes: Fungistasis and Microbial Biomarkers

    PubMed Central

    Yrjälä, Kim; Alakukku, Laura; Palojärvi, Ansa

    2012-01-01

    The exploitation of soil ecosystem services by agricultural management strategies requires knowledge of microbial communities in different management regimes. Crop cover by no-till management protects the soil surface, reducing the risk of erosion and nutrient leaching, but might increase straw residue-borne and soilborne plant-pathogenic fungi. A cross-site study of soil microbial communities and Fusarium fungistasis was conducted on six long-term agricultural fields with no-till and moldboard-plowed treatments. Microbial communities were studied at the topsoil surface (0 to 5 cm) and bottom (10 to 20 cm) by general bacterial and actinobacterial terminal restriction fragment length polymorphism (T-RFLP) and phospholipid fatty acid (PLFA) analyses. Fusarium culmorum soil fungistasis describing soil receptivity to plant-pathogenic fungi was explored by using the surface layer method. Soil depth had a significant impact on general bacterial as well as actinobacterial communities and PLFA profiles in no-till treatment, with a clear spatial distinction of communities (P < 0.05), whereas the depth-related separation of microbial communities was not observed in plowed fields. The fungal biomass was higher in no-till surface soil than in plowed soil (P < 0.07). Soil total microbial biomass and fungal biomass correlated with fungistasis (P < 0.02 for the sum of PLFAs; P < 0.001 for PLFA 18:2ω6). Our cross-site study demonstrated that agricultural management strategies can have a major impact on soil microbial community structures, indicating that it is possible to influence the soil processes with management decisions. The interactions between plant-pathogenic fungi and soil microbial communities are multifaceted, and a high level of fungistasis could be linked to the high microbial biomass in soil but not to the specific management strategy. PMID:22983972

  10. Direct Evidence Linking Soil Organic Matter Development to Microbial Communities

    NASA Astrophysics Data System (ADS)

    Kallenbach, C.; Grandy, S.

    2013-12-01

    Despite increasing recognition of microbial contributions to soil organic matter (SOM) formation there is little experimental evidence linking microbial processes to SOM development and the mechanisms responsible remain unclear. Specifically, if stable SOM is largely comprised of microbial products, we need to better understand the soil conditions that influence microbial biomass production and ultimately its stability. Microbial physiology, such as microbial growth efficiency (MGE) and rate (MGR) have direct influences on microbial biomass production and are highly sensitive to resource quality. Therefore, the importance of resource quality on SOM is not necessarily a function of resistance to decay but the degree to which it optimizes microbial biomass production. While resource quality may have an indirect effect on SOM abundance via its influence on microbial physiology, SOM stabilization of labile microbial products may rely heavily on a soil's capacity to form organo-mineral interactions. To examine the relative importance of soil microbial community function, resource quality and mineralogy on direct microbial contributions to SOM formation and stability, an ongoing 15-mo incubation experiment was set up using artificial, initially C- and microbial-free soils. Soil microcosms were constructed by mixing sand with either kaolinite or montmorillonite clays followed with a natural soil microbial inoculum. For both soil mineral treatments, weekly additions of glucose, cellobiose, or syringol are carried out, with an additional treatment of plant leachate to serve as a reference. This simplified system allows us to determine if, in the absence of plant-derived C, microbial products using simple substrates can result in chemically complex SOM similar to natural soils. Over the course of the incubation, MGE, MGR, microbial activity, and SOM accumulation rates are monitored. Pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) is used to track the microbial

  11. The Critical Link: Community Colleges and the Workforce.

    ERIC Educational Resources Information Center

    Falcone, Lisa, Ed.

    In 1993, the American Association of Community Colleges (AACC) sponsored five activities designed to build the capacity of community colleges to respond to workforce development needs of employers and employees through contract training services. Three of these activities targeted community college-based business/industry liaisons, who provide a…

  12. Discovering link communities in complex networks by an integer programming model and a genetic algorithm.

    PubMed

    Li, Zhenping; Zhang, Xiang-Sun; Wang, Rui-Sheng; Liu, Hongwei; Zhang, Shihua

    2013-01-01

    Identification of communities in complex networks is an important topic and issue in many fields such as sociology, biology, and computer science. Communities are often defined as groups of related nodes or links that correspond to functional subunits in the corresponding complex systems. While most conventional approaches have focused on discovering communities of nodes, some recent studies start partitioning links to find overlapping communities straightforwardly. In this paper, we propose a new quantity function for link community identification in complex networks. Based on this quantity function we formulate the link community partition problem into an integer programming model which allows us to partition a complex network into overlapping communities. We further propose a genetic algorithm for link community detection which can partition a network into overlapping communities without knowing the number of communities. We test our model and algorithm on both artificial networks and real-world networks. The results demonstrate that the model and algorithm are efficient in detecting overlapping community structure in complex networks.

  13. Metal-linked Immunosorbent Assay (MeLISA): the Enzyme-Free Alternative to ELISA for Biomarker Detection in Serum.

    PubMed

    Yu, Ru-Jia; Ma, Wei; Liu, Xiao-Yuan; Jin, Hong-Ying; Han, Huan-Xing; Wang, Hong-Yang; Tian, He; Long, Yi-Tao

    2016-01-01

    Determination of disease biomarkers in clinical samples is of crucial significance for disease monitoring and public health. The dominating format is enzyme-linked immunosorbent assay (ELISA), which subtly exploits both the antigen-antibody reaction and biocatalytic property of enzymes. Although enzymes play an important role in this platform, they generally suffer from inferior stability and less tolerant of temperature, pH condition compared with general chemical product. Here, we demonstrate a metal-linked immunosorbent assay (MeLISA) based on a robust signal amplification mechanism that faithfully replaces the essential element of the enzyme. As an enzyme-free alternative to ELISA, this methodology works by the detection of α-fetoprotein (AFP), prostatic specific antigen (PSA) and C-reactive protein (CRP) at concentrations of 0.1 ng mL(-1), 0.1 ng mL(-1) and 1 ng mL(-1) respectively. It exhibits approximately two magnitudes higher sensitivity and is 4 times faster for chromogenic reaction than ELISA. The detection of AFP and PSA was further confirmed by over a hundred serum samples from hepatocellular carcinoma (HCC) and prostate cancer patients respectively. PMID:27446504

  14. Metal-linked Immunosorbent Assay (MeLISA): the Enzyme-Free Alternative to ELISA for Biomarker Detection in Serum

    PubMed Central

    Yu, Ru-Jia; Ma, Wei; Liu, Xiao-Yuan; Jin, Hong-Ying; Han, Huan-Xing; Wang, Hong-Yang; Tian, He; Long, Yi-Tao

    2016-01-01

    Determination of disease biomarkers in clinical samples is of crucial significance for disease monitoring and public health. The dominating format is enzyme-linked immunosorbent assay (ELISA), which subtly exploits both the antigen-antibody reaction and biocatalytic property of enzymes. Although enzymes play an important role in this platform, they generally suffer from inferior stability and less tolerant of temperature, pH condition compared with general chemical product. Here, we demonstrate a metal-linked immunosorbent assay (MeLISA) based on a robust signal amplification mechanism that faithfully replaces the essential element of the enzyme. As an enzyme-free alternative to ELISA, this methodology works by the detection of α-fetoprotein (AFP), prostatic specific antigen (PSA) and C-reactive protein (CRP) at concentrations of 0.1 ng mL-1, 0.1 ng mL-1 and 1 ng mL-1 respectively. It exhibits approximately two magnitudes higher sensitivity and is 4 times faster for chromogenic reaction than ELISA. The detection of AFP and PSA was further confirmed by over a hundred serum samples from hepatocellular carcinoma (HCC) and prostate cancer patients respectively. PMID:27446504

  15. Linking Workforce Development to Economic Development: A Casebook for Community Colleges

    ERIC Educational Resources Information Center

    Rothwell, William J., Ed.; Gerity, Patrick E., Ed.

    2008-01-01

    "Linking Workforce Development to Economic Development: A Casebook for Community Colleges" is a compilation of best practice examples, which illustrate what it takes for community colleges to achieve their goal of helping people acquire education and skills, helping employers, supporting communities, and building the nation. The book is written…

  16. Local Route to the Info Superhighway: How Schools Can Forge Community Links.

    ERIC Educational Resources Information Center

    Blenz-Clucas, Beth

    1996-01-01

    Describes how schools and public libraries can link with their communities in public networks (freenets) to provide access to the Internet and other community and educational resources. Discusses the origins of cybercasting, how freenets are used, an educational online service called Academy One, telecommunications community projects in Montana…

  17. Utilization of DNA-protein cross-links as a biomarker of chromium exposure.

    PubMed Central

    Zhitkovich, A; Voitkun, V; Kluz, T; Costa, M

    1998-01-01

    Human exposure to carcinogenic Cr(VI) compounds is found among workers in a large number of professional groups, and it can also occur through environmental pollution. A significant number of toxic waste sites contain Cr as a major contaminant. In this paper we summarize our efforts to apply measurements of DNA-protein cross-links (DPC) as test for biologically active doses of Cr(VI). DPC were found at elevated levels in lymphocytes in several human populations with low to medium Cr exposures. At high exposure to Cr(VI), exemplified by a group of Bulgarian chromeplaters, DPC plateaued and adducts' levels were similar to those found in environmentally exposed individuals. Lymphocytic DPC correlated strongly with Cr levels in erythrocytes that are indicative of Cr(VI) exposure. DPC in lymphocytes were not confounded by such variables as smoking, age, body weight, gender, or ethnicity. A new version of the cross-link assay offers improved sensitivity and requires a small amount of biologic material. Preliminary results indicate that the ability of DPC to reach detectable levels at low levels of Cr exposure could be related to a lack of repair of these lesions in lymphoid cells. Cr(III)-mediated cross-links of DNA with peptide glutathione or single amino acids were mutagenic in human cells, with a relationship of higher molecular weight of the peptide/amino acid correlating with a more potent mutagenic response. We speculate that bulky DPC could also have a significant promutagenic effect. The current methodology does not allow specific determination of Cr-induced DPC; however, demonstrated sensitivity of DPC measurements and the assay's large sample capacity may allow this assay to be used as the initial screening test for the occurrence of DNA damage in Cr(VI)-exposed populations. PMID:9703480

  18. Linking community programs in environment to programs in population: towards sustainable communities that sustain sanctuaries.

    PubMed

    Cincotta, R P

    1994-01-01

    This article briefly reviews several nongovernmental organization (NGO) programs that address environmental and population issues. A framework is constructed that identifies how linked programs are supposed to work. The potential for sustainable communities is explored. It is concluded that sanctuaries in developing countries will not survive unless population in surrounding communities is stabilized and the economic and ecological relationships between the community and the sanctuary ecosystem are sustainable. In developed countries resource needs must be identified in regional planning in order for environmental protection to occur. The author finds that NGOs can be instrumental in securing community participation in environmental protection. NGOs operating in Chiapas, Mexico, provide management assistance and public health and family planning awareness to displaced indigenous farmers and conservative professionals. Another NGO outside the Ranthambhore National Park in Rajasthan, India, works to promote alternative fuel and grazing sources among local farmers. Near Chautara, in Nepal, farmers are aided by NGOs in laying sanitary water pipes, which reduces the amount of women's time required for fetching water and increases the amount of time women can spend gardening or getting involved in environmental projects. NGO efforts that reduce women's time absorbed by domestic burdens help women fulfill family planning desires and allow for greater investment in the education of children. Environmental sustainability will be dependent on family planning and other population-related processes and on the awareness that public health is an environmental issue. Opposition to integrated environment and population programs stems from donor opposition, opposition to investment in low-density areas, and a priority on biodiversity issues over development of public health services near sanctuaries. This paper was presented at an international forum at the George Washington

  19. Free health clinic links college, church, and community.

    PubMed

    Carey, Rebekah Albrecht; Fricke, Jonathan

    2011-01-01

    Granville Neighborhood Health Center (GNHC) in Milwaukee, Wisconsin, was conceived out of community need and the vision of Risen Savior Lutheran Church, Wisconsin Lutheran College (WLC), and community leaders. GNHC offers free healthcare services monthly to the uninsured and a service-learning and clinical site for nursing and other students at the college.

  20. Socio-Economic Importance of Links between Campuses, Communities, and International Students and Alumni: Perceptions of Collegiate and Community Leaders.

    ERIC Educational Resources Information Center

    Smith, Harold A.

    A Mississippi State University study investigated the perceptions of community and higher education leaders (N=197) concerning the potential socio-economic importance to Americans of establishing continuing links among communities, colleges and universities, and international students and alumni. Individuals surveyed include academic vice…

  1. Modelling Optimal Control of Cholera in Communities Linked by Migration.

    PubMed

    Njagarah, J B H; Nyabadza, F

    2015-01-01

    A mathematical model for the dynamics of cholera transmission with permissible controls between two connected communities is developed and analysed. The dynamics of the disease in the adjacent communities are assumed to be similar, with the main differences only reflected in the transmission and disease related parameters. This assumption is based on the fact that adjacent communities often have different living conditions and movement is inclined toward the community with better living conditions. Community specific reproduction numbers are given assuming movement of those susceptible, infected, and recovered, between communities. We carry out sensitivity analysis of the model parameters using the Latin Hypercube Sampling scheme to ascertain the degree of effect the parameters and controls have on progression of the infection. Using principles from optimal control theory, a temporal relationship between the distribution of controls and severity of the infection is ascertained. Our results indicate that implementation of controls such as proper hygiene, sanitation, and vaccination across both affected communities is likely to annihilate the infection within half the time it would take through self-limitation. In addition, although an infection may still break out in the presence of controls, it may be up to 8 times less devastating when compared with the case when no controls are in place. PMID:26246850

  2. Principles To Link By. Integrating Education, Health, and Human Services for Children, Youth, and Families: Systems That Are Community-Based and School-Linked. Final Report.

    ERIC Educational Resources Information Center

    American Academy of Pediatrics, Washington, DC.

    This report describes the importance, collaboration procedure, and principles of linking integrated service systems that are community-based and school-linked, established by the National Consensus Building Conference on School Linked Integrated Service Systems. The consensus principles aim to create comprehensive, effective, community-based…

  3. Linking community resources in diabetes care: a role for technology?

    PubMed

    Tung, Elizabeth L; Peek, Monica E

    2015-07-01

    Designing and implementing effective lifestyle modification strategies remains one of the great challenges in diabetes care. Historically, programs have focused on individual behavior change with little or no attempt to integrate change within the broader social framework or community context. However, these contextual factors have been shown to be associated with poor diabetes outcomes, particularly in low-income minority populations. Recent evidence suggests that one way to address these disparities is to match patient needs to existing community resources. Not only does this position patients to more quickly adapt behavior in a practical way, but this also refers patients back to their local communities where a support mechanism is in place to sustain healthy behavior. Technology offers a new and promising platform for connecting patients to meaningful resources (also referred to as "assets"). This paper summarizes several noteworthy innovations that use technology as a practical bridge between healthcare and community-based resources that promote diabetes self-care. PMID:25994856

  4. Linking community resources in diabetes care: a role for technology?

    PubMed

    Tung, Elizabeth L; Peek, Monica E

    2015-07-01

    Designing and implementing effective lifestyle modification strategies remains one of the great challenges in diabetes care. Historically, programs have focused on individual behavior change with little or no attempt to integrate change within the broader social framework or community context. However, these contextual factors have been shown to be associated with poor diabetes outcomes, particularly in low-income minority populations. Recent evidence suggests that one way to address these disparities is to match patient needs to existing community resources. Not only does this position patients to more quickly adapt behavior in a practical way, but this also refers patients back to their local communities where a support mechanism is in place to sustain healthy behavior. Technology offers a new and promising platform for connecting patients to meaningful resources (also referred to as "assets"). This paper summarizes several noteworthy innovations that use technology as a practical bridge between healthcare and community-based resources that promote diabetes self-care.

  5. Testing pathways linking exposure to community violence and sexual behaviors among African American youth.

    PubMed

    Voisin, Dexter R; Hotton, Anna L; Neilands, Torsten B

    2014-09-01

    Exposure to community violence and HIV sexual risks are two major public health concerns among youth. This study tests various pathways linking exposure to community violence and sexual behaviors among African American adolescents. Using a sample of 563 (61% females) African American youth attending high school we examined whether problematic psychological symptoms, low school engagement, and/or negative perceptions of peer norms about safer sex functioned as pathways linking exposure to community violence and sexual behaviors. Major findings indicated that, for boys, the relationship between exposure to community violence and sexual début and sexual risk behaviors were linked by aggression. In addition, the relationship between exposure to community violence and sexual risk behaviors were linked by negative perceptions of peer attitudes about safer sex. For girls, the relationship between exposure to community violence and sexual début was linked by aggression and negative perceptions of peer attitudes about safer sex. These findings provide support for pathways linking exposure to community violence to sexual behaviors.

  6. An edge-centric perspective on the human connectome: link communities in the brain.

    PubMed

    de Reus, Marcel A; Saenger, Victor M; Kahn, René S; van den Heuvel, Martijn P

    2014-10-01

    Brain function depends on efficient processing and integration of information within a complex network of neural interactions, known as the connectome. An important aspect of connectome architecture is the existence of community structure, providing an anatomical basis for the occurrence of functional specialization. Typically, communities are defined as groups of densely connected network nodes, representing clusters of brain regions. Looking at the connectome from a different perspective, instead focusing on the interconnecting links or edges, we find that the white matter pathways between brain regions also exhibit community structure. Eleven link communities were identified: five spanning through the midline fissure, three through the left hemisphere and three through the right hemisphere. We show that these link communities are consistently identifiable and investigate the network characteristics of their underlying white matter pathways. Furthermore, examination of the relationship between link communities and brain regions revealed that the majority of brain regions participate in multiple link communities. In particular, the highly connected and central hub regions showed a rich level of community participation, supporting the notion that these hubs play a pivotal role as confluence zones in which neural information from different domains merges.

  7. An edge-centric perspective on the human connectome: link communities in the brain

    PubMed Central

    de Reus, Marcel A.; Saenger, Victor M.; Kahn, René S.; van den Heuvel, Martijn P.

    2014-01-01

    Brain function depends on efficient processing and integration of information within a complex network of neural interactions, known as the connectome. An important aspect of connectome architecture is the existence of community structure, providing an anatomical basis for the occurrence of functional specialization. Typically, communities are defined as groups of densely connected network nodes, representing clusters of brain regions. Looking at the connectome from a different perspective, instead focusing on the interconnecting links or edges, we find that the white matter pathways between brain regions also exhibit community structure. Eleven link communities were identified: five spanning through the midline fissure, three through the left hemisphere and three through the right hemisphere. We show that these link communities are consistently identifiable and investigate the network characteristics of their underlying white matter pathways. Furthermore, examination of the relationship between link communities and brain regions revealed that the majority of brain regions participate in multiple link communities. In particular, the highly connected and central hub regions showed a rich level of community participation, supporting the notion that these hubs play a pivotal role as confluence zones in which neural information from different domains merges. PMID:25180305

  8. "A Culture-Brain Link: Negative Age Stereotypes Predict Alzheimer's Disease Biomarkers": Correction to Levy et al. (2016).

    PubMed

    2016-02-01

    Reports an error in "A Culture-Brain Link: Negative Age Stereotypes Predict Alzheimer's Disease Biomarkers" by Becca R. Levy, Luigi Ferrucci, Alan B. Zonderman, Martin D. Slade, Juan Troncoso and Susan M. Resnick (Psychology and Aging, Advanced Online Publication, Dec 7, 2015, np). In the article, the correct analyses were reported for bootstrapping; however, the sizes of the bootstrapping samples for Studies 1 and 2 were reversed. (The following abstract of the original article appeared in record 2015-54839-001.) Although negative age stereotypes have been found to predict adverse outcomes among older individuals, it was unknown whether the influence of stereotypes extends to brain changes associated with Alzheimer's disease. To consider this possibility, we drew on dementia-free participants, in the Baltimore Longitudinal Study of Aging, whose age stereotypes were assessed decades before yearly magnetic resonance images and brain autopsies were performed. Those holding more-negative age stereotypes earlier in life had significantly steeper hippocampal-volume loss and significantly greater accumulation of neurofibrillary tangles and amyloid plaques, adjusting for relevant covariates. These findings suggest a new pathway to identifying mechanisms and potential interventions related to the pathology of Alzheimer's disease.

  9. C26:0-Carnitine Is a New Biomarker for X-Linked Adrenoleukodystrophy in Mice and Man

    PubMed Central

    van de Beek, Malu-Clair; Dijkstra, Inge M. E.; van Lenthe, Henk; Ofman, Rob; Goldhaber-Pasillas, Dalia; Schauer, Nicolas; Schackmann, Martin; Engelen-Lee, Joo-Yeon; Vaz, Frédéric M.; Kulik, Wim; Wanders, Ronald J. A.; Engelen, Marc; Kemp, Stephan

    2016-01-01

    X-linked adrenoleukodystrophy (ALD), a progressive neurodegenerative disease, is caused by mutations in ABCD1 and characterized by very-long-chain fatty acids (VLCFA) accumulation. Virtually all males develop progressive myelopathy (AMN). A subset of patients, however, develops a fatal cerebral demyelinating disease (cerebral ALD). Hematopoietic stem cell transplantation is curative for cerebral ALD provided the procedure is performed in an early stage of the disease. Unfortunately, this narrow therapeutic window is often missed. Therefore, an increasing number of newborn screening programs are including ALD. To identify new biomarkers for ALD, we developed an Abcd1 knockout mouse with enhanced VLCFA synthesis either ubiquitous or restricted to oligodendrocytes. Biochemical analysis revealed VLCFA accumulation in different lipid classes and acylcarnitines. Both C26:0-lysoPC and C26:0-carnitine were highly elevated in brain, spinal cord, but also in bloodspots. We extended the analysis to patients and confirmed that C26:0-carnitine is also elevated in bloodspots from ALD patients. We anticipate that validation of C26:0-carnitine for the diagnosis of ALD in newborn bloodspots may lead to a faster inclusion of ALD in newborn screening programs in countries that already screen for other inborn errors of metabolism. PMID:27124591

  10. Building healthy communities for children: The transportation link

    SciTech Connect

    Holmes, H.

    1995-09-01

    Two concepts are essential to a definition of a healthy community: social justice and ecological sustainability. These principles must be at the heart of creating healthy communities, cities, and regions. Children and young people are an integral part of socially just and ecologically sustainable communities. Transportation and land-use policies are critical tools for shaping healthy communities, cities, and regions. The health impacts of the private automobile and its full cost to society, including public health and environmental damage costs, need to be clearly understood. The developing physiology of children put them at particular risk to medical impacts of automobile emissions and air pollution. The public health impacts of transportation and land-use policies cannot be divorced from the planning and decision-making process. Transit, bicycle, and pedestrian-oriented transportation modes can serve the transportation needs of children and can stimulate land uses more conducive to a healthy social, economic, and environmental quality of life. This article comments on the combined issues of social justice and ecological sustainability for building the best communities for meeting the needs of children and young adults. 3 refs.

  11. Structured decision making as a method for linking quantitative decision support to community fundamental objectives

    EPA Science Inventory

    Decision support intended to improve ecosystem sustainability requires that we link stakeholder priorities directly to quantitative tools and measures of desired outcomes. Actions taken at the community level can have large impacts on production and delivery of ecosystem service...

  12. Injuries and Safe Communities Accreditation: Is there a link?

    PubMed

    Sinelnikov, Sergey; Friedman, Lee S; Chavez, Emily A

    2016-06-01

    Safe Communities (SC) is a global movement that brings together community stakeholders to collaboratively address injury concerns. SC accreditation is a formal process through which communities are recognized for strengthening local injury prevention capacity. Six million Americans live in 25 SC sites, but no research has been done to understand the model's potential impact on this population. This study explored the temporal relationship between SC accreditation and injury trends in three SC sites from the state of Illinois-Arlington Heights, Itasca, and New Lenox. Hospitalization data, including patient demographics, exposure information, injury outcomes, and economic variables, were obtained from a statewide hospital discharge database for a 12-year period (1999-2011). Joinpoint regression models were fitted to identify any periods of significant change, examine the direction of the injury trend, and to estimate monthly percent changes in injury counts and rates. Poisson random-intercept regression measured the average total change since the official SC accreditation for the three communities combined and compared them to three matched control sites. In joinpoint regression, one of the SC sites showed a 10-year increase in hospitalization cases and rates followed by a two-year decline, and the trend reversal occurred while the community was pursuing the SC accreditation. Injury hospitalizations decreased after accreditation compared to the pre-accreditation period when SC sites were compared to their control counterparts using Poisson modeling. Our findings suggest that the SC model may be a promising approach to reduce injuries. Further research is warranted to replicate these findings in other communities.

  13. Community Involvement: Linking Parents and Non-Parents.

    ERIC Educational Resources Information Center

    Kenner, Lynn; Gribbin, Randall

    1992-01-01

    To ensure the success of its enrichment activities program, a Texas elementary school formed principal assistants committees (PACs) comprised of highly diverse community volunteer coordinators. In the PAC program, parents, nonparents, and educators work together, sharing problems and solutions while supporting each others' efforts. Sidebars list…

  14. Linking Schools and Communities; Kids Building Portfolios of Their Lives.

    ERIC Educational Resources Information Center

    Shelton, Jack

    2000-01-01

    Place makes learning relevant and underlies identity. When schools give kids tools and expectations and integrate them into their curricular and extracurricular activities, the school becomes a creative force in a community. Then students can produce outcomes that demonstrate their abilities, enhance the reputation of their schools, and make a…

  15. "Why Fly That Way?" Linking Community and Academic Achievement.

    ERIC Educational Resources Information Center

    Greely, Kathy

    This book tells the story of a year in one middle school teacher's class full of lively young adolescents, highlighting exemplary ways of learning and types of schooling. This alternative model of education shows how a strong, supportive community is essential in helping students reach their highest potential. The book includes: specific projects…

  16. Linking Microbial Community Structure to Function in Representative Simulated Systems

    PubMed Central

    Marcus, Ian M.; Wilder, Hailey A.; Quazi, Shanin J.

    2013-01-01

    Pathogenic bacteria are generally studied as a single strain under ideal growing conditions, although these conditions are not the norm in the environments in which pathogens typically proliferate. In this investigation, a representative microbial community along with Escherichia coli O157:H7, a model pathogen, was studied in three environments in which such a pathogen could be found: a human colon, a septic tank, and groundwater. Each of these systems was built in the lab in order to retain the physical/chemical and microbial complexity of the environments while maintaining control of the feed into the models. The microbial community in the colon was found to have a high percentage of bacteriodetes and firmicutes, while the septic tank and groundwater systems were composed mostly of proteobacteria. The introduction of E. coli O157:H7 into the simulated systems elicited a shift in the structures and phenotypic cell characteristics of the microbial communities. The fate and transport of the microbial community with E. coli O157:H7 were found to be significantly different from those of E. coli O157:H7 studied as a single isolate, suggesting that the behavior of the organism in the environment was different from that previously conceived. The findings in this study clearly suggest that to gain insight into the fate of pathogens, cells should be grown and analyzed under conditions simulating those of the environment in which the pathogens are present. PMID:23396331

  17. The effect of a community-based, primary health care exercise program on inflammatory biomarkers and hormone levels.

    PubMed

    Papini, Camila Bosquiero; Nakamura, Priscila M; Zorzetto, Lucas P; Thompson, Janice L; Phillips, Anna C; Kokubun, Eduardo

    2014-01-01

    The aim of this study was to analyze the impact of a community-based exercise program in primary care on inflammatory biomarkers and hormone levels. The 1-year quasiexperimental study involved 13 women (mean age = 56.8 ± 11.4 years) and it was developed in two basic health care units in Rio Claro City, Brazil. The physical exercise intervention was comprised of two, 60-minute sessions/week. The inflammatory biomarkers were measured at baseline, 6 months, and 1 year. Repeated measures ANOVA analyses indicated that the intervention was effective in reducing CRP and TNFα after 1 year compared to baseline and 6 months (P < 0.05). There were no changes in IL10, IL6, and insulin after 1 year. However, leptin significantly increased at 1 year (P = 0.016). The major finding of this study is that a community-based exercise program can result in a decrease or maintenance of inflammatory biomarkers after 1 year, and thus has the potential to be a viable public health approach for chronic disease prevention. PMID:25136143

  18. The Effect of a Community-Based, Primary Health Care Exercise Program on Inflammatory Biomarkers and Hormone Levels

    PubMed Central

    Papini, Camila Bosquiero; Nakamura, Priscila M.; Zorzetto, Lucas P.; Thompson, Janice L.; Phillips, Anna C.; Kokubun, Eduardo

    2014-01-01

    The aim of this study was to analyze the impact of a community-based exercise program in primary care on inflammatory biomarkers and hormone levels. The 1-year quasiexperimental study involved 13 women (mean age = 56.8 ± 11.4 years) and it was developed in two basic health care units in Rio Claro City, Brazil. The physical exercise intervention was comprised of two, 60-minute sessions/week. The inflammatory biomarkers were measured at baseline, 6 months, and 1 year. Repeated measures ANOVA analyses indicated that the intervention was effective in reducing CRP and TNFα after 1 year compared to baseline and 6 months (P < 0.05). There were no changes in IL10, IL6, and insulin after 1 year. However, leptin significantly increased at 1 year (P = 0.016). The major finding of this study is that a community-based exercise program can result in a decrease or maintenance of inflammatory biomarkers after 1 year, and thus has the potential to be a viable public health approach for chronic disease prevention. PMID:25136143

  19. The effect of a community-based, primary health care exercise program on inflammatory biomarkers and hormone levels.

    PubMed

    Papini, Camila Bosquiero; Nakamura, Priscila M; Zorzetto, Lucas P; Thompson, Janice L; Phillips, Anna C; Kokubun, Eduardo

    2014-01-01

    The aim of this study was to analyze the impact of a community-based exercise program in primary care on inflammatory biomarkers and hormone levels. The 1-year quasiexperimental study involved 13 women (mean age = 56.8 ± 11.4 years) and it was developed in two basic health care units in Rio Claro City, Brazil. The physical exercise intervention was comprised of two, 60-minute sessions/week. The inflammatory biomarkers were measured at baseline, 6 months, and 1 year. Repeated measures ANOVA analyses indicated that the intervention was effective in reducing CRP and TNFα after 1 year compared to baseline and 6 months (P < 0.05). There were no changes in IL10, IL6, and insulin after 1 year. However, leptin significantly increased at 1 year (P = 0.016). The major finding of this study is that a community-based exercise program can result in a decrease or maintenance of inflammatory biomarkers after 1 year, and thus has the potential to be a viable public health approach for chronic disease prevention.

  20. Linking Research and Practice through Teacher Communities: A Place Where Formal and Practical Knowledge Meet?

    ERIC Educational Resources Information Center

    Pareja Roblin, Natalie N.; Ormel, Bart J. B.; McKenney, Susan E.; Voogt, Joke M.; Pieters, Jules M.

    2014-01-01

    This study characterises the links between research and practice across 12 projects concerned with the collaborative design of lesson plans by teacher communities (TCs). Analyses focused on sources of knowledge used to inform lesson design, participants' roles and knowledge generated by the teacher community. Three patterns emerged pertaining…

  1. The Community Links of a Sample of People with Intellectual Disabilities

    ERIC Educational Resources Information Center

    Hall, Louise; Hewson, Simon

    2006-01-01

    Background: In 1995, an unpublished study (S. Hewson & C. Waters) showed that the community links of residents in 11 local National Health Services (NHS) trust houses were meagre, despite the service's stated commitment to community presence and participation. The 1995 study was repeated for the same 11 houses in 2002 to examine whether any…

  2. Concerns about School-Linked Services: Institution-Based versus Community-Based Models.

    ERIC Educational Resources Information Center

    Chaskin, Robert J.; Richman, Harold A.

    1993-01-01

    Reviews concerns about school-linked services programs, exploring institutional-based versus community-based models of service delivery. It is argued that the community is the appropriate context for providing and facilitating access to services and opportunities. Too strong an institutional bias runs the risk of limiting access and community…

  3. Engaging Students in Authentic Science through School-Community Links: Learning from the Rural Experience

    ERIC Educational Resources Information Center

    Tytler, Russell; Symington, David; Kirkwood, Valda; Malcolm, Cliff

    2008-01-01

    There is an increase in school-community linked initiatives in school science. A substantial proportion of these involve rural schools. This article asks the question: In what ways do these initiatives offer possibilities for better engaging rural students with school science? The paper draws on information from a number of school-community linked…

  4. Phospholipid fatty acid biomarkers in a freshwater periphyton community exposed to uranium: discovery by non-linear statistical learning

    SciTech Connect

    Webb-Robertson, Bobbie-Jo M.; Bunn, Amoret L.; Bailey, Vanessa L.

    2011-01-01

    Phospholipid fatty acids (PLFA) have been widely used to characterize environmental microbial communities, generating community profiles that can distinguish phylogenetic or functional groups within the community. The poor specificity of organism groups with fatty acid biomarkers in the classic PLFA-microorganism associations is a confounding factor in many of the statistical classification/clustering approaches traditionally used to interpret PLFA profiles. In this paper we demonstrate that non-linear statistical learning methods, such as a support vector machine (SVM), can more accurately find patterns related to uranyl nitrate exposure in a freshwater periphyton community than linear methods, such as partial least squares discriminant analysis. In addition, probabilistic models of exposure can be derived from the identified lipid biomarkers to demonstrate the potential model-based approach that could be used in remediation. The SVM probability model separates dose groups at accuracies of ~87.0%, ~71.4%, ~87.5%, and 100% for the four groups; Control (non-amended system), low-dose (amended at 10 µg U L-1), medium dose (amended at 100 µg U L-1), and high dose (500 µg U L-1). The SVM model achieved an overall cross-validated classification accuracy of ~87% in contrast to ~59% for the best linear classifier.

  5. Geochip: A high throughput genomic tool for linking community structure to functions

    SciTech Connect

    Van Nostrand, Joy D.; Liang, Yuting; He, Zhili; Li, Guanghe; Zhou, Jizhong

    2009-01-30

    GeoChip is a comprehensive functional gene array that targets key functional genes involved in the geochemical cycling of N, C, and P, sulfate reduction, metal resistance and reduction, and contaminant degradation. Studies have shown the GeoChip to be a sensitive, specific, and high-throughput tool for microbial community analysis that has the power to link geochemical processes with microbial community structure. However, several challenges remain regarding the development and applications of microarrays for microbial community analysis.

  6. Enzyme-linked immunosorbent assay for detection of organophosphorylated butyrylcholinesterase: A biomarker of exposure to organophosphate agents

    SciTech Connect

    Wang, Liming; Du, Dan; Lu, Donglai; Lin, Chiann Tso; Smith, Jordan N.; Timchalk, Charles; Liu, Fengquan; Wang, Jun; Lin, Yuehe

    2011-05-05

    A sandwich enzyme-linked immunosorbent assay (sELISA) is developed for detection of organophosphorylated butyrylcholinesterase (OP-BChE), a potential biomarker for human exposure to organophosphate insecticides and nerve agents. A pair of antibodies specific to OP-BChE adduct were identified through systematic screening of several anti BChE antibodies (anti-BChE) and anti-phosphoserine antibodies (anti-Pser) from different sources. The selected anti-BChE (set as capture antibody) antibodies recognize both phosphorylated and nonphosphorylated BChE. These antibodies can therefore be used to capture both BChE and OP-BChE from the sample matrices. The anti- Pser (set as detecting antibody) was used to recognize the OP moiety of OP-BChE adducts. With the combination of the selected antibody pair, several key parameters (such as the concentration of anti-BChE and anti-Pser, and the blocking agent) were optimized to enhance the sensitivity and selectivity of the sELISA. Under the optimal conditions, the sELISA has shown a wide linear range from 0.03 nM to 30 nM, with a detection limit of 0.03 nM. Furthermore, the sELISA was successfully applied to detect OP-BChE using in-vitro biological samples such as rat plasma spiked with OP-BChE with excellent adduct recovery (z>99 %). These results demonstrate that this novel approach holds great promise to develop an ELISA kit and offers a simple and cost-effective tool for screening/evaluating exposure to organophosphate insecticides and nerve agents.

  7. Linking microbial community structure and microbial processes: An empirical and conceptual overview

    USGS Publications Warehouse

    Bier, R.L.; Bernhardt, E.S.;; Boot, C.M.; Graham, E.B.;; Hall, E.K.; Lennon, J.T.; Nemergut, D.R.; Osborne, B.B.; Ruiz-Gonzalez, C.; Schimel, J.P.; Waldrop, Mark P.; Wallenstein, M.D.

    2015-01-01

    A major goal of microbial ecology is to identify links between microbial community structure and microbial processes. Although this objective seems straightforward, there are conceptual and methodological challenges to designing studies that explicitly evaluate this link. Here, we analyzed literature documenting structure and process responses to manipulations to determine the frequency of structure-process links and whether experimental approaches and techniques influence link detection. We examined nine journals (published 2009–13) and retained 148 experimental studies measuring microbial community structure and processes. Many qualifying papers (112 of 148) documented structure and process responses, but few (38 of 112 papers) reported statistically testing for a link. Of these tested links, 75% were significant and typically used Spearman or Pearson's correlation analysis (68%). No particular approach for characterizing structure or processes was more likely to produce significant links. Process responses were detected earlier on average than responses in structure or both structure and process. Together, our findings suggest that few publications report statistically testing structure-process links. However, when links are tested for they often occur but share few commonalities in the processes or structures that were linked and the techniques used for measuring them.

  8. Using the Women's Community Education Approach to Deliver Community Employment Training: A Case Study from Longford Women's Link

    ERIC Educational Resources Information Center

    Patterson, Lorne; Dowd, Kathleen

    2010-01-01

    The recent economic downturn and surge in unemployment has focused attention on education and training as a strategic response to Ireland's socio-economic crisis. However, that attention has been concentrated on training through statutory institutions, particularly FAS and the VECs. Longford Women's Link, a Women's Community Education centre in Co…

  9. Link prediction based on hyperbolic mapping with community structure for complex networks

    NASA Astrophysics Data System (ADS)

    Wang, Zuxi; Wu, Yao; Li, Qingguang; Jin, Fengdong; Xiong, Wei

    2016-05-01

    Link prediction is becoming a concerned topic in the complex network field in recent years. However, the existing link prediction methods are unsatisfactory for processing topological information and have high time complexity. This paper presents a novel method of Link Prediction with Community Structure (LPCS) based on hyperbolic mapping. Different from the existing link prediction methods, to utilize global structure information of the network, LPCS deals with the network from an overall perspective. LPCS takes full advantage of the community structure and its hierarchical organization to map networks into hyperbolic space, and obtains the hyperbolic coordinates which depict the global structure information of the network, then uses hyperbolic distance to describe the similarity between the nodes, finally predicts missing links according to the degree of the similarity between unconnected node pairs. The combination of the hyperbolic geometry framework and the community structure makes LPCS perform well in predicting missing links, and the time complexity of LPCS is linear, which makes LPCS can be applied to handle large scale networks in acceptable time. LPCS outperforms many state-of-the-art link prediction methods in the networks obeying power-law degree distribution.

  10. Environmental quality assessment combining sediment metal levels, biomarkers and macrobenthic communities: application to the Óbidos coastal lagoon (Portugal).

    PubMed

    Pereira, Patrícia; Carvalho, Susana; Pereira, Fábio; de Pablo, Hilda; Gaspar, Miguel B; Pacheco, Mário; Vale, Carlos

    2012-12-01

    Macroinvertebrate benthic communities are one of the key biological components considered for the assessment of benthic integrity in the context of the Water Framework Directive (WFD). However, under moderate contamination scenarios, the assessment of macrobenthic alterations at community level alone could be insufficient to discriminate the environmental quality of coastal and transitional waters. Keeping this in view, sediment quality of moderately contaminated sites in a coastal lagoon (Óbidos lagoon, Portugal) was assessed by the combination of sediment metal levels, Carcinus maenas biomarkers (accumulated metals and oxidative stress responses) and macrobenthic communities. Two sites were selected in confined inner branches (BS and BB) and a third one in the middle lagoon (ML). The site BB presented slightly higher levels of metals in sediment but biological variables calculated for macrobenthic data were not significantly different between sites. The biotic index M-AMBI that is being applied to assess environmental quality of transitional waters in the scope of the WFD pointed either to high (site ML) or good quality status (BS and BB) in the selected sites. However, crabs from BB site presented significantly higher levels of Ni in hepatopancreas than those from ML and macrobenthic community structure was significantly different between BB and ML. Additionally, spatial differences were obtained for oxidative stress parameters suggesting that BB site presented stressors for crabs (higher GST and lower GSH(t) at BB site). Factor analysis (PCA) integrating sediment contamination, biomarkers in crabs and macrobenthic data also distinguished BB site as the most environmentally disturbed. On the other hand, at ML site, some macrobenthic variables (equitability and polychaetes' diversity) were found to be enhanced by current environmental conditions, suggesting the existence of a better sediment quality. Current results pointed to the usefulness of integrating

  11. Hypersaline Microbial Mat Lipid Biomarkers

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Embaye, Tsegereda; Turk, Kendra A.; Summons, Roger E.

    2002-01-01

    Lipid biomarkers and compound specific isotopic abundances are powerful tools for studies of contemporary microbial ecosystems. Knowledge of the relationship of biomarkers to microbial physiology and community structure creates important links for understanding the nature of early organisms and paleoenvironments. Our recent work has focused on the hypersaline microbial mats in evaporation ponds at Guerrero Negro, Baja California Sur, Mexico. Specific biomarkers for diatoms, cyanobacteria, archaea, green nonsulfur (GNS), sulfate reducing, sulfur oxidizing and methanotrophic bacteria have been identified. Analyses of the ester-bound fatty acids indicate a highly diverse microbial community, dominated by photosynthetic organisms at the surface. The delta C-13 of cyanobacterial biomarkers such as the monomethylalkanes and hopanoids are consistent with the delta C-13 measured for bulk mat (-10%o), while a GNS biomarker, wax esters (WXE), suggests a more depleted delta C-13 for GNS biomass (-16%o). This isotopic relationship is different than that observed in mats at Octopus Spring, Yellowstone National Park (YSNP) where GNS appear to grow photoheterotrophic ally. WXE abundance, while relatively low, is most pronounced in an anaerobic zone just below the cyanobacterial layer. The WXE isotope composition at GN suggests that these bacteria utilize photoautotrophy incorporating dissolved inorganic carbon (DIC) via the 3-hydroxypropionate pathway using H2S or H2.

  12. Links between plant and fungal communities across a deforestation chronosequence in the Amazon rainforest.

    PubMed

    Mueller, Rebecca C; Paula, Fabiana S; Mirza, Babur S; Rodrigues, Jorge L M; Nüsslein, Klaus; Bohannan, Brendan J M

    2014-07-01

    Understanding the interactions among microbial communities, plant communities and soil properties following deforestation could provide insights into the long-term effects of land-use change on ecosystem functions, and may help identify approaches that promote the recovery of degraded sites. We combined high-throughput sequencing of fungal rDNA and molecular barcoding of plant roots to estimate fungal and plant community composition in soil sampled across a chronosequence of deforestation. We found significant effects of land-use change on fungal community composition, which was more closely correlated to plant community composition than to changes in soil properties or geographic distance, providing evidence for strong links between above- and below-ground communities in tropical forests.

  13. Geriatric nursing education in community health: CareLink--partnering for excellence.

    PubMed

    Clemmens, Donna; Goldstein, Jill M; Clarke, Kitty; Moriarty, Mari; Soberman, Rhonda Karp; Gardner, Daniel S

    2009-04-01

    The purpose of the study was to evaluate how participation in the CareLink program influenced the community health knowledge and skill of baccalaureate nursing students regarding the care of community-dwelling older adults. Students were assigned three to four clients each during their 14-week clinical placement with a home care agency, situated in a naturally occurring retirement community or senior center. Students contracted with their clients to set goals and provided standardized health assessments and teaching. Students completed pretest and posttest surveys, and attended focus groups to address their learning. Students' public health nursing and cultural competence improved significantly. The CareLink program provides a meaningful learning experience for baccalaureate nursing students. Attitudes toward older adults and community health nursing in general shifted to acknowledge that older adults have strengths and resilience not previously acknowledged.

  14. Biomarker-derived phytoplankton community for summer monsoon reconstruction in the western South China Sea over the past 450 ka

    NASA Astrophysics Data System (ADS)

    Li, Li; Li, Qianyu; He, Juan; Wang, Hui; Ruan, Yanming; Li, Jianru

    2015-12-01

    Marine algal-derived lipid biomarkers (alkenones, brassicasterol, dinosterol, and long-chain diol/keto-ol representing haptophytes, diatoms, dinoflagellates, and eustigmatophytes, respectively) were used to evaluate the phytoplankton productivity and community structure changes in core MD05-2901 from the western South China Sea, which features distinct summer upwelling induced by southwest Asian monsoon. The results revealed substantial differences in the distribution patterns between the four major marine primary producers. Diatom and dinoflagellate biomarkers displayed slightly higher abundances, mostly in interglacials especially after MIS 8, while alkenones exhibited lower values in MIS 12 and MIS 1, with higher values in between especially in the middle of MIS 7, but eustigmatophytes increased in most glaciations, indicating complex responses of different phytoplanktons to paleoclimatic and paleoenvironmental changes over the past 450 ka. The sum of the four phytoplanktons shows subtle glacial-interglacial patterns, probably reflecting the combined hydrological dynamics driven by enhanced summer monsoon during summer/interglacials and enhanced winter monsoon during winter/glacials in the region. The biomarker-based community structure showed relative high contribution from diatoms and dinoflagellates during interglacials, high contribution in the middle part of the section centered at ~210 ka from the coccolithophorids, but varying levels from the eustigmatophytes with high percentages in most glacials. Diatoms show strong nutrient sensitivity and positive relation with other paleo-proxies, and their enrichments during interglacials can be attributed to enhanced nutrient level induced by the East Asian summer monsoon, which could have been coupled with the influence of the global ice volume, the summer insolation and the Southern Hemisphere latent heat.

  15. Lipid biomarker and microbial community of 49.6°E hydrothermal field at Southwest Indian Ocean Ridge

    NASA Astrophysics Data System (ADS)

    Lei, J.; Chu, F.; Yu, X.; Li, X.; Tao, C.

    2012-12-01

    In 2007, Chinese Research Cruises Discovered the First Active Hydrothermal Vent Field at the Ultraslow Spreading Southwest Indian Ridge. This study intent to get composition, evolution and origin information of lipid compounds in SWIR, and recognize the style of lipid biomarkers which have obviously indicative significance for community structure.Soluble organic matter were extracted from geological samples (including chimney sulfide, oxide, around hydrothermal vents) in Southwest Indian Ridge (SWIR), and divided into hydrocarbon, fatty acid component by column chromatography. GC, GC-MS, HPLC-MS were applied for composition and abundance analysis. Lipid in hydrothermal sulfide contains obvious isoprenoidal hydrocarbon biomarkers (Sq, IS40) and GDGTs (m/z=653) that associated with methanogenic archaea which belongs to Euryarchaeota, and iso /anti-iso fatty acid (iC15:0, aiC15:0, iC17:0, aiC17:0)which may originated from sulfate reducing bacteria (SRB).Lipids extracted from hydrothermal oxide lack isoprenoidal hydrocarbon, and Ph/C18 (0.57) is much lower than sulfide (1.22). Fatty acid compound of oxide include abundant saturated fatty (C16:0, C18:0) acid and mono-unsaturated fatty acids (C16:1n7, C18:1n7), but much less iso/anti-iso was detected. Lipid composition of hydrothermal oxide showed that archaea activity was seldom in hydrothermal oxide, and sulfur-oxidizing bacteria was the main microbial community.Study of Jaeschke (2010) showed that high temperature hydrothermal venting encompassed different microbial community from low temperature hydrothermal venting. Our study showed that in different stage of hydrothermal, microbial community structure may be distinct.

  16. Learning Communities: Linking the Basic Course to the Greater University Community.

    ERIC Educational Resources Information Center

    Leonard, Jessica Grassmann

    Learning communities, freshman interest groups, or cluster classes are a relatively new trend on college and university campuses. In addition to improving freshman retention and performance, these courses create a bridge between the basic course and other courses. Learning communities are curricular structures that promote academic success by…

  17. Integrating the environment, the economy, and community health: a Community Health Center's initiative to link health benefits to smart growth.

    PubMed

    McAvoy, Peter V; Driscoll, Mary Beth; Gramling, Benjamin J

    2004-04-01

    The Sixteenth Street Community Health Center (SSCHC) in Milwaukee, Wis, is making a difference in the livability of surrounding neighborhoods and the overall health of the families it serves. SSCHC is going beyond traditional health care provider models and working to link the environment, the economy, and community health through urban brownfield redevelopment and sustainable land-use planning. In 1997, SSCHC recognized that restoration of local air and water quality and other environmental conditions, coupled with restoring family-supporting jobs in the neighborhood, could have a substantial impact on the overall health of families. Recent events indicate that SSCHC's pursuit of smart growth strategies has begun to pay off. PMID:15053995

  18. Forging links between nutrition and healthcare using community-based partnerships.

    PubMed

    Biel, Melissa; Evans, Susan H; Clarke, Peter

    2009-01-01

    This pilot project tested the feasibility of a community-based partnership between community clinics and food pantries as an approach to combat diet-related illnesses and engage low-income individuals in healthcare. Many communities possess both kinds of agencies, which serve similar clienteles and are geographically near each other, but these types of agencies rarely have partnered. The "LINKS" program built partnerships between clinics and food pantries at 2 sites. For more than 6 months, the clinics conducted health screenings and provided referrals during scheduled pantry food distributions. Results indicate that clinics can effectively partner with food pantries, an overlooked resource for health promotion.

  19. Cold-spotting: linking primary care and public health to create communities of solution.

    PubMed

    Westfall, John M

    2013-01-01

    By providing enhanced primary care and social services to patients with high utilization of expensive emergency and hospital care, there is evidence that their health can improve and their costs can be lowered. This type of "hot-spotting" improves the care of individual patients. It may be that these patients live in communities with disintegrated social determinants of health, little community support, and poor access to primary care. These "cold spots" in the community may be amenable to interventions targeted at linking primary care and public health at broader community and population levels. Building local communities of solution that address the individual and population may help decrease these cold spots, thereby eliminating the hot spots as well.

  20. Ten Ways Community Organizations Can Link Children to Medicaid (and Other Public Health Insurance Programs).

    ERIC Educational Resources Information Center

    Center on Budget and Policy Priorities, Washington, DC.

    Ten ways community organizations, which may include schools, can link children to Medicaid and other public health insurance programs are listed. They are: (1) disseminate information about the availability of health insurance for children in low-income families; (2) incorporate Medicaid income eligibility screening as part of the program's…

  1. Raising Standards: Opening Doors. Developing Links between Schools and Their Communities.

    ERIC Educational Resources Information Center

    Department for Education and Employment, London (England).

    This booklet offers guidance to help schools open up their premises and facilities for outside use and to enhance their links with the local community. It highlights the benefits of partnership and offers real examples of the type of activity which is already undertaken in many schools and how it is organized and funded. Also covered are the legal…

  2. Red Blood Cell Fatty Acids and Biomarkers of Inflammation: A Cross-sectional Study in a Community-based Cohort

    PubMed Central

    Fontes, João D.; Rahman, Faisal; Lacey, Sean; Larson, Martin G.; Vasan, Ramachandran S.; Benjamin, Emelia J.; Harris, William S.; Robins, Sander J.

    2015-01-01

    Introduction Inflammation and inflammatory biomarkers have emerged as integral components and predictors of incident cardiovascular (CV) disease. Omega-3 fatty acids, particularly eicosapentaenoic and docosahexaenoic acids (EPA and DHA) have anti-inflammatory properties, and have been variably associated with lower blood pressure, favorable blood lipid changes, and reduced CV events. Methods and Results We examined the cross-sectional association of red blood cell (RBC) fatty acids, representative of body membrane fatty acid composition, with 10 biomarkers active in multiple inflammatory pathways in 2724 participants (mean age 66±9 years, 54% women, 8% minorities) from the Framingham Offspring and minority Omni Cohorts. . After multivariable adjustment, the RBC EPA and DHA content was inversely correlated (all P≤0.001) with 8 markers of inflammation, receptors, or pathways: urinary isoprostanes (r=−0.16); and soluble interleukin-6 (r=−0.10); C-reactive protein (r=−0.08); tumor necrosis factor receptor 2 (r=−0.08); intercellular adhesion molecule-1 (r=−0.08); P-selectin (r=−0.06); lipoprotein-associated phospholipase-A2 mass (r=−0.11) and activity (r=−0.08). The correlations for monocyte chemoattractant protein-1 was −0.05, P=0.006 and osteoprotegerin (r= −0.06, P=0.002) were only nominally significant. Conclusion In our large community-based study, we observed modest inverse associations between several types of inflammatory biomarkers with RBC omega-3 fatty acid levels. Our findings are consistent with the hypothesis that omega-3 fatty acids have anti-inflammatory properties. PMID:25897795

  3. Methods for Linking Community Views to Measureable Outcomes in a Youth Violence Prevention Program

    PubMed Central

    McDonald, Catherine C.; Richmond, Therese S.; Guerra, Terry; Thomas, Nicole A.; Walker, Alia; Branas, Charles C.; TenHave, Thomas R.; Vaughn, Nicole A.; Leff, Stephen S.; Hausman, Alice J.

    2013-01-01

    Background All parties in community–academic partnerships have a vested interest prevention program success. Markers of success that reflect community’s experiences of programmatic prevention success are not always measurable, but critically speak to community-defined needs. Objective The purpose of this manuscript was to (1) describe our systematic process for linking locally relevant community views (community-defined indicators) to measurable outcomes in the context of a youth violence prevention program and (2) discuss lessons learned, next steps, and recommendations for others trying to replicate a similar process. Methods A research team composed of both academic and community researchers conducted a systematic process of matching community-defined indicators of youth violence prevention programmatic success to standardized youth survey items being administered in the course of a program evaluation. The research team of three community partners and Five academic partners considered 43 community-defined indicators and 208 items from the youth surveys being utilized within the context of a community-based aggression prevention program. At the end of the matching process, 92 youth survey items were identified and agreed upon as potential matches to 11 of the community-defined indicators. Conclusions We applied rigorous action steps to match community-defined indicators to survey data collected in the youth violence prevention intervention. We learned important lessons that inform recommendations for others interested in such endeavors. The process used to derive and assess community-defined indicators of success emphasized the principles of community-based participatory research (CBPR) and use of existing and available data to reduce participant burden. PMID:23221296

  4. Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

    PubMed

    Navarrete, Acacio Aparecido; Soares, Tielle; Rossetto, Raffaella; van Veen, Johannes Antonie; Tsai, Siu Mui; Kuramae, Eiko Eurya

    2015-09-01

    Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions. PMID:26184407

  5. Biomarkers of Manganese Exposure in Pregnant Women and Children Living in an Agricultural Community in California

    PubMed Central

    2015-01-01

    Manganese (Mn) is an essential nutrient but at high exposure levels is a neurotoxicant. There is no well-validated biomarker to assess perinatal Mn exposure. A total of 75 mother-child pairs provided blood, urine, and/or deciduous tooth samples. We analyzed Mn in dentin and enamel of shed teeth; maternal, cord, and child blood; and maternal and child urine and examined the interrelationships of Mn levels in all matrices. We observed higher Mn levels in prenatal than postnatal dentin (geometric mean (GM) = 0.51 vs 0.16 Mn:Ca, p < 0.001), maternal blood at delivery than 26 weeks gestation (GM = 20.7 vs. 14.6 μg/L, p = 0.001), and cord blood than child blood at 24 months of age (39.9 vs 25.0 μg/L, p = 0.005). There were no significant correlations between Mn in dentin and Mn concentrations in maternal blood or maternal or child urine. Levels of Mn in prenatal dentin, prenatal maternal blood, and 24 month urine were higher (p < 0.05) among mothers and children living with a farm worker. Prenatal Mn levels in dentin were correlated with Mn loadings and concentrations in prenatal house dust. Levels of Mn measured in tooth dentin constitute a promising biomarker of perinatal exposure. PMID:25390650

  6. Carotenoid biomarkers as an imperfect reflection of the anoxygenic phototrophic community in meromictic Fayetteville Green Lake.

    PubMed

    Meyer, K M; Macalady, J L; Fulton, J M; Kump, L R; Schaperdoth, I; Freeman, K H

    2011-07-01

    Organic biomarkers in marine sedimentary rocks hold important clues about the early history of Earth's surface environment. The chemical relicts of carotenoids from anoxygenic sulfur bacteria are of particular interest to geoscientists because of their potential to signal episodes of marine photic-zone euxinia such as those proposed for extended periods in the Proterozoic as well as brief intervals during the Phanerozoic. It is therefore critical to constrain the environmental and physiological factors that influence carotenoid production and preservation in modern environments. Here, we present the results of coupled pigment and nucleic acid clone library analyses from planktonic and benthic samples collected from a microbially dominated meromictic lake, Fayetteville Green Lake (New York). Purple sulfur bacteria (PSB) are abundant and diverse both in the water column at the chemocline and in benthic mats below oxygenated shallow waters, with different PSB species inhabiting the two environments. Okenone (from PSB) is an abundant carotenoid in both the chemocline waters and in benthic mats. Green sulfur bacteria and their primary pigment Bchl e are also represented in and below the chemocline. However, the water column and sediments are devoid of the green sulfur bacteria carotenoid isorenieratene. The unexpected absence of isorenieratene and apparent benthic production of okenone provide strong rationale for continued exploration of the microbial ecology of biomarker production in modern euxinic environments. PMID:21682840

  7. Carotenoid biomarkers as an imperfect reflection of the anoxygenic phototrophic community in meromictic Fayetteville Green Lake.

    PubMed

    Meyer, K M; Macalady, J L; Fulton, J M; Kump, L R; Schaperdoth, I; Freeman, K H

    2011-07-01

    Organic biomarkers in marine sedimentary rocks hold important clues about the early history of Earth's surface environment. The chemical relicts of carotenoids from anoxygenic sulfur bacteria are of particular interest to geoscientists because of their potential to signal episodes of marine photic-zone euxinia such as those proposed for extended periods in the Proterozoic as well as brief intervals during the Phanerozoic. It is therefore critical to constrain the environmental and physiological factors that influence carotenoid production and preservation in modern environments. Here, we present the results of coupled pigment and nucleic acid clone library analyses from planktonic and benthic samples collected from a microbially dominated meromictic lake, Fayetteville Green Lake (New York). Purple sulfur bacteria (PSB) are abundant and diverse both in the water column at the chemocline and in benthic mats below oxygenated shallow waters, with different PSB species inhabiting the two environments. Okenone (from PSB) is an abundant carotenoid in both the chemocline waters and in benthic mats. Green sulfur bacteria and their primary pigment Bchl e are also represented in and below the chemocline. However, the water column and sediments are devoid of the green sulfur bacteria carotenoid isorenieratene. The unexpected absence of isorenieratene and apparent benthic production of okenone provide strong rationale for continued exploration of the microbial ecology of biomarker production in modern euxinic environments.

  8. Effects of Adenotonsillectomy on Plasma Inflammatory Biomarkers in Obese Children with Obstructive Sleep Apnea: A Community-Based Study

    PubMed Central

    Kheirandish-Gozal, Leila; Gileles-Hillel, Alex; Alonso-Álvarez, María Luz; Peris, Eduard; Bhattacharjee, Rakesh; Terán-Santos, Joaquin; Duran-Cantolla, Joaquin; Gozal, David

    2015-01-01

    Background Obesity and obstructive sleep apnea syndrome (OSA) are highly prevalent and frequently overlapping conditions in children that lead to systemic inflammation, the latter being implicated in the various end-organ morbidities associated with these conditions. Aim To examine the effects of adenotonsillectomy (T&A) on plasma levels of inflammatory markers in obese children with polysomnographically diagnosed OSA who were prospectively recruited from the community. Methods Obese children prospectively diagnosed with OSA, underwent T&A and a second overnight polysomnogram (PSG) after surgery. Plasma fasting morning samples obtained after each of the 2 PSG were assayed for multiple inflammatory and metabolic markers including interleukin-6 (IL-6), IL-18, plasminogen activator inhibitor-1 (PAI-1), monocyte chemoattractant protein-1 (MCP-1), matrix metalloproteinase- (MMP-9), adiponectin, apelin C, leptin and osteocrin. Results Out of 122 potential candidates, 100 obese children with OSA completed the study with only 1/3 exhibiting normalization of their PSG after T&A (i.e., AHI≤1/hrTST). However, overall significant decreases in MCP-1, PAI-1, MMP-9, IL-18 and IL-6, and increases in adropin and osteocrin plasma concentrations occurred after T&A. Several of the T&A responsive biomarkers exhibited excellent sensitivity and moderate specificity to predict residual OSA (i.e., AHI≥/hrTST). Conclusions A defined subset of systemic inflammatory and metabolic biomarkers is reversibly altered in the context of OSA among community-based obese children, further reinforcing the concept on the interactive pro-inflammatory effects of sleep disorders such as OSA and obesity contributing to downstream end-organ morbidities. PMID:25801692

  9. Characterization of the deep-sea microbial community and investigation of their carbon sources using lipid biomarkers

    NASA Astrophysics Data System (ADS)

    Rampen, S. W.; Sinninghe Damsté, J. S.; Schouten, S.; Middelburg, J. J.

    2012-12-01

    Most marine microbiology studies so far have been devoted to the photic zone, as this is the area where most of the primary production occurs. However, recently several groups of autotrophic organisms belonging to the Thaumarchaeota have been identified in the deep-sea. Thaumarchaeota belong to the Archaea, which form one of the three Domains of life, next to the Eukarya and the Bacteria. While until the 1990s the Archaea were viewed as extremophilic organisms, results obtained over the last twenty years indicate that Thaumarchaeota are an ubiquitous component of marine plankton, being among the most widely distributed and most abundant groups of microorganisms on the planet; Thaumarchaeota even exceed Bacteria in abundance below 1000 m water depth. Despite these findings, our understanding on their physiology and their biogeochemical function remains mostly speculative because only very few of these organisms could be cultivated. The aim of our project is 1) to characterize the microbial community in the deep-sea using lipid biomarkers for Bacteria, Archaea and Eukarya, 2) to investigate the carbon sources for these organisms using compound specific 13C and 14C analyses and 3) to elucidate the flow of carbon in deep-sea microbial communities using 13C labeling studies. To this end, organic matter has been collected from several locations in the Mediterranean Sea and from the Iceland Basin. Water volumes up to 160 liters were sampled using Niskin bottles which were then filtered on board, while larger volumes, up to 5000 liters, were sampled by deployment of two McLane in-situ pumps at depth. Additional water samples were filtered from the subsurface to distinguish in-situ production from settling organic biomass produced in the upper water column. In addition, 13C labeled glucose, amino acids and sodium bicarbonate were each added to deep-sea water kept in separate 20 liter Nalgene bottles. Incubated water samples and control samples were kept at deep

  10. The application of a biometric identification technique for linking community and hospital data in rural Ghana

    PubMed Central

    Odei-Lartey, Eliezer Ofori; Boateng, Dennis; Danso, Samuel; Kwarteng, Anthony; Abokyi, Livesy; Amenga-Etego, Seeba; Gyaase, Stephaney; Asante, Kwaku Poku; Owusu-Agyei, Seth

    2016-01-01

    Background The reliability of counts for estimating population dynamics and disease burdens in communities depends on the availability of a common unique identifier for matching general population data with health facility data. Biometric data has been explored as a feasible common identifier between the health data and sociocultural data of resident members in rural communities within the Kintampo Health and Demographic Surveillance System located in the central part of Ghana. Objective Our goal was to assess the feasibility of using fingerprint identification to link community data and hospital data in a rural African setting. Design A combination of biometrics and other personal identification techniques were used to identify individual's resident within a surveillance population seeking care in two district hospitals. Visits from resident individuals were successfully recorded and categorized by the success of the techniques applied during identification. The successes of visits that involved identification by fingerprint were further examined by age. Results A total of 27,662 hospital visits were linked to resident individuals. Over 85% of those visits were successfully identified using at least one identification method. Over 65% were successfully identified and linked using their fingerprints. Supervisory support from the hospital administration was critical in integrating this identification system into its routine activities. No concerns were expressed by community members about the fingerprint registration and identification processes. Conclusions Fingerprint identification should be combined with other methods to be feasible in identifying community members in African rural settings. This can be enhanced in communities with some basic Demographic Surveillance System or census information. PMID:26993473

  11. Linking physical education with community sport and recreation: a program for adolescent girls.

    PubMed

    Casey, Meghan; Mooney, Amanda; Eime, Rochelle; Harvey, Jack; Smyth, John; Telford, Amanda; Payne, Warren

    2013-09-01

    The engagement of adolescent girls in physical activity (PA) is a persistent challenge. School-based PA programs have often met with little success because of the lack of linkages between school and community PA settings. The Triple G program aimed to improve PA levels of secondary school girls (12-15 years) in regional Victoria, Australia. The program included a school-based physical education (PE) component that uniquely incorporated student-centered teaching and behavioral skill development. The school component was conceptually and practically linked to a community component that emphasized appropriate structures for participation. The program was informed by ethnographic fieldwork to understand the contextual factors that affect girls' participation in PA. A collaborative intervention design was undertaken to align with PE curriculum and coaching and instructional approaches in community PA settings. The theoretical framework for the intervention was the socioecological model that was underpinned by both individual-level (social cognitive theory) and organizational-level (building organizational/community capacity) strategies. The program model provides an innovative conceptual framework for linking school PE with community sport and recreation and may benefit other PA programs seeking to engage adolescent girls. The objective of this article is to describe program development and the unique theoretical framework and curriculum approaches.

  12. Linking soil microbial communities to vascular plant abundance along a climate gradient.

    PubMed

    Bragazza, Luca; Bardgett, Richard D; Mitchell, Edward A D; Buttler, Alexandre

    2015-02-01

    The ongoing expansion of shrub cover in response to climate change represents a unique opportunity to explore the link between soil microbial communities and vegetation changes. This link is particularly important in peatlands where shrub expansion is expected to feed back negatively on the carbon sink capacity of these ecosystems. Microbial community structure and function were measured seasonally in four peatlands located along an altitude gradient representing a natural gradient of climate and associated vascular plant abundance. We show that increased soil temperature and reduced water content are associated with greater vascular plant biomass, in particular that of ericoids, and that this, in turn, is correlated with greater microbial biomass. More specifically, microbial community structure is characterized by an increasing dominance of fungi over bacteria with improved soil oxygenation. We also found that the carbon and nitrogen stoichiometry of microbial biomass differs in relation to soil microbial community structure and that this is ultimately associated with a different investment in extracellular enzymatic activity. Our findings highlight the fact that the determination of the structural identity of microbial communities can help to explain the biogeochemical dynamics of organic matter and provide a better understanding of ecosystem response to environmental changes.

  13. Structural changes in soil communities after triclopyr application in soils invaded by Acacia dealbata Link.

    PubMed

    Souza-Alonso, Pablo; Guisande, Alejandra; González, Luís

    2015-01-01

    Triclopyr is a commonly used herbicide in the control of woody plants and can exhibit toxic effects to soil microorganisms. However, the impact on soils invaded by plant exotics has not yet been addressed. Here, we present the results of an 18-month field study conducted to evaluate the impact of triclopyr on the structure of fungal and bacterial communities in soils invaded by Acacia dealbata Link, through the use of denature gradient gel electrophoresis. After triclopyr application, analyses of bacterial fingerprints suggested a change in the structure of the soil bacterial community, whereas the structure of the soil fungal community remained unaltered. Bacterial density and F:B ratio values changed across the year but were not altered due to herbicide spraying. On the contrary, fungal diversity was increased in plots sprayed with triclopyr 5 months after the first application. Richness and diversity (H') of both bacteria and fungi were not modified after triclopyr application. PMID:25602151

  14. Structural changes in soil communities after triclopyr application in soils invaded by Acacia dealbata Link.

    PubMed

    Souza-Alonso, Pablo; Guisande, Alejandra; González, Luís

    2015-01-01

    Triclopyr is a commonly used herbicide in the control of woody plants and can exhibit toxic effects to soil microorganisms. However, the impact on soils invaded by plant exotics has not yet been addressed. Here, we present the results of an 18-month field study conducted to evaluate the impact of triclopyr on the structure of fungal and bacterial communities in soils invaded by Acacia dealbata Link, through the use of denature gradient gel electrophoresis. After triclopyr application, analyses of bacterial fingerprints suggested a change in the structure of the soil bacterial community, whereas the structure of the soil fungal community remained unaltered. Bacterial density and F:B ratio values changed across the year but were not altered due to herbicide spraying. On the contrary, fungal diversity was increased in plots sprayed with triclopyr 5 months after the first application. Richness and diversity (H') of both bacteria and fungi were not modified after triclopyr application.

  15. Signature lipid biomarkers for in situ microbial biomass, community structure and nutritional status of deep subsurface microbiota in relation to geochemical gradients. Final technical report

    SciTech Connect

    White, D.C.; Ringelberg, D.B.

    1998-02-01

    To obtain a better understanding of the microbial ecology of the deep subsurface, it was necessary to employ alternate techniques for the identification of microorganisms in situ. Classical microbiological techniques assay only those organisms which are culturable with bias occurring towards the media selected. Since culturable microorganisms typically represents only 0.1 to 10% of the extant microbiota, techniques for the direct assay of microorganisms in situ were needed. The analysis of cellular lipid biomarkers is a technique whereby microbial communities can be assayed directly in a variety of environmental matrices. Through the quantitative recovery of lipid biomarkers, estimations of cell biomass, community composition and community nutritional and/or physiological status can be obtained.

  16. In situ experiments to assess effects of constraints linked to caging on ecotoxicity biomarkers of the three-spined stickleback (Gasterosteus aculeatus L.).

    PubMed

    Le Guernic, Antoine; Sanchez, Wilfried; Palluel, Olivier; Bado-Nilles, Anne; Turies, Cyril; Chadili, Edith; Cavalié, Isabelle; Adam-Guillermin, Christelle; Porcher, Jean-Marc; Geffard, Alain; Betoulle, Stéphane; Gagnaire, Béatrice

    2016-04-01

    The aim of this study was to evaluate the effects of caging constraints on multiple fish biomarkers used during ecotoxicological studies (biometric data, immune and antioxidant systems, and energetic status). Two of these constraints were linked to caging: starvation and fish density in cages, and one in relation to the post-caging handling: a short transport. Three in situ experiments were conducted with three-spined sticklebacks (Gasterosteus aculeatus). The first experiment compared the effects of three densities (low, medium, and high). The second experiment compared effects of starvation in fish fed every two days with fish that were not fed. Finally comparisons between sticklebacks which have suffered a short car transport after caging and sticklebacks killed without preliminary transport were made. The lack of food had no effect on fish energetic reserves but negatively affected their condition index and their immune system. Transport and high density induced oxidative stress, defined as an overproduction of reactive oxygen species and a stimulation of the antioxidant system. These two constraints also harmed the leucocyte viability. In order not to have any impact on ecotoxicity biomarkers during in situ experiments, it is preferable to decrease fish density in cages, prevent transport before dissections, and feed fish when the caging lasts more than two weeks.

  17. Proteomic profiling of N-linked glycoproteins identifies ConA-binding procathepsin D as a novel serum biomarker for hepatocellular carcinoma.

    PubMed

    Qi, Yi-Jun; Ward, Douglas G; Pang, Chun; Wang, Qi-Ming; Wei, Wenbin; Ma, Jin; Zhang, Juan; Lou, Qiang; Shimwell, Neil J; Martin, Ashley; Wong, Nathalie; Chao, Wei-Xia; Wang, Ming; Ma, Yuan-Fang; Johnson, Philip J

    2014-02-01

    The aim of this study was to identify novel biomarkers for the diagnosis of, and potential therapeutic targets for, hepatocellular carcinoma (HCC). Multilectin affinity chromatography was used to enrich N-linked glycoproteins from nontumorous liver and HCC tissues followed by 2DE and protein identification by MS. Twenty-eight differentially expressed proteins were identified. Western blotting validated consistently lower concentrations of human liver carboxylesterase 1 and haptoglobin, and higher concentration of procathepsin D (pCD) in HCC tissues. Knockdown of cathepsin D (CD) expression mediated by siRNA significantly inhibited the in vitro invasion of two HCC cell lines, SNU449 and SNU473, which normally secrete high-levels of CD. Prefractionation using individual lectins demonstrated an elevation in ConA-binding glycoforms of proCD and CD in HCC tissues. In the serum of HCC patients, "ConA-binding proCD" (ConA-pCD) is significantly increased in concentration and this increase is comprised of several distinct upregulated acidic isoforms (pI 4.5-5.5). Receiver operating characteristic analysis showed that the sensitivity and specificity of serum ConA-pCD for HCC diagnosis were 85% and 80%, respectively. This is the first report that serum ConA-pCD is increased significantly in HCC and is potentially useful as a serological biomarker for diagnosis of HCC.

  18. Galectin‐3, a Biomarker Linking Oxidative Stress and Inflammation With the Clinical Outcomes of Patients With Atherothrombosis

    PubMed Central

    Madrigal‐Matute, Julio; Lindholt, Jes Sandal; Fernandez‐Garcia, Carlos Ernesto; Benito‐Martin, Alberto; Burillo, Elena; Zalba, Guillermo; Beloqui, Oscar; Llamas‐Granda, Patricia; Ortiz, Alberto; Egido, Jesus; Blanco‐Colio, Luis Miguel; Martin‐Ventura, Jose Luis

    2014-01-01

    Background Galectin‐3 (Gal‐3) participates in different mechanisms involved in atherothrombosis, such as inflammation, proliferation, or macrophage chemotaxis. Thus, there have been committed intensive efforts to elucidate the function of Gal‐3 in cardiovascular (CV) diseases. The role of Gal‐3 as a circulating biomarker has been demonstrated in patients with heart failure, but its importance as a biomarker in atherothrombosis is still unknown. Methods and Results Because Gal‐3 is involved in monocyte‐to‐macrophage transition, we used fresh isolated monocytes and the in vitro model of macrophage differentiation of THP‐1 cells stimulated with phorbol myristate acetate (PMA). Gal‐3 release is increased by PMA in human monocytes and macrophages, a process involving exosomes and regulated by reactive oxygen species/NADPH oxidase activity. In asymptomatic subjects (n=199), Gal‐3 plasma levels are correlated with NADPH oxidase activity in peripheral blood mononuclear cells (r=0.476; P<0.001) and carotid intima‐media thickness (r=0.438; P<0.001), a surrogate marker of atherosclerosis. Accordingly, Gal‐3 plasma concentrations are increased in patients with carotid atherosclerosis (n=158), compared to control subjects (n=115; 14.3 [10.7 to 16.9] vs. 10.4 [8.6 to 12.5] ng/mL; P<0.001). Finally, on a 5‐year follow‐up study in patients with peripheral artery disease, Gal‐3 concentrations are significantly and independently associated with an increased risk for CV mortality (hazard ratio=2.24, 95% confidence interval: 1.06 to 4.73, P<0.05). Conclusions Gal‐3 extracellular levels could reflect key underlying mechanisms involved in atherosclerosis etiology, development, and plaque rupture, such as inflammation, infiltration of circulating cells and oxidative stress. Moreover, circulating Gal‐3 concentrations are associated with clinical outcomes in patients with atherothrombosis. PMID:25095870

  19. Spatial patterns and links between microbial community composition and function in cyanobacterial mats

    PubMed Central

    Al-Najjar, Mohammad A. A.; Ramette, Alban; Kühl, Michael; Hamza, Waleed; Klatt, Judith M.; Polerecky, Lubos

    2014-01-01

    We imaged reflectance and variable fluorescence in 25 cyanobacterial mats from four distant sites around the globe to assess, at different scales of resolution, spatial variabilities in the physiological parameters characterizing their photosynthetic capacity, including the absorptivity by chlorophyll a (Achl), maximum quantum yield of photosynthesis (Ymax), and light acclimation irradiance (Ik). Generally, these parameters significantly varied within individual mats on a sub-millimeter scale, with about 2-fold higher variability in the vertical than in the horizontal direction. The average vertical profiles of Ymax and Ik decreased with depth in the mat, while Achl exhibited a sub-surface maximum. The within-mat variability was comparable to, but often larger than, the between-sites variability, whereas the within-site variabilities (i.e., between samples from the same site) were generally lowest. When compared based on averaged values of their photosynthetic parameters, mats clustered according to their site of origin. Similar clustering was found when the community composition of the mats' cyanobacterial layers were compared by automated ribosomal intergenic spacer analysis (ARISA), indicating a significant link between the microbial community composition and function. Although this link is likely the result of community adaptation to the prevailing site-specific environmental conditions, our present data is insufficient to identify the main factors determining these patterns. Nevertheless, this study demonstrates that the spatial variability in the photosynthetic capacity and light acclimation of benthic phototrophic microbial communities is at least as large on a sub-millimeter scale as it is on a global scale, and suggests that this pattern of variability scaling is similar for the microbial community composition. PMID:25147548

  20. Common neighbours and the local-community-paradigm for topological link prediction in bipartite networks

    NASA Astrophysics Data System (ADS)

    Daminelli, Simone; Thomas, Josephine Maria; Durán, Claudio; Vittorio Cannistraci, Carlo

    2015-11-01

    Bipartite networks are powerful descriptions of complex systems characterized by two different classes of nodes and connections allowed only across but not within the two classes. Unveiling physical principles, building theories and suggesting physical models to predict bipartite links such as product-consumer connections in recommendation systems or drug-target interactions in molecular networks can provide priceless information to improve e-commerce or to accelerate pharmaceutical research. The prediction of nonobserved connections starting from those already present in the topology of a network is known as the link-prediction problem. It represents an important subject both in many-body interaction theory in physics and in new algorithms for applied tools in computer science. The rationale is that the existing connectivity structure of a network can suggest where new connections can appear with higher likelihood in an evolving network, or where nonobserved connections are missing in a partially known network. Surprisingly, current complex network theory presents a theoretical bottle-neck: a general framework for local-based link prediction directly in the bipartite domain is missing. Here, we overcome this theoretical obstacle and present a formal definition of common neighbour index and local-community-paradigm (LCP) for bipartite networks. As a consequence, we are able to introduce the first node-neighbourhood-based and LCP-based models for topological link prediction that utilize the bipartite domain. We performed link prediction evaluations in several networks of different size and of disparate origin, including technological, social and biological systems. Our models significantly improve topological prediction in many bipartite networks because they exploit local physical driving-forces that participate in the formation and organization of many real-world bipartite networks. Furthermore, we present a local-based formalism that allows to intuitively

  1. Biological database of images and genomes: tools for community annotations linking image and genomic information.

    PubMed

    Oberlin, Andrew T; Jurkovic, Dominika A; Balish, Mitchell F; Friedberg, Iddo

    2013-01-01

    Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype-genotype connection linking the two types of data is lagging behind. While there are many types of software that enable the manipulation and analysis of image data and genomic data as separate entities, there is no framework established for linking the two. We present a generic set of software tools, BioDIG, that allows linking of image data to genomic data. BioDIG tools can be applied to a wide range of research problems that require linking images to genomes. BioDIG features the following: rapid construction of web-based workbenches, community-based annotation, user management and web services. By using BioDIG to create websites, researchers and curators can rapidly annotate a large number of images with genomic information. Here we present the BioDIG software tools that include an image module, a genome module and a user management module. We also introduce a BioDIG-based website, MyDIG, which is being used to annotate images of mycoplasmas. PMID:23550062

  2. Biological Database of Images and Genomes: tools for community annotations linking image and genomic information

    PubMed Central

    Oberlin, Andrew T; Jurkovic, Dominika A; Balish, Mitchell F; Friedberg, Iddo

    2013-01-01

    Genomic data and biomedical imaging data are undergoing exponential growth. However, our understanding of the phenotype–genotype connection linking the two types of data is lagging behind. While there are many types of software that enable the manipulation and analysis of image data and genomic data as separate entities, there is no framework established for linking the two. We present a generic set of software tools, BioDIG, that allows linking of image data to genomic data. BioDIG tools can be applied to a wide range of research problems that require linking images to genomes. BioDIG features the following: rapid construction of web-based workbenches, community-based annotation, user management and web services. By using BioDIG to create websites, researchers and curators can rapidly annotate a large number of images with genomic information. Here we present the BioDIG software tools that include an image module, a genome module and a user management module. We also introduce a BioDIG-based website, MyDIG, which is being used to annotate images of mycoplasmas. Database URL: BioDIG website: http://biodig.org BioDIG source code repository: http://github.com/FriedbergLab/BioDIG The MyDIG database: http://mydig.biodig.org/ PMID:23550062

  3. Variation in Parasite Communities in Spottail Shiners (Notropis hudsonius) Linked with Precipitation.

    PubMed

    Marcogliese, David J; Locke, Sean A; Gélinas, Malorie; Gendron, Andrée D

    2016-02-01

    The Richelieu River, Quebec, is a highly-regulated waterway subject to numerous anthropogenic influences from municipal effluents and agricultural activities. Parasite communities in 234 spottail shiners (Notropis hudsonius) were examined from 4 localities in late spring 2003 and 2004. Component species richness varied between 15 and 18 species in 2003 but declined to 9 to 13 in 2004, while total parasite abundance was consistently lower in 2003. Parasite component community similarity among localities could not be directly linked to available upstream water quality measurements or anthropogenic activity and was best explained by precipitation. Total precipitation in May 2003 was approximately 40% more than in May 2004, presumably altering patterns of runoff, river flow rates, and water quality. This study suggests that fish parasite species composition and richness in the Richelieu River are influenced by environmental parameters which in turn ultimately are driven by a combination of climatic conditions and anthropogenic activities in the watershed. PMID:26465386

  4. Value Co-creation and Co-innovation: Linking Networked Organisations and Customer Communities

    NASA Astrophysics Data System (ADS)

    Romero, David; Molina, Arturo

    Strategic networks such as Collaborative Networked Organisations (CNOs) and Virtual Customer Communities (VCCs) show a high potential as drivers of value co-creation and collaborative innovation in today’s Networking Era. Both look at the network structures as a source of jointly value creation and open innovation through access to new skills, knowledge, markets and technologies by sharing risk and integrating complementary competencies. This collaborative endeavour has proven to be able to enhance the adaptability and flexibility of CNOs and VCCs value creating systems in order to react in response to external drivers such as collaborative (business) opportunities. This paper presents a reference framework for creating interface networks, also known as ‘experience-centric networks’, as enablers for linking networked organisations and customer communities in order to support the establishment of user-driven and collaborative innovation networks.

  5. Invader Assisted Enzyme-Linked Immunosorbent Assay for Colorimetric Detection of Disease Biomarkers Using Oligonucleotide Probe-Modified Gold Nanoparticles.

    PubMed

    Song, Qinxin; Qi, Xiemin; Jia, Huning; He, Liang; Kumar, Shalen; Pitman, Janet L; Zou, Bingjie; Zhou, Guohua

    2016-04-01

    We successfully developed an invader assisted ELISA assay (iaELISA) for sensitive detection of disease biomarkers. The method includes three key steps as follows; biotinylated detection antibody was at first used to capture targeted antigen by sandwich ELISA. The biotinylated oligonucleotide was then attached to detection antibody via streptavidin. Finally, the cascade invader reactions were employed to amplify the biotinylated oligonucleotide specific to the antigen so that detection of the antigen was transformed into signal amplification of the antigen-specific DNA. To achieve colorimetric detection, oligonucleotide probe and modified gold nanoparticles (AuNPs) were coupled with the invader assay. Utilization of the hairpin probes in the invader reaction brought about free AuNPs, resulting in the positive read-out (red color). On the other hand, aggregation of the AuNPs occurred when the hairpin probes were not utilized in the reaction. This method was successfully used to detect as low as 2.4 x 10(-11) g/mL of HBsAg by both naked eye and spectrophotometer. This sensitivity was about 100 times higher than that of conventional ELISA method. The method was also used to assay 16 serum specimens from HBV-infected patients and 8 serum specimens from HBV-negative donors and results were in good agreement with those obtained from the conventional ELISA. As the invader assay is sensitive to one base sequence, a good specificity was also obtained by detecting other antigens like hepatitis A virus (HAV) and BSA. The method has therefore much potential for ultrasensitive and cost-effective detection of targeted proteins that have clinical importance.

  6. Invader Assisted Enzyme-Linked Immunosorbent Assay for Colorimetric Detection of Disease Biomarkers Using Oligonucleotide Probe-Modified Gold Nanoparticles.

    PubMed

    Song, Qinxin; Qi, Xiemin; Jia, Huning; He, Liang; Kumar, Shalen; Pitman, Janet L; Zou, Bingjie; Zhou, Guohua

    2016-04-01

    We successfully developed an invader assisted ELISA assay (iaELISA) for sensitive detection of disease biomarkers. The method includes three key steps as follows; biotinylated detection antibody was at first used to capture targeted antigen by sandwich ELISA. The biotinylated oligonucleotide was then attached to detection antibody via streptavidin. Finally, the cascade invader reactions were employed to amplify the biotinylated oligonucleotide specific to the antigen so that detection of the antigen was transformed into signal amplification of the antigen-specific DNA. To achieve colorimetric detection, oligonucleotide probe and modified gold nanoparticles (AuNPs) were coupled with the invader assay. Utilization of the hairpin probes in the invader reaction brought about free AuNPs, resulting in the positive read-out (red color). On the other hand, aggregation of the AuNPs occurred when the hairpin probes were not utilized in the reaction. This method was successfully used to detect as low as 2.4 x 10(-11) g/mL of HBsAg by both naked eye and spectrophotometer. This sensitivity was about 100 times higher than that of conventional ELISA method. The method was also used to assay 16 serum specimens from HBV-infected patients and 8 serum specimens from HBV-negative donors and results were in good agreement with those obtained from the conventional ELISA. As the invader assay is sensitive to one base sequence, a good specificity was also obtained by detecting other antigens like hepatitis A virus (HAV) and BSA. The method has therefore much potential for ultrasensitive and cost-effective detection of targeted proteins that have clinical importance. PMID:27301208

  7. Beyond the Classroom: International Education and the Community College. Volume III: Creating Institutional Links in Asia and the Pacific.

    ERIC Educational Resources Information Center

    Franco, Robert W., Ed.; Shimabukuro, James N., Ed.

    Part of a four-volume set in which community college educators discuss their efforts to internationalize the educational experience of the students and communities they serve, volume III in this series addresses the development of programmatic links among five two-year colleges and institutions in Japan, Taiwan, the People's Republic of China,…

  8. An Ontario initiative to enhance the effectiveness of AIDS Service Organizations: Community-Linked Evaluation of AIDS Resources.

    PubMed

    Browne, Gina; Browne, Joseph A; McGee, Frank

    2005-01-01

    This report describes the rationale, process, and early outcomes of establishing a community-based research unit. The AIDS Bureau of the Ontario Provincial Government established the Community-Linked Evaluation of AIDS Resources Unit (CLEAR), which works in partnership with the AIDS Bureau and 31 of 74 AIDS Service Organizations (ASOs) in Ontario.

  9. Two Different Bacterial Community Types Are Linked with the Low-Methane Emission Trait in Sheep

    PubMed Central

    Kittelmann, Sandra; Pinares-Patiño, Cesar S.; Seedorf, Henning; Kirk, Michelle R.; Ganesh, Siva; McEwan, John C.; Janssen, Peter H.

    2014-01-01

    The potent greenhouse gas methane (CH4) is produced in the rumens of ruminant animals from hydrogen produced during microbial degradation of ingested feed. The natural animal-to-animal variation in the amount of CH4 emitted and the heritability of this trait offer a means for reducing CH4 emissions by selecting low-CH4 emitting animals for breeding. We demonstrate that differences in rumen microbial community structure are linked to high and low CH4 emissions in sheep. Bacterial community structures in 236 rumen samples from 118 high- and low-CH4 emitting sheep formed gradual transitions between three ruminotypes. Two of these (Q and S) were linked to significantly lower CH4 yields (14.4 and 13.6 g CH4/kg dry matter intake [DMI], respectively) than the third type (H; 15.9 g CH4/kg DMI; p<0.001). Low-CH4 ruminotype Q was associated with a significantly lower ruminal acetate to propionate ratio (3.7±0.4) than S (4.4±0.7; p<0.001) and H (4.3±0.5; p<0.001), and harbored high relative abundances of the propionate-producing Quinella ovalis. Low-CH4 ruminotype S was characterized by lactate- and succinate-producing Fibrobacter spp., Kandleria vitulina, Olsenella spp., Prevotella bryantii, and Sharpea azabuensis. High-CH4 ruminotype H had higher relative abundances of species belonging to Ruminococcus, other Ruminococcaceae, Lachnospiraceae, Catabacteriaceae, Coprococcus, other Clostridiales, Prevotella, other Bacteroidales, and Alphaproteobacteria, many of which are known to form significant amounts of hydrogen. We hypothesize that lower CH4 yields are the result of bacterial communities that ferment ingested feed to relatively less hydrogen, which results in less CH4 being formed. PMID:25078564

  10. Linked hydrologic and social systems that support resilience of traditional irrigation communities

    NASA Astrophysics Data System (ADS)

    Fernald, A.; Guldan, S.; Boykin, K.; Cibils, A.; Gonzales, M.; Hurd, B.; Lopez, S.; Ochoa, C.; Ortiz, M.; Rivera, J.; Rodriguez, S.; Steele, C.

    2015-01-01

    Southwestern US irrigated landscapes are facing upheaval due to water scarcity and land use conversion associated with climate change, population growth, and changing economics. In the traditionally irrigated valleys of northern New Mexico, these stresses, as well as instances of community longevity in the face of these stresses, are apparent. Human systems have interacted with hydrologic processes over the last 400 years in river-fed irrigated valleys to create linked systems. In this study, we ask if concurrent data from multiple disciplines could show that human-adapted hydrologic and socioeconomic systems have created conditions for resilience. Various types of resiliencies are evident in the communities. Traditional local knowledge about the hydrosocial cycle of community water management and ability to adopt new water management practices is a key response to disturbances such as low water supply from drought. Livestock producers have retained their irrigated land by adapting: changing from sheep to cattle and securing income from outside their livestock operations. Labor-intensive crops decreased as off-farm employment opportunities became available. Hydrologic resilience of the system can be affected by both human and natural elements. We find, for example, that there are multiple hydrologic benefits of traditional irrigation system water seepage: it recharges the groundwater that recharges rivers, supports threatened biodiversity by maintaining riparian vegetation, and ameliorates impacts of climate change by prolonging streamflow hydrographs. Human decisions to transfer water out of agriculture or change irrigation management, as well as natural changes such as long-term drought or climate change, can result in reduced seepage and the benefits it provides. We have worked with the communities to translate the multidisciplinary dimensions of these systems into a common language of causal loop diagrams, which form the basis for modeling future scenarios to

  11. Mechanistic links between gut microbial community dynamics, microbial functions and metabolic health

    PubMed Central

    Ha, Connie WY; Lam, Yan Y; Holmes, Andrew J

    2014-01-01

    Gut microbes comprise a high density, biologically active community that lies at the interface of an animal with its nutritional environment. Consequently their activity profoundly influences many aspects of the physiology and metabolism of the host animal. A range of microbial structural components and metabolites directly interact with host intestinal cells and tissues to influence nutrient uptake and epithelial health. Endocrine, neuronal and lymphoid cells in the gut also integrate signals from these microbial factors to influence systemic responses. Dysregulation of these host-microbe interactions is now recognised as a major risk factor in the development of metabolic dysfunction. This is a two-way process and understanding the factors that tip host-microbiome homeostasis over to dysbiosis requires greater appreciation of the host feedbacks that contribute to regulation of microbial community composition. To date, numerous studies have employed taxonomic profiling approaches to explore the links between microbial composition and host outcomes (especially obesity and its comorbidities), but inconsistent host-microbe associations have been reported. Available data indicates multiple factors have contributed to discrepancies between studies. These include the high level of functional redundancy in host-microbiome interactions combined with individual variation in microbiome composition; differences in study design, diet composition and host system between studies; and inherent limitations to the resolution of rRNA-based community profiling. Accounting for these factors allows for recognition of the common microbial and host factors driving community composition and development of dysbiosis on high fat diets. New therapeutic intervention options are now emerging. PMID:25469018

  12. Oxygen-18 isotope of breath CO2 linking to erythrocytes carbonic anhydrase activity: a biomarker for pre-diabetes and type 2 diabetes

    PubMed Central

    Ghosh, Chiranjit; Banik, Gourab D.; Maity, Abhijit; Som, Suman; Chakraborty, Arpita; Selvan, Chitra; Ghosh, Shibendu; Chowdhury, Subhankar; Pradhan, Manik

    2015-01-01

    Carbonic anhydrase (CA), a well-characterized metalloenzyme, is associated with oxygen-18 ( 18O)-isotopic fractionations of CO2. To investigate how CA activity links the 18O of breath CO2 to pre-diabetes (PD) and type 2 diabetes (T2D) during metabolism, we studied pre- and post-dose CA activities in erythrocytes with simultaneous monitoring of 18O/ 16O-isotope ratios of breath CO2 and thereafter elucidated potential metabolic pathways underlying CA alteration in the pathogenesis of T2D. Here we show that the post-dose CA activity in both T2D and PD was markedly enhanced, whereas the non-diabetic controls (NDC) exhibited a considerable reduction in post-dose CA activity when compared with their basal CA activities. However, T2D and PD exhibited isotopic enrichments of 18O in breath CO2, while a marked depletion of 18O in CO2 was manifested in NDC. Thus, the isotopic enrichments and depletions of 18O in breath CO2 were well correlated with the changes in CA activities for controls, PD and T2D. Our findings suggest the changes in CA activities in erythrocytes may contribute to the pathogenesis of T2D and the breath C 18O 16O regulated by the CA activity as a potential biomarker for non-invasive assessment of T2D, and thus may open a new method for treating T2D. PMID:25633556

  13. A randomised controlled trial linking mental health inpatients to community smoking cessation supports: A study protocol

    PubMed Central

    2011-01-01

    Background Mental health inpatients smoke at higher rates than the general population and are disproportionately affected by tobacco dependence. Despite the advent of smoke free policies within mental health hospitals, limited systems are in place to support a cessation attempt post hospitalisation, and international evidence suggests that most smokers return to pre-admission smoking levels following discharge. This protocol describes a randomised controlled trial that will test the feasibility, acceptability and efficacy of linking inpatient smoking care with ongoing community cessation support for smokers with a mental illness. Methods/Design This study will be conducted as a randomised controlled trial. 200 smokers with an acute mental illness will be recruited from a large inpatient mental health facility. Participants will complete a baseline survey and will be randomised to either a multimodal smoking cessation intervention or provided with hospital smoking care only. Randomisation will be stratified by diagnosis (psychotic, non-psychotic). Intervention participants will be provided with a brief motivational interview in the inpatient setting and options of ongoing smoking cessation support post discharge: nicotine replacement therapy (NRT); referral to Quitline; smoking cessation groups; and fortnightly telephone support. Outcome data, including cigarettes smoked per day, quit attempts, and self-reported 7-day point prevalence abstinence (validated by exhaled carbon monoxide), will be collected via blind interview at one week, two months, four months and six months post discharge. Process information will also be collected, including the use of cessation supports and cost of the intervention. Discussion This study will provide comprehensive data on the potential of an integrated, multimodal smoking cessation intervention for persons with an acute mental illness, linking inpatient with community cessation support. Trial Registration Australian and New Zealand

  14. A method linking the toxic effects at community-level with contaminant concentrations.

    PubMed

    Wang, Changyou; Su, Rongguo; Zhang, Yong; Liu, Gang

    2016-11-01

    In this study, we developed a method to quantify and link the toxic effects in community-level ecosystems with concentrations of petroleum hydrocarbons. The densities of Platymonas helgolandica var. tsingtaoensis, Isochrysis galbana, and Brachionus plicatilis in single-species tests and customized ecosystems were examined in response to a concentration gradient of petroleum hydrocarbons ranging from 0 to 8.0mgL(-1). A three-population ecological model with interspecies competition-grazing relationships was used to characterize population sizes with concentrations of petroleum hydrocarbons. A threshold concentration of the simplified plankton ecosystem of 0.376mgL(-1) for petroleum hydrocarbons was calculated from the proposed model, which was higher than the no-effect concentration of 0.056mgL(-1) derived from the single-species toxicity tests and the predicted no-effect concentration of 0.076mgL(-1) calculated from the species sensitivity distribution. This finding indicates that interspecies competition and grazing reduced the toxic effect of petroleum hydrocarbons at the community level. The sensitivity analysis for model parameters demonstrates that plankton population biomasses are highly sensitive to filtration rates. Antagonism between interspecies interactions and petroleum hydrocarbon toxicity was attributed to the reduced filtration rate and zooplankton grazing pressure. The proposed method is a simple means to address the concern regarding the impacts of ecological interactions on ecological risk assessments of pollutants.

  15. A Reemerging Political Space for Linking Person and Community Through Primary Health Care

    PubMed Central

    Bazemore, Andrew; Phillips, Robert L.; Etz, Rebecca S.; Stange, Kurt C.

    2012-01-01

    Objectives. We sought to understand how national policy key informants perceive the value and changing role of primary care in the context of emerging political opportunities. Methods. We conducted 13 semistructured interviews in May 2011 with leaders of federal agencies, think tanks, nonprofits, and quality standard–defining organizations with influence over health care reform policies and implementation. We recorded the interviews and used an editing and immersion–crystallization analysis approach to identify themes. Results. We identified 4 themes: (1) affirmation of primary care as the foundation of a more effective health care system, (2) the patient-centered medical home as a transitional step to foster practice innovation and payment reform, (3) the urgent need for an increased focus on community and population health in primary care, and (4) the ongoing need for advocacy and research efforts to keep primary care on public and policy agendas. Conclusions. Current efforts to reform primary care are only intermediate steps toward a system with a greater focus on community and population health. Transformed and policy-enabled primary care is an essential link between personalized care and population health. PMID:22690969

  16. Linking genes to communities and ecosystems: Daphnia as an ecogenomic model.

    PubMed

    Miner, Brooks E; De Meester, Luc; Pfrender, Michael E; Lampert, Winfried; Hairston, Nelson G

    2012-05-22

    How do genetic variation and evolutionary change in critical species affect the composition and functioning of populations, communities and ecosystems? Illuminating the links in the causal chain from genes up to ecosystems is a particularly exciting prospect now that the feedbacks between ecological and evolutionary changes are known to be bidirectional. Yet to fully explore phenomena that span multiple levels of the biological hierarchy requires model organisms and systems that feature a comprehensive triad of strong ecological interactions in nature, experimental tractability in diverse contexts and accessibility to modern genomic tools. The water flea Daphnia satisfies these criteria, and genomic approaches capitalizing on the pivotal role Daphnia plays in the functioning of pelagic freshwater food webs will enable investigations of eco-evolutionary dynamics in unprecedented detail. Because its ecology is profoundly influenced by both genetic polymorphism and phenotypic plasticity, Daphnia represents a model system with tremendous potential for developing a mechanistic understanding of the relationship between traits at the genetic, organismal and population levels, and consequences for community and ecosystem dynamics. Here, we highlight the combination of traits and ecological interactions that make Daphnia a definitive model system, focusing on the additional power and capabilities enabled by recent molecular and genomic advances. PMID:22298849

  17. Benthic macroinvertebrate and fish communities in Lake Huron are linked to submerged groundwater vents

    USGS Publications Warehouse

    Garrison, Sanders T.; Biddanda, B.A.; Stricker, C.A.; Nold, S.C.

    2011-01-01

    Groundwater can be an important source of nutrients and energy to aquatic ecosystems, but quantifying the inputs and biogeochemical importance remains challenging. A series of submerged groundwater vents in northern Lake Huron were examined to determine the linkage between groundwater nutrients and aquatic food webs. We collected samples of key food-web components from groundwater vent and reference habitats and analyzed them for 13C, 15N, and 34S isotopes. Dissolved inorganic carbon (DIC) in the groundwater was depleted in 13C, while aqueous sulfate was enriched in 34S (mean differences between groundwater and reference sites were -3.9% and +12.0%, respectively). Benthic primary producers, macroinvertebrates, and benthivorous fish had significantly lower ??13C values in groundwater environments, and benthivorous fish were somewhat depleted (-2.5%) in ??34S at groundwater sites compared to reference sites. However, ??15N values were not different between groundwater and reference sites, and pelagic components of the ecosystems (plankton and planktivorous and piscivorous fish) were similar in both ??13C and ??15N. These data suggest benthic metazoan communities surrounding groundwater vents are partially linked to groundwater-derived benthic primary production, while planktivorous and piscivorous communities not directly associated with the benthos do not rely on groundwater nutrients. ?? Inter-Research 2011.

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

    PubMed

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

    2011-08-23

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

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

    PubMed Central

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

    2011-01-01

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

  20. Making the links between community structure and individual well-being: community quality of life in Riverdale, Toronto, Canada.

    PubMed

    Raphael, D; Renwick, R; Brown, I; Steinmetz, B; Sehdev, H; Phillips, S

    2001-09-01

    An inquiry into community quality of life was carried out within a framework that recognizes the complex relationship between community structures and individual well-being. Through use of focus groups and key informant interviews, community members, service providers, and elected representatives in a Toronto community considered aspects of their community that affected quality of life. Community members identified strengths of access to amenities, caring and concerned people, community agencies, low-cost housing, and public transportation. Service providers and elected representatives recognized diversity, community agencies and resources, and presence of culturally relevant food stores and services as strengths. At one level, findings were consistent with emerging concepts of social capital. At another level, threats to the community were considered in relation to the hypothesized role neo-liberalism plays in weakening the welfare state. PMID:11439254

  1. Validation of biomarkers of CVD risk from dried blood spots in community-based research: Methodologies and study-specific serum equivalencies

    PubMed Central

    Samuelsson, Laura B.; Hall, Martica H.; McLean, Shakir; Porter, James H.; Berkman, Lisa; Marino, Miguel; Sembajwe, Grace; McDade, Thomas W.; Buxton, Orfeu M.

    2016-01-01

    Objective Dried blood spot (DBS) methodology offers significant advantages over venipuncture in vulnerable populations or large-scale studies, including reduced participant burden and higher response rates. Uncertainty about validity of cardiovascular risk biomarkers remains a barrier to wide-scale use. We determined the validity of DBS-derived biomarkers of CVD risk versus gold-standard assessments, and study-specific, serum-equivalency values for clinical relevance of DBS-derived values. Methods Concurrent venipuncture serum and DBS samples (n=150 adults) were assayed in CLIA-certified and DBS laboratories, respectively. Time controls of DBS standard samples were assayed single-blind along with test samples. Linear regression analyses evaluated DBS-to-serum equivalency values; agreement and bias were assessed via Bland-Altman plots. Results Linear regressions of venipuncture values on DBS-to-serum equivalencies provided R2 values for TC, HDL-C, CRP of 0.484, 0.118, 0.666, respectively. Bland-Altman plots revealed minimal systematic bias between DBS-to-serum and venipuncture values; precision worsened at higher mean values of CRP. Time controls reveal little degradation or change in analyte values for HDL-C and CRP over 30 weeks. Conclusions DBS-assessed biomarkers represent a valid alternative to venipuncture assessments. Large studies using DBS should include study-specific serum-equivalency determinations to optimize individual-level sensitivity, viability of detecting intervention effects, and generalizability in community-level, primary prevention interventions. PMID:26652683

  2. Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

    PubMed Central

    Cassman, Noriko A.; Leite, Marcio F. A.; Pan, Yao; de Hollander, Mattias; van Veen, Johannes A.; Kuramae, Eiko E.

    2016-01-01

    Inorganic fertilization and mowing alter soil factors with subsequent effects–direct and indirect - on above- and below-ground communities. We explored direct and indirect effects of long-term fertilization (N, P, NPK, Liming) and twice yearly mowing on the plant, bacterial and fungal communities and soil factors. We analyzed co-variation using 16S and 18S rRNA genes surveys, and plant frequency and edaphic factors across treatments. The plant and fungal communities were distinct in the NPK and L treatments, while the bacterial communities and soil factors were distinct in the N and L treatments. Plant community diversity and evenness had low diversity in the NPK and high diversity in the liming treatment, while the diversity and evenness of the bacterial and fungal communities did not differ across treatments, except of higher diversity and evenness in the liming treatment for the bacteria. We found significant co-structures between communities based on plant and fungal comparisons but not between plant and bacterial nor bacterial and fungal comparisons. Our results suggested that the plant and fungal communities are more tightly linked than either community with the bacterial community in fertilized soils. We found co-varying plant, bacterial and fungal taxa in different treatments that may indicate ecological interactions. PMID:27020916

  3. Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland

    NASA Astrophysics Data System (ADS)

    Cassman, Noriko A.; Leite, Marcio F. A.; Pan, Yao; de Hollander, Mattias; van Veen, Johannes A.; Kuramae, Eiko E.

    2016-03-01

    Inorganic fertilization and mowing alter soil factors with subsequent effects–direct and indirect - on above- and below-ground communities. We explored direct and indirect effects of long-term fertilization (N, P, NPK, Liming) and twice yearly mowing on the plant, bacterial and fungal communities and soil factors. We analyzed co-variation using 16S and 18S rRNA genes surveys, and plant frequency and edaphic factors across treatments. The plant and fungal communities were distinct in the NPK and L treatments, while the bacterial communities and soil factors were distinct in the N and L treatments. Plant community diversity and evenness had low diversity in the NPK and high diversity in the liming treatment, while the diversity and evenness of the bacterial and fungal communities did not differ across treatments, except of higher diversity and evenness in the liming treatment for the bacteria. We found significant co-structures between communities based on plant and fungal comparisons but not between plant and bacterial nor bacterial and fungal comparisons. Our results suggested that the plant and fungal communities are more tightly linked than either community with the bacterial community in fertilized soils. We found co-varying plant, bacterial and fungal taxa in different treatments that may indicate ecological interactions.

  4. Biomarkers in Parkinson's disease: a venture capitalist's perspective.

    PubMed

    Eckstein, Jens W

    2010-10-01

    The emergence of biomarkers linking disease and treatment effects in a clear manner presents an opportunity to change the current drug development paradigm, which could lead to more cost-efficient and higher-quality clinical trials. This has raised the hopes of venture capital investors, who may be able to better navigate the stormy and risky sea of early-stage life science investments, to find a way out of the current funding crisis for novel, nonvalidated drugs and their clinical development. The following survey paints a snapshot of the current perception of biomarkers as a paradigm changer in the eyes of the venture capital community.

  5. Urinary Biomarkers KIM-1 and NGAL for Detection of Chronic Kidney Disease of Uncertain Etiology (CKDu) among Agricultural Communities in Sri Lanka.

    PubMed

    De Silva, Pallagae Mangala C S; Mohammed Abdul, Khaja Shameem; Eakanayake, Eakanayake M D V; Jayasinghe, Sudheera Sammanthi; Jayasumana, Channa; Asanthi, Hewa Bandulage; Perera, Hettiarachigae S D; Chaminda, Gamage G Tushara; Chandana, Ediriweera P S; Siribaddana, Sisira H

    2016-09-01

    Chronic Kidney Disease of uncertain etiology (CKDu) is an emerging epidemic among farming communities in rural Sri Lanka. Victims do not exhibit common causative factors, however, histopathological studies revealed that CKDu is a tubulointerstitial disease. Urine albumin or albumin-creatinine ratio is still being used as a traditional diagnostic tool to identify CKDu, but accuracy and prevalence data generated are questionable. Urinary biomarkers have been used in similar nephropathy and are widely recognised for their sensitivity, specificity and accuracy in determining CKDu and early renal injury. However, these biomarkers have never been used in diagnosing CKDu in Sri Lanka. Male farmers (n = 1734) were recruited from 4 regions in Sri Lanka i.e. Matara and Nuwara Eliya (farming locations with no CKDu prevalence) and two CKDu emerging locations from Hambantota District in Southern Sri Lanka; Angunakolapelessa (EL1) and Bandagiriya (EL2). Albuminuria (ACR ≥ 30mg/g); serum creatinine based estimation of glomerular filtration rate (eGFR); creatinine normalized urinary kidney injury molecule (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL) were measured. Fourteen new CKDu cases (18%) from EL1 and nine CKDu cases (9%) from EL2 were recognized for the first time from EL1, EL2 locations, which were previously considered as non-endemic of the disease and associated with persistent albuminuria (ACR ≥ 30mg/g Cr). No CKDu cases were identified in non-endemic study locations in Matara (CM) and Nuwara Eliya (CN). Analysis of urinary biomarkers showed urinary KIM-1 and NGAL were significantly higher in new CKDu cases in EL1 and EL2. However, we also reported significantly higher KIM-1 and NGAL in apparently healthy farmers in EL 1 and EL 2 with comparison to both control groups. These observations may indicate possible early renal damage in absence of persistent albuminuria and potential capabilities of urinary KIM-1 and NGAL in early detection of renal injury

  6. Urinary Biomarkers KIM-1 and NGAL for Detection of Chronic Kidney Disease of Uncertain Etiology (CKDu) among Agricultural Communities in Sri Lanka

    PubMed Central

    Mohammed Abdul, Khaja Shameem; Eakanayake, Eakanayake M. D. V.; Jayasinghe, Sudheera Sammanthi; Jayasumana, Channa; Asanthi, Hewa Bandulage; Perera, Hettiarachigae S. D.; Chaminda, Gamage G. Tushara; Chandana, Ediriweera P. S.; Siribaddana, Sisira H.

    2016-01-01

    Chronic Kidney Disease of uncertain etiology (CKDu) is an emerging epidemic among farming communities in rural Sri Lanka. Victims do not exhibit common causative factors, however, histopathological studies revealed that CKDu is a tubulointerstitial disease. Urine albumin or albumin-creatinine ratio is still being used as a traditional diagnostic tool to identify CKDu, but accuracy and prevalence data generated are questionable. Urinary biomarkers have been used in similar nephropathy and are widely recognised for their sensitivity, specificity and accuracy in determining CKDu and early renal injury. However, these biomarkers have never been used in diagnosing CKDu in Sri Lanka. Male farmers (n = 1734) were recruited from 4 regions in Sri Lanka i.e. Matara and Nuwara Eliya (farming locations with no CKDu prevalence) and two CKDu emerging locations from Hambantota District in Southern Sri Lanka; Angunakolapelessa (EL1) and Bandagiriya (EL2). Albuminuria (ACR ≥ 30mg/g); serum creatinine based estimation of glomerular filtration rate (eGFR); creatinine normalized urinary kidney injury molecule (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL) were measured. Fourteen new CKDu cases (18%) from EL1 and nine CKDu cases (9%) from EL2 were recognized for the first time from EL1, EL2 locations, which were previously considered as non-endemic of the disease and associated with persistent albuminuria (ACR ≥ 30mg/g Cr). No CKDu cases were identified in non-endemic study locations in Matara (CM) and Nuwara Eliya (CN). Analysis of urinary biomarkers showed urinary KIM-1 and NGAL were significantly higher in new CKDu cases in EL1 and EL2. However, we also reported significantly higher KIM-1 and NGAL in apparently healthy farmers in EL 1 and EL 2 with comparison to both control groups. These observations may indicate possible early renal damage in absence of persistent albuminuria and potential capabilities of urinary KIM-1 and NGAL in early detection of renal injury

  7. Urinary Biomarkers KIM-1 and NGAL for Detection of Chronic Kidney Disease of Uncertain Etiology (CKDu) among Agricultural Communities in Sri Lanka.

    PubMed

    De Silva, Pallagae Mangala C S; Mohammed Abdul, Khaja Shameem; Eakanayake, Eakanayake M D V; Jayasinghe, Sudheera Sammanthi; Jayasumana, Channa; Asanthi, Hewa Bandulage; Perera, Hettiarachigae S D; Chaminda, Gamage G Tushara; Chandana, Ediriweera P S; Siribaddana, Sisira H

    2016-09-01

    Chronic Kidney Disease of uncertain etiology (CKDu) is an emerging epidemic among farming communities in rural Sri Lanka. Victims do not exhibit common causative factors, however, histopathological studies revealed that CKDu is a tubulointerstitial disease. Urine albumin or albumin-creatinine ratio is still being used as a traditional diagnostic tool to identify CKDu, but accuracy and prevalence data generated are questionable. Urinary biomarkers have been used in similar nephropathy and are widely recognised for their sensitivity, specificity and accuracy in determining CKDu and early renal injury. However, these biomarkers have never been used in diagnosing CKDu in Sri Lanka. Male farmers (n = 1734) were recruited from 4 regions in Sri Lanka i.e. Matara and Nuwara Eliya (farming locations with no CKDu prevalence) and two CKDu emerging locations from Hambantota District in Southern Sri Lanka; Angunakolapelessa (EL1) and Bandagiriya (EL2). Albuminuria (ACR ≥ 30mg/g); serum creatinine based estimation of glomerular filtration rate (eGFR); creatinine normalized urinary kidney injury molecule (KIM-1) and neutrophil gelatinase-associated lipocalin (NGAL) were measured. Fourteen new CKDu cases (18%) from EL1 and nine CKDu cases (9%) from EL2 were recognized for the first time from EL1, EL2 locations, which were previously considered as non-endemic of the disease and associated with persistent albuminuria (ACR ≥ 30mg/g Cr). No CKDu cases were identified in non-endemic study locations in Matara (CM) and Nuwara Eliya (CN). Analysis of urinary biomarkers showed urinary KIM-1 and NGAL were significantly higher in new CKDu cases in EL1 and EL2. However, we also reported significantly higher KIM-1 and NGAL in apparently healthy farmers in EL 1 and EL 2 with comparison to both control groups. These observations may indicate possible early renal damage in absence of persistent albuminuria and potential capabilities of urinary KIM-1 and NGAL in early detection of renal injury

  8. Rural Student Entrepreneurs: Linking Commerce and Community. (Benefits)[Squared]: The Exponential Results of Linking School Improvement and Community Development, Issue Number Three.

    ERIC Educational Resources Information Center

    Boethel, Martha

    In many rural areas, both communities and schools are threatened by decreasing population and changing economic conditions. To boost both the local economy and student achievement, a growing number of rural schools are turning to entrepreneurial education. In school entrepreneurship programs, students create small businesses under the guidance of…

  9. Maintaining Scientific Community Vocabularies in Drupal through Consumption of Linked Open Data and Web Services

    NASA Astrophysics Data System (ADS)

    Shepherd, A.; Arko, R. A.; Maffei, A. R.; Chandler, C. L.

    2012-12-01

    In the Summer of 2011, a one-year pilot project was funded by the National Science Foundation to build a pre-cruise planning application using the Drupal content management system (CMS). This application will be used to assist the individual operators of research vessels in the UNOLS fleet. A large portion of the operator's pre-cruise process revolves around a questionnaire presented to the principal investigator(PI) that is used to gather information about the nature of their upcoming cruise. The Drupal-based application will be delivered as a distribution for use by any operator of a UNOLS vessel to construct customized questionnaires and provide an interface for the PI to complete this questionnaire at their leisure. A major goal of the project is to develop an application that will require as little programming maintenance as possible after the initial development effort. One of the strategies employed is the reuse of existing controlled vocabularies and linked open data wherever possible for fields of the questionnaire - most notably to populate the concepts of Country, Organization, Port, and Ship. The Rolling Deck to Repository (R2R) program manages controlled vocabularies for these concepts and currently exposes these concepts as linked open data. Furthermore, R2R has identified the authoritative source for pertinent oceanographic community vocabularies as ICES for Ship, UNOLS for Port, IANA for Organization, ISO for Country, ISO for Language, SeaDataNet for Device, FIPS for State, and IHO for Sea Area as described at http://www.rvdata.us/voc. The scope of the terms provided by these sources matches the scope of the operator's needs for these concepts, and so the application is being designed to automatically consume served information about these vocabulary terms to populate and update Drupal taxonomies for use in the questionnaire. Where newer terms are required for a PI to complete a questionnaire (before they appear in the vocabularies), the Drupal

  10. Linking leaf veins to growth and mortality rates: an example from a subtropical tree community.

    PubMed

    Iida, Yoshiko; Sun, I-Fang; Price, Charles A; Chen, Chien-Teh; Chen, Zueng-Sang; Chiang, Jyh-Min; Huang, Chun-Lin; Swenson, Nathan G

    2016-09-01

    A fundamental goal in ecology is to link variation in species function to performance, but functional trait-performance investigations have had mixed success. This indicates that less commonly measured functional traits may more clearly elucidate trait-performance relationships. Despite the potential importance of leaf vein traits, which are expected to be related to resource delivery rates and photosynthetic capacity, there are few studies, which examine associations between these traits and demographic performance in communities. Here, we examined the associations between species traits including leaf venation traits and demographic rates (Relative Growth Rate, RGR and mortality) as well as the spatial distributions of traits along soil environment for 54 co-occurring species in a subtropical forest. Size-related changes in demographic rates were estimated using a hierarchical Bayesian approach. Next, Kendall's rank correlations were quantified between traits and estimated demographic rates at a given size and between traits and species-average soil environment. Species with denser venation, smaller areoles, less succulent, or thinner leaves showed higher RGR for a wide range of size classes. Species with leaves of denser veins, larger area, cheaper construction costs or thinner, or low-density wood were associated with high mortality rates only in small size classes. Lastly, contrary to our expectations, acquisitive traits were not related to resource-rich edaphic conditions. This study shows that leaf vein traits are weakly, but significantly related to tree demographic performance together with other species traits. Because leaf traits associated with an acquisitive strategy such as denser venation, less succulence, and thinner leaves showed higher growth rate, but similar leaf traits were not associated with mortality, different pathways may shape species growth and survival. This study suggests that we are still not measuring some of key traits related to

  11. Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird–plant network

    PubMed Central

    Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

    2014-01-01

    Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird–plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought. PMID:24552835

  12. Processes entangling interactions in communities: forbidden links are more important than abundance in a hummingbird-plant network.

    PubMed

    Vizentin-Bugoni, Jeferson; Maruyama, Pietro Kiyoshi; Sazima, Marlies

    2014-04-01

    Understanding the relative importance of multiple processes on structuring species interactions within communities is one of the major challenges in ecology. Here, we evaluated the relative importance of species abundance and forbidden links in structuring a hummingbird-plant interaction network from the Atlantic rainforest in Brazil. Our results show that models incorporating phenological overlapping and morphological matches were more accurate in predicting the observed interactions than models considering species abundance. This means that forbidden links, by imposing constraints on species interactions, play a greater role than species abundance in structuring the ecological network. We also show that using the frequency of interaction as a proxy for species abundance and network metrics to describe the detailed network structure might lead to biased conclusions regarding mechanisms generating network structure. Together, our findings suggest that species abundance can be a less important driver of species interactions in communities than previously thought.

  13. Responses of Soil Bacterial Communities to Nitrogen Deposition and Precipitation Increment Are Closely Linked with Aboveground Community Variation.

    PubMed

    Li, Hui; Xu, Zhuwen; Yang, Shan; Li, Xiaobin; Top, Eva M; Wang, Ruzhen; Zhang, Yuge; Cai, Jiangping; Yao, Fei; Han, Xingguo; Jiang, Yong

    2016-05-01

    It has been predicted that precipitation and atmospheric nitrogen (N) deposition will increase in northern China; yet, ecosystem responses to the interactive effects of water and N remain largely unknown. In particular, responses of belowground microbial community to projected global change and their potential linkages to aboveground macro-organisms are rarely studied. In this study, we examined the responses of soil bacterial diversity and community composition to increased precipitation and multi-level N deposition in a temperate steppe in Inner Mongolia, China, and explored the diversity linkages between aboveground and belowground communities. It was observed that N addition caused the significant decrease in bacterial alpha-diversity and dramatic changes in community composition. In addition, we documented strong correlations of alpha- and beta-diversity between plant and bacterial communities in response to N addition. It was found that N enriched the so-called copiotrophic bacteria, but reduced the oligotrophic groups, primarily by increasing the soil inorganic N content and carbon availability and decreasing soil pH. We still highlighted that increased precipitation tended to alleviate the effects of N on bacterial diversity and dampen the plant-microbe connections induced by N. The counteractive effects of N addition and increased precipitation imply that even though the ecosystem diversity and function are predicted to be negatively affected by N deposition in the coming decades; the combination with increased precipitation may partially offset this detrimental effect.

  14. Step 5: has clearly defined policies, procedures for collaboration, consultation, links to community resources: the coalition for improving maternity services:.

    PubMed

    Salt, Karen

    2007-01-01

    Step 5 of the Ten Steps of Mother-Friendly Care ensures that the hospital, birth center, or home birth service has clearly defined policies and procedures for collaborating and consulting with other maternity services and for linking the mother and baby to appropriate community services during both the prenatal and the postpartum periods. The rationales and evidence in support of this step are presented. PMID:18523674

  15. Linking Geology and Microbiology: Inactive Pockmarks Affect Sediment Microbial Community Structure

    PubMed Central

    Haverkamp, Thomas H. A.; Hammer, Øyvind; Jakobsen, Kjetill S.

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment. PMID:24475066

  16. Linking geology and microbiology: inactive pockmarks affect sediment microbial community structure.

    PubMed

    Haverkamp, Thomas H A; Hammer, Øyvind; Jakobsen, Kjetill S

    2014-01-01

    Pockmarks are geological features that are found on the bottom of lakes and oceans all over the globe. Some are active, seeping oil or methane, while others are inactive. Active pockmarks are well studied since they harbor specialized microbial communities that proliferate on the seeping compounds. Such communities are not found in inactive pockmarks. Interestingly, inactive pockmarks are known to have different macrofaunal communities compared to the surrounding sediments. It is undetermined what the microbial composition of inactive pockmarks is and if it shows a similar pattern as the macrofauna. The Norwegian Oslofjord contains many inactive pockmarks and they are well suited to study the influence of these geological features on the microbial community in the sediment. Here we present a detailed analysis of the microbial communities found in three inactive pockmarks and two control samples at two core depth intervals. The communities were analyzed using high-throughput amplicon sequencing of the 16S rRNA V3 region. Microbial communities of surface pockmark sediments were indistinguishable from communities found in the surrounding seabed. In contrast, pockmark communities at 40 cm sediment depth had a significantly different community structure from normal sediments at the same depth. Statistical analysis of chemical variables indicated significant differences in the concentrations of total carbon and non-particulate organic carbon between 40 cm pockmarks and reference sample sediments. We discuss these results in comparison with the taxonomic classification of the OTUs identified in our samples. Our results indicate that microbial communities at the sediment surface are affected by the water column, while the deeper (40 cm) sediment communities are affected by local conditions within the sediment.

  17. Linking community, parenting, and depressive symptom trajectories: testing resilience models of adolescent agency based on race/ethnicity and gender.

    PubMed

    Williams, Amanda L; Merten, Michael J

    2014-09-01

    Family stress models illustrate how communities affect youth outcomes through effects on parents and studies consistently show the enduring effects of early community context. The present study takes a different approach identifying human agency during adolescence as a potentially significant promotive factor mediating the relationship between community, parenting, and mental health. While agency is an important part of resilience, its longitudinal effects are unknown, particularly based on gender and race/ethnicity. The purpose of this research was to model the long-term effects of community structural adversity and social resources as predictors of adolescent depressive symptom trajectories via indirect effects of parental happiness, parent-child relationships, and human agency. Latent growth analyses were conducted with 1,796 participants (53% female; 56% White) across four waves of the National Longitudinal Study of Adolescent Health spanning adolescence (Wave 1) through adulthood (Wave 4). The results identified agency as an important promotive factor during adolescence with long-term mental health benefits, but only for White and male participants. For these individuals, community social resources and the quality of the parent-child relationship were related to higher levels of agency and more positive mental health trajectories. Although community social resources similarly benefitted parenting and agency among females and non-White participants, there were no significant links between agency and depressive symptoms for these youth. The results suggest that agency remains an important, but poorly understood concept and additional work is necessary to continue unpacking its meaning for diverse groups of youth. PMID:24907892

  18. Linking community, parenting, and depressive symptom trajectories: testing resilience models of adolescent agency based on race/ethnicity and gender.

    PubMed

    Williams, Amanda L; Merten, Michael J

    2014-09-01

    Family stress models illustrate how communities affect youth outcomes through effects on parents and studies consistently show the enduring effects of early community context. The present study takes a different approach identifying human agency during adolescence as a potentially significant promotive factor mediating the relationship between community, parenting, and mental health. While agency is an important part of resilience, its longitudinal effects are unknown, particularly based on gender and race/ethnicity. The purpose of this research was to model the long-term effects of community structural adversity and social resources as predictors of adolescent depressive symptom trajectories via indirect effects of parental happiness, parent-child relationships, and human agency. Latent growth analyses were conducted with 1,796 participants (53% female; 56% White) across four waves of the National Longitudinal Study of Adolescent Health spanning adolescence (Wave 1) through adulthood (Wave 4). The results identified agency as an important promotive factor during adolescence with long-term mental health benefits, but only for White and male participants. For these individuals, community social resources and the quality of the parent-child relationship were related to higher levels of agency and more positive mental health trajectories. Although community social resources similarly benefitted parenting and agency among females and non-White participants, there were no significant links between agency and depressive symptoms for these youth. The results suggest that agency remains an important, but poorly understood concept and additional work is necessary to continue unpacking its meaning for diverse groups of youth.

  19. ECO TECH LINK: PT3 Grant Builds Technology Circles in the K-18 Community.

    ERIC Educational Resources Information Center

    Klinger, Katie; Duckett, Jane; Medrano, Maria; Crow, Nedra; Stowers, Gwen

    Through the vehicle of the PT3 grant program, ECO TECH LINK has built a strong consortium to support technology circles of government, education and business in order to raise student achievement scores, shorten the time it takes to earn a teaching credential, and enhance the quality of teacher credential courses. The ECO TECH LINK grant enables…

  20. Exploring ancient microbial community assemblages by creating complex lipid biomarker profiles for stromatolites and microbial mats in Hamelin Pool, Shark Bay, Australia

    NASA Astrophysics Data System (ADS)

    Myers, E.; Summons, R. E.; Schubotz, F.; Matys, E. D.

    2015-12-01

    Stromatolites that are biogenic in origin, a characteristic that can be determined by the coexistence of microbial mats (active microbial communities) and stromatolites (lithified structures) like in Hamelin Pool, comprise one of the best modern analogs to ancient microbial community assemblages. Comprehensive lipid biomarker profiles that include lipids of varying persistence in the rock record can help determine how previously living microbial communities are represented in lithified stromatolites. To create these profiles, the samples analyzed included non-lithified smooth, pustular, and colloform microbial mats, as well as smooth and colloform stromatolites. Select samples were separated into upper and lower layers of 5cm depth each. Intact polar lipids, glycerol dialkyl glycerol tetraethers, and bacteriohopanepolyols were analyzed via liquid chromatography-mass spectrometry (LC-MS) coupled to a Quadropole Time-of-Flight (QTOF) mass spectrometer; additionally, fatty acids from each sample were analyzed using gas chromatography-mass spectrometry (GC-MS) to prove consistent signatures with those determined by Allen et al. in 2010 for similar microbial mat samples. In accordance with those findings, 2-methylhopanoids were detected, as well as limited signals from higher (vascular) plants, the latter of which suggests terrestrial inputs, potentially from runoff. The rarely detected presence of 3-methylhopanoids appears in a significant portion of the samples, though further isolations of the molecule are needed to confirm. While all lipid profiles were relatively similar, certain differences in relative composition are likely attributable to morphological differences of the mats, some of which allow deeper oxygen and/or sunlight penetration, which influence the microbial community. However, overall similarities of transient and persistent lipids suggest that the microbial communities of both the non-lithified microbial mats and stromatolites are similar.

  1. The GEOSS Science and Technology Stakeholder Network and Service Suite: Linking S&T Communities and GEOSS

    NASA Astrophysics Data System (ADS)

    Plag, Hans-Peter; Jules-Plag, Shelley

    2015-04-01

    The Global Earth Observation System of Systems (GEOSS) developed by the Group on Earth Observations (GEO) aims to provide practice-relevant knowledge in support of decision making in a wide range of societal benefit areas. Generating this practice-relevant knowledge based on Earth observations, socio-economic data and models often depends on research, and utilization of the societal benefits of EOs requires the involvement of science and research communities. Building a GEOSS responding to the needs of a wide range of users necessitates contributions from many science and technology (S&T) communities. In particular, a strong engagement of science and technology (S&T) communities in both the development and use of GEOSS is necessary to address the complex issues associated with the on-going transition out of the Holocene. S&T support is needed to improve interoperability between global observing, modeling, and information systems; to enable data integration across disciplinary boundaries; to facilitate data sharing, archiving, dissemination, and reanalysis; to optimize the recording of observations, assimilation of data into models, and generation of data products; to enhance the value of observations from individual observing systems through their integration in the SBAs; and to harmonize well-calibrated, highly accurate, stable, sustained in-situ and satellite observations of the same variable recorded by different sensors and different agencies. Consequently, the GEO Work Plan includes several Tasks focusing on outreach to S&T communities, and most of the GEO Community of Practice have a strong S&T component. The GEOSS S&T Stakeholder Network facilitates input from S&T communities to GEO. Infrastructure serving and linking S&T users communities and GEOSS has been developed and is integrated into a GEOSS S&T Service Suite (GSTSS). The GSTSS has several outreach components for the demonstration of GEOSS and its value for S&T communities, and for services supporting

  2. Linking Parent and Community Involvement with Student Achievement: Comparing Principal and Teacher Perceptions of Stakeholder Influence

    ERIC Educational Resources Information Center

    Gordon, Molly F.; Louis, Karen Seashore

    2009-01-01

    Expanding the sources of leadership in schools has been a reform theme since the mid 1980s. Using exploratory factor analysis and regression, we examine the following questions: (1) How does leadership style affect principals' openness to community involvement? (2) Is a principal's openness to community involvement related to student achievement?…

  3. Linking Scholarship and Practice: Community College Leaders, State Mandates, and Leadership Competencies

    ERIC Educational Resources Information Center

    Hebert-Swartzer, Cathleen A.; McNair, Delores E.

    2010-01-01

    To be an effective leader in today's community college requires a sophisticated set of skills that are often learned through on the job training, mentoring, and professional development activities. Using case study methodology, this study examined how community college leaders in California use their skills to implement a state mandate related to…

  4. Change and Diversity: Communities Link with Higher Education: Reconsidering the Nature of Service Partnerships.

    ERIC Educational Resources Information Center

    Shadiow, Linda K.

    This paper discusses how higher education involvement with community service can be sustained and strengthened. There has been increased discussion of community and university partnerships during the last few years, as exemplified by the summer 1991 issue of "Teachers College Record." Higher education is challenged to integrate service activities…

  5. Linking Community Communication to Conservation of the Maned Wolf in Central Brazil

    ERIC Educational Resources Information Center

    Bizerril, Marcelo Ximenes A.; Soares, Carla Cruz; Santos, Jean Pierre

    2011-01-01

    This article describes the environmental education (EE) program developed in the neighboring community of Serra da Canastra National Park based on a research project focused on the maned wolf conservation. The article assesses three tools used to foster the community's participation in discussing local issues: (1) communal production of a book…

  6. Understanding the Link between Social Organization and Crime in Rural Communities

    PubMed Central

    Chilenski, Sarah M.; Syvertsen, Amy K.; Greenberg, Mark T.

    2015-01-01

    Rural communities make up much of America's heartland, yet we know little about their social organization, and how elements of their social organization relate to crime rates. The current study sought to remedy this gap by examining the associations between two measures of social organization – collective efficacy and social trust – with a number of structural community characteristics, local crime rates, and perceptions of safety in a sample of 27 rural and small town communities in two states. Measures of collective efficacy, social trust, and perceived safety, were gathered from key community members in 2006; other measures were drawn from the 2000 Census and FBI Uniform Crime Reporting system. A series of competing hypotheses were tested to examine the relative importance of social trust and collective efficacy in predicting local crime rates. Results do not support the full generalization of the social disorganization model. Correlational analyses showed that neither collective efficacy nor social trust had a direct association with community crime, nor did they mediate the associations between community structural characteristics and crime. However, perceived safety mediated the association between community crime and both measures of social organization. Analyses suggest that social trust may be more important than collective efficacy when understanding the effect of crime on a community's culture in rural areas. Understanding these associations in rural settings can aid decision makers in shaping policies to reduce crime and juvenile delinquency. PMID:26120326

  7. Structured decision making as a framework for linking quantitative decision support to community values

    EPA Science Inventory

    Community-level decisions can have large impacts on production and delivery of ecosystem services, which ultimately affects community well-being. But engaging stakeholders in a process to explore these impacts is a significant challenge. The principles of Structured Decision Ma...

  8. Exploring Links between Empowerment and Community-Based Arts and Cultural Practices: Perspectives from Barcelona Practitioners

    ERIC Educational Resources Information Center

    Carrasco, Ruben David Fernández; Monferrer, Moisés Carmona; Tarditi, Andrés Di Masso

    2016-01-01

    In this paper, we reflect on the development of community-based arts and cultural (CBAC) practices to promote psychosocial, group/organisational and community changes from the perspective of empowerment. We draw on findings from an initial exploratory phase of an ongoing action-research project in Spain about creative tools that empower artists…

  9. Veterans Coming Home to the Community College: Linking Research to Practice

    ERIC Educational Resources Information Center

    Persky, Karen R.; Oliver, Diane E.

    2011-01-01

    Community colleges must prepare for change as increasing numbers of students who are veterans of the Iraq and Afghanistan Wars use their post-9/11 GI Bill benefits to join the colleges' diverse student bodies. Based on the findings of a mixed methods case study, needs of veterans at the community college are framed and discussed within five major…

  10. Linking Environmental Science Students to External Community Partners: A Critical Assessment of a Service Learning Course

    ERIC Educational Resources Information Center

    Grossman, Julie; Cooper, Terrence

    2004-01-01

    This article describes a course that integrates environmental science students into local community organizations. Despite initially high expectations, students who completed the course held negative opinions about their experience because of inadequate community partner preparation. Based on the course's successes and challenges, in this article,…

  11. Literacy Outreach: The Community Link. A Guide to Working with Literacy Helpers.

    ERIC Educational Resources Information Center

    Green, Karen Reed; And Others

    This guide, which is addressed to community-based organizations desiring to start or expand existing adult literacy programs, deals with recruiting and training volunteer literacy tutors. Outlined in the guide are strategies for expanding community outreach efforts (identifying who needs help and where help is typically obtained, learning from…

  12. Standing Alone No More: Linking Research to a Writing Course in a Learning Community

    ERIC Educational Resources Information Center

    Rapchak, Marcia; Cipr, Ava

    2015-01-01

    Collaborating with teaching faculty is a well-established method of making library instruction more meaningful and engaging to students, and learning communities provide an excellent opportunity to work closely with both teaching faculty and a cohort of students. A typical learning community brings students together around a similar discipline or…

  13. Landscapes for Learning: Growing Children, Youth, Schools, and Communities. Linking Learning with Life.

    ERIC Educational Resources Information Center

    Vander Mey, Brenda J.; McDonald, Sian I.

    This booklet provides information on implementing the Landscapes for Learning (LFL) program, which was conceived to bring children, youths, and communities together to learn about landscaping while beautifying local schools and communities. The booklet begins with a discussion of the concept of environmental stewardship. Described next are the…

  14. NABIR Assessment Element, Expanded Rapid, Comprehensive, Lipid Biomarker Analysis for Subsurface, Community Composition and Nutritional/Physiological Status as Monitors of Remediation and Detoxification Effectiveness

    SciTech Connect

    David C. White

    2005-09-14

    NABIR funding at the University of Tennessee Center for Biomarker Analysis (CBA) has led to several key contributions to the investigation of bioremediation of metals and radionuclides. This lab has played an integral part in assessing microbial communities at the field scale at the ORNL FRC (Istok et al., 2004) and two UMTRA sites (Anderson et al., 2003, Chang et al., 2001). Our work over the period of the grant has resulted in 42-peer reviewed publications, 62 presentations (14 of which were international), and one patent pending. Currently CBA has 2 papers in press. The main objectives relating to the field portion of this program were to provide comprehensive biomarker analysis for NABIR collaborators to enhance the understanding of microbial geo-bioprocesses involved in the effective immobilization of metals (We have worked with and published or currently are publishing with 10 groups of NAIBR investigators). The laboratory portion of our research centered on methods development and has led to three major innovations that could result in a systematic way of evaluating sites for potential bioremediation. The first of these is the development of an in situ sampling device (Peacock et al., 2004, Anderson et al., 2003, Istok et al., 2004) for the collection and concentration of microbial biomass. The second is the development of expanded lipid analysis based on the significantly greater sensitivity and selectivity of the LC/MS/MS that allows the analysis of respiratory quinones, diglycerides, sterols, intact phospholipids, poly-hydroxyalkonates, and potentially archaeol, and caldarchaeols from archea. These new analyses are accomplished more rapidly and with increased sensitivities and resolution than in the past (Lytle et al., 2000a, 2000b, 2001a, Geyer et al., 2004). The third advance is the coupling of lipid analysis with 13C enrichment experiments (Lytle et al., 2001b, Geyer et al. 2005). With this technique it is now possible to follow the active portion of

  15. Linking DNRA community structure and activity in a shallow lagoonal estuarine system

    PubMed Central

    Song, Bongkeun; Lisa, Jessica A.; Tobias, Craig R.

    2014-01-01

    Dissimilatory nitrate reduction to ammonium (DNRA) and denitrification are two nitrate respiration pathways in the microbial nitrogen cycle. Diversity and abundance of denitrifying bacteria have been extensively examined in various ecosystems. However, studies on DNRA bacterial diversity are limited, and the linkage between the structure and activity of DNRA communities has yet to be discovered. We examined the composition, diversity, abundance, and activities of DNRA communities at five sites along a salinity gradient in the New River Estuary, North Carolina, USA, a shallow temporal/lagoonal estuarine system. Sediment slurry incubation experiments with 15N-nitrate were conducted to measure potential DNRA rates, while the abundance of DNRA communities was calculated using quantitative PCR of nrfA genes encoding cytochrome C nitrite reductase, commonly found in DNRA bacteria. A pyrosequencing method targeting nrfA genes was developed using an Ion Torrent sequencer to examine the diversity and composition of DNRA communities within the estuarine sediment community. We found higher levels of nrfA gene abundance and DNRA activities in sediments with higher percent organic content. Pyrosequencing analysis of nrfA genes revealed spatial variation of DNRA communities along the salinity gradient of the New River Estuary. Percent abundance of dominant populations was found to have significant influence on overall activities of DNRA communities. Abundance of dominant DNRA bacteria and organic carbon availability are important regulators of DNRA activities in the eutrophic New River Estuary. PMID:25232351

  16. Advanced primary care in San Antonio: linking practice and community strategies to improve health.

    PubMed

    Ferrer, Robert L; Gonzalez Schlenker, Carolina; Lozano Romero, Raquel; Poursani, Ramin; Bazaldua, Oralia; Davidson, DeWayne; Ann Gonzales, Melissa; Dehoyos, Janie; Castilla, Martha; Corona, Betty A; Tysinger, James; Alsip, Bryan; Trejo, Jonathan; Jaén, Carlos Roberto

    2013-01-01

    Improving health among people living in poverty often transcends narrowly focused illness care. Meaningful success is unlikely without confronting the complex social origins of illness. We describe an emerging community of solution to improve health outcomes for a population of 6000 San Antonio, Texas, residents enrolled in a county health care program. The community of solution comprises a county health system, a family medicine residency program, a metropolitan public health department, and local nonprofit organizations and businesses. Community-based activities responding to the needs of individuals and their neighborhoods are driven by a cohort of promotores (community health workers) whose mission encompasses change at both the individual and community levels. Centered on patients' functional goals, promotores mobilize family and community resources and consider what community-level action will address the social determinants of health. On the clinical side, care teams implement population-based risk assessment and nurse care management with a focus on care transitions as well as other measures to meet the needs of patients with high morbidity and high use of health care. Population-based outcome metrics include reductions in hospitalizations, emergency department and urgent care visits, and the associated charges. Promotores also assess patients' progress along the trajectory of their selected functional goals.

  17. Fine-scale community and genetic structure are tightly linked in species-rich grasslands

    PubMed Central

    Whitlock, Raj; Bilton, Mark C.; Grime, J. Phil; Burke, Terry

    2011-01-01

    Recent evidence indicates that grassland community structure and species diversity are influenced by genetic variation within species. We review what is known regarding the impact of intraspecific diversity on grassland community structure, using an ancient limestone pasture as a focal example. Two genotype-dependent effects appear to modify community structure in this system. First, the abundance of individual constituent species can depend upon the combined influence of direct genetic effects stemming from individuals within the population. Second, the outcome of localized interspecific interactions occurring within the community can depend on the genotypes of participating individuals (indicating indirect genetic effects). Only genotypic interactions are thought to be capable of allowing the long-term coexistence of both genotypes and species. We discuss the implications of these effects for the maintenance of diversity in grasslands. Next, we present new observations indicating that losses of genotypic diversity from each of two species can be predicted by the abundance of other coexisting species within experimental grassland communities. These results suggest genotype-specific responses to abundance in other coexisting species. We conclude that both direct and indirect genetic effects are likely to shape community structure and species coexistence in grasslands, implying tight linkage between fine-scale genetic and community structure. PMID:21444309

  18. Linking above and belowground responses to global change at community and ecosystem scales.

    SciTech Connect

    Antoninka, Anita; Wolf, Julie; Bowker, Matt; Classen, Aimee T; JohnsonPhD, Dr Nancy C

    2009-01-01

    Cryptic belowground organisms are difficult to observe and their responses to global changes are not well understood. Nevertheless, there is reason to believe that interactions among above- and belowground communities may mediate ecosystem responses to global change. We used grassland mesocosms to manipulate the abundance of one important group of soil organisms, arbuscular mycorrhizal (AM) fungi, and to study community and ecosystem responses to CO2 and N enrichment. After two growing seasons, biomass responses of plant communities were recorded, and soil community responses were measured using microscopy, phospholipid fatty acids (PLFA) and community-level physiological profiles (CLPP). Ecosystem responses were examined by measuring net primary production (NPP), evapotranspiration, total soil organic matter (SOM), and extractable mineral N. Structural equation modeling was used to examine the causal relationships among treatments and response variables. We found that while CO2 and N tended to directly impact ecosystem functions (evapotranspiration and NPP, respectively), AM fungi indirectly impacted ecosystem functions by strongly influencing the composition of plant and soil communities. For example, the presence of AM fungi had a strong influence on other root and soil fungi and soil bacteria. We found that the mycotrophic status of the dominant plant species in the mesocosms determined whether the presence of AM fungi increased or decreased NPP. Mycotrophic grasses dominated the mesocosm communities during the first growing season, and thus, the mycorrhizal treatments had the highest NPP. In contrast, non-mycotrophic forbs were dominant during the second growing season and thus, the mycorrhizal treatments had the lowest NPP. The composition of the plant community strongly influenced soil N; and the composition of the soil organisms strongly influenced SOM accumulation in the mesocosms. These results show how linkages between above- and belowground communities

  19. Microbial-algal community changes during the latest Permian ecological crisis: Evidence from lipid biomarkers at Cili, South China

    NASA Astrophysics Data System (ADS)

    Luo, Genming; Wang, Yongbiao; Grice, Kliti; Kershaw, Steve; Algeo, Thomas J.; Ruan, Xiaoyan; Yang, Hao; Jia, Chengling; Xie, Shucheng

    2013-06-01

    Microbialites flourished globally immediately following the latest Permian mass extinction. In this study, lipid biomarker records were analyzed in the Cili section (Hunan Province, South China) in order to determine the types of microbes involved in microbialite formation and their response to contemporaneous environmental changes. Various biomarkers were identified in the aliphatic and aromatic fractions using gas chromatography (GC) and GC-mass spectrometry (GC-MS). Low abundance of steranes in the microbialite layer suggests that it did not contain large amounts of algae, in striking contrast to the abundant algal fossils and algal-derived steranes present in the underlying (pre-crisis) skeletal limestone. Although pristine/phytane (Pr/Ph) ratios increased in the microbialite layer, covariation of Pr/Ph with the ratio of low- to high-molecular-weight n-alkanes (C20 -/C20 +) suggests that the former proxy was controlled by microbial (particularly cyanobacterial) inputs rather than by redox conditions. The microbialite also yielded low ratios of hopanes to short-chain n-alkanes (HP/Lalk) and high abundances of C21n-alkylcyclohexane, indicating that, in addition to cyanobacteria, anaerobic bacteria, archaea, and possibly acritarchs flourished in the aftermath of the marine extinction event. The upper part of the thinly bedded micritic limestone overlying the microbialite exhibits a bimodal distribution of n-alkanes as well as increased abundances of extended tricyclic terpanes and steranes, suggesting a return of habitable shallow-marine conditions for eukaryotic algae several hundred thousand years after the latest Permian mass extinction. Increases in the dibenzofuran ratio (i.e., DBF/(DBF + DBT + F)) and in the coronene to phenanthrene ratio (Cor/P) in the skeletal limestone immediately below the microbialite are evidence of enhanced soil erosion rates and wildfire intensity, marking the collapse of terrestrial ecosystems. The terrestrial crisis thus slightly

  20. Linking personal and public health information: a vision for community-centered health information systems.

    PubMed

    Kwiatkowski, K; Brennan, P F

    2001-01-01

    As health care in the U.S. and worldwide has shifted from a centralized, institution-based model to a distributed process occurring largely in the communities, Integrated Advanced Information Management Systems (IAIMS) initiatives must also move toward addressing the challenges of integrating health information at the community level. The Wisconsin IAIMS initiative strives to create such a solution, anchoring its efforts in a regional health information technology architecture by partnering with Wisconsin-area communities as the foundation that will ensure the establishment of the appropriate collaborations to gain adequate investment and generate sustainable solutions for health information integration.

  1. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest

    PubMed Central

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient—namely, Santa Virginia, Picinguaba and Restinga—we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms—ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning. PMID:26752633

  2. Linking the Composition of Bacterial and Archaeal Communities to Characteristics of Soil and Flora Composition in the Atlantic Rainforest.

    PubMed

    Lima-Perim, Julia Elidia; Romagnoli, Emiliana Manesco; Dini-Andreote, Francisco; Durrer, Ademir; Dias, Armando Cavalcante Franco; Andreote, Fernando Dini

    2016-01-01

    The description of microbiomes as intrinsic fractions of any given ecosystem is an important issue, for instance, by linking their compositions and functions with other biotic and abiotic components of natural systems and hosts. Here we describe the archaeal and bacterial communities from soils of the Atlantic Rainforest in Brazil. Based on the comparison of three areas located along an altitudinal gradient-namely, Santa Virginia, Picinguaba and Restinga-we detected the most abundant groups of Bacteria (Acidobacteria and Proteobacteria) and Archaea (Thaumarchaeota, Crenarchaeota and Euryarchaeota). The particular composition of such communities in each of these areas was first evidenced by PCR-DGGE patterns [determined for Bacteria, Archaea and ammonia-oxidizing organisms-ammonia-oxidizing archaea (AOA) and bacteria (AOB)]. Moreover, sequence-based analysis provided a better resolution of communities, which indicated distinct frequencies of archaeal phyla and bacterial OTUs across areas. We found, as indicated by the Mantel test and multivariate analyses, a potential effect of the flora composition that outpaces the effect of soil characteristics (either physical and chemical) influencing the assembly of these microbial communities in soils. Our results indicate a collective role of the ecosystem underlying observed differences in microbial communities in these soils. Particularly, we posit that rainforest preservation also needs to take into account the maintenance of the soil biodiversity, as this is prompted to influence major processes that affect ecosystem functioning.

  3. Linking with Community To Reclaim Natural Areas for Education: The McLane Elementary School Project.

    ERIC Educational Resources Information Center

    Spencer, Melinda; Smith, Kathy Kurtz

    2002-01-01

    Describes a project in which students, teachers, and the community work to reclaim neglected wetlands and forested areas for use as an environmental study site for interdisciplinary learning. (Author/MM)

  4. Creating community action plans for obesity prevention using the ANGELO (Analysis Grid for Elements Linked to Obesity) Framework.

    PubMed

    Simmons, A; Mavoa, H M; Bell, A C; De Courten, M; Schaaf, D; Schultz, J; Swinburn, B A

    2009-12-01

    Community-based interventions are an important component of obesity prevention efforts. The literature provides little guidance on priority-setting for obesity prevention in communities, especially for socially and culturally diverse populations. This paper reports on the process of developing prioritized, community-participatory action plans for obesity prevention projects in children and adolescents using the ANGELO (Analysis Grid for Elements Linked to Obesity) Framework. We combined stakeholder engagement processes, the ANGELO Framework (scans for environmental barriers, targeted behaviours, gaps in skills and knowledge) and workshops with key stakeholders to create action plans for six diverse obesity prevention projects in Australia (n = 3), New Zealand, Fiji and Tonga from 2002 to 2005. Some sites included sociocultural contextual analyses in the environmental scans. Target groups were under-5-year-olds (Australia), 4-12-year-olds (Australia) and 13-18-year-olds (all four countries). Over 120 potential behavioural, knowledge, skill and environmental elements were identified for prioritization leading into each 2-day workshop. Many elements were common across the diverse cultural communities; however, several unique sociocultural elements emerged in some cultural groups which informed their action plans. Youth were actively engaged in adolescent projects, allowing their needs to be incorporated into the action plans initiating the process of ownership. A common structure for the action plan promoted efficiencies in the process while allowing for community creativity and innovation. The ANGELO is a flexible and efficient way of achieving an agreed plan for obesity prevention with diverse communities. It is responsive to community needs, combines local and international knowledge and creates stakeholder ownership of the action plan.

  5. Modeling the Biodegradation of Bacterial Community Assembly Linked Antibiotics in River Sediment Using a Deterministic-Stochastic Combined Model.

    PubMed

    Zhang, Wenlong; Li, Yi; Wang, Chao; Wang, Peifang; Hou, Jun; Yu, Zhongbo; Niu, Lihua; Wang, Linqiong; Wang, Jing

    2016-08-16

    To understand the interaction between bacterial community assembly and the assembly linked antibiotics biodegradation, a unique model framework containing a Monod kinetic, a logistic kinetic, and a stochastic item was established to describe the biodegradation of bacterial community assembly linked sulfamethoxazole (SMX) in river sediment. According to the modeling results, both deterministic and stochastic processes driving bacterial population variations played important roles in controlling SMX biodegradation, and the relative importance depended on the in situ concentration of SMX. A threshold concentration of SMX, which was biodegraded in the experimental river sediment depending on different processes, was obtained (i.e., 20 μg/kg). The higher introduced concentration of SMX (>20 μg/kg) was found to promote the acclimation of antibiotic degradation bacteria in microbial community through niche differentiation, which resulted in the specific microbial metabolization of SMX. In contrast, the lower introduced concentration of SMX (<20 μg/kg) was not able to lead to a significant increase of deterministic processes and resulted in the biodegradation of SMX through co-metabolism by the coexisting microorganisms. The developed model can be considered a useful tool for improving the technologies of water environmental protection and remediation. PMID:27428250

  6. Integrating the Environment, the Economy, and Community Health: A Community Health Center’s Initiative to Link Health Benefits to Smart Growth

    PubMed Central

    McAvoy, Peter V.; Driscoll, Mary Beth; Gramling, Benjamin J.

    2004-01-01

    The Sixteenth Street Community Health Center (SSCHC) in Milwaukee, Wis, is making a difference in the livability of surrounding neighborhoods and the overall health of the families it serves. SSCHC is going beyond traditional health care provider models and working to link the environment, the economy, and community health through urban brownfield redevelopment and sustainable land-use planning. In 1997, SSCHC recognized that restoration of local air and water quality and other environmental conditions, coupled with restoring family-supporting jobs in the neighborhood, could have a substantial impact on the overall health of families. Recent events indicate that SSCHC’s pursuit of smart growth strategies has begun to pay off. PMID:15053995

  7. Linking fungal communities to wood density loss after 12 years of log decay.

    PubMed

    Kubartová, Ariana; Ottosson, Elisabet; Stenlid, Jan

    2015-05-01

    Changes in biodiversity might alter decomposition processes and, consequently, carbon and nutrient cycling. We examined fungal diversity and density loss in experimental Norway spruce logs after 12 years of decay in a hemiboreal forest. Between 28 and 50% of the original wood biomass remained, depending on the fungal community composition in the log, operational taxonomic unit (OTU) richness had only a minor effect on the log biomass. Although the communities were OTU rich (190-340 OTUs per log), the majority of OTUs were infrequent or rare; wood degradation therefore depended mostly on the most abundant OTUs and their decomposing abilities. The least decayed logs were characterized by continuous dominance of an earlier colonizer and by high within-log community diversity, which was significantly related to sample variables (position in log, density and moisture). In the most decayed logs, the earlier colonizers were generally replaced by white-rot species able to exploit the highly decomposed wood. The communities were relatively spatially uniform within whole logs, independent of the sample variables, whereas among-log diversity was high. Importance of fungal community composition in decomposition processes should be taken into account when studying and modeling carbon dynamics in forest ecosystems.

  8. Linking community and disease ecology: the impact of biodiversity on pathogen transmission.

    PubMed

    Roche, Benjamin; Dobson, Andrew P; Guégan, Jean-François; Rohani, Pejman

    2012-10-19

    The increasing number of zoonotic diseases spilling over from a range of wild animal species represents a particular concern for public health, especially in light of the current dramatic trend of biodiversity loss. To understand the ecology of these multi-host pathogens and their response to environmental degradation and species extinctions, it is necessary to develop a theoretical framework that takes into account realistic community assemblages. Here, we present a multi-host species epidemiological model that includes empirically determined patterns of diversity and composition derived from community ecology studies. We use this framework to study the interaction between wildlife diversity and directly transmitted pathogen dynamics. First, we demonstrate that variability in community composition does not affect significantly the intensity of pathogen transmission. We also show that the consequences of community diversity can differentially impact the prevalence of pathogens and the number of infectious individuals. Finally, we show that ecological interactions among host species have a weaker influence on pathogen circulation than inter-species transmission rates. We conclude that integration of a community perspective to study wildlife pathogens is crucial, especially in the context of understanding and predicting infectious disease emergence events.

  9. Linking fungal communities to wood density loss after 12 years of log decay.

    PubMed

    Kubartová, Ariana; Ottosson, Elisabet; Stenlid, Jan

    2015-05-01

    Changes in biodiversity might alter decomposition processes and, consequently, carbon and nutrient cycling. We examined fungal diversity and density loss in experimental Norway spruce logs after 12 years of decay in a hemiboreal forest. Between 28 and 50% of the original wood biomass remained, depending on the fungal community composition in the log, operational taxonomic unit (OTU) richness had only a minor effect on the log biomass. Although the communities were OTU rich (190-340 OTUs per log), the majority of OTUs were infrequent or rare; wood degradation therefore depended mostly on the most abundant OTUs and their decomposing abilities. The least decayed logs were characterized by continuous dominance of an earlier colonizer and by high within-log community diversity, which was significantly related to sample variables (position in log, density and moisture). In the most decayed logs, the earlier colonizers were generally replaced by white-rot species able to exploit the highly decomposed wood. The communities were relatively spatially uniform within whole logs, independent of the sample variables, whereas among-log diversity was high. Importance of fungal community composition in decomposition processes should be taken into account when studying and modeling carbon dynamics in forest ecosystems. PMID:25873458

  10. Linking frontline work and state-of-the-art knowledge: a community exchange system.

    PubMed

    Indyk, D; Belville, R

    1995-01-01

    When challenged by complex medical and social conditions, local providers must participate in information exchanges, resource sharing, continuing education, and service coordination. A community exchange system, flexible enough to share and adapt new knowledge, and able to provide continuing multidisciplinary training and education across different practice settings, was established for the prevention and treatment of HIV/AIDS in East Harlem, New York City. The HIV/AIDS community exchange system supports linkages among disciplines within a medical center, communication among the local community-based organizations, and networks between the two settings. The system, as a model, is applicable to complex socio-medical problems such as diabetes, substance abuse, violence, tuberculosis, or geriatrics.

  11. Linking seasonal inorganic nitrogen shift to the dynamics of microbial communities in the Chesapeake Bay.

    PubMed

    Hong, Yiguo; Xu, Xiongrong; Kan, Jinjun; Chen, Feng

    2014-04-01

    Seasonal shifts of dissolved inorganic nitrogen (DIN) and the dynamics of microbial communities for nitrogen transformation were investigated in the water column of Chesapeake Bay. The relative abundance of nitrogen over phosphorus (N) showed a strong seasonal and spatial pattern: gradually decreased from upstream to downstream; high in winter and low in summer. Because the phosphorus concentration remained relatively stable, the spatiotemporal pattern of N implied that a substantial fraction of DIN was removed in the bay, especially in summer. Correlation analyses indicated the functional microbial communities and environmental variables, such as temperature, dissolved oxygen, salinity, played important roles for connecting the seasonal variation of N. Among them, temperature was the trigger factor. High temperature in the summer induced the growth of functional microbes, which subsequently consumed a large portion of DIN inputted from the tributaries and reduced the N. The current study provided the relative importance of microbial communities and environmental variables in driving the DIN loss in the bay.

  12. Biomarkers for antipsychotic therapies.

    PubMed

    Pich, Emilio Merlo; Vargas, Gabriel; Domenici, Enrico

    2012-01-01

    Molecular biomarkers for antipsychotic treatments have been conceptually linked to the measurements of dopamine functions, mostly D(2) receptor occupancy, either by imaging using selective PET/SPECT radioactive tracers or by assessing plasma prolactin levels. A quest for novel biomarkers was recently proposed by various academic, health service, and industrial institutions driven by the need for better treatments of psychoses. In this review we conceptualize biomarkers within the Translational Medicine paradigm whose goal was to provide support to critical decision-making in drug discovery. At first we focused on biomarkers as outcome measure of clinical studies by searching into the database clinicaltrial.gov. The results were somewhat disappointing, showing that out of 1,659 antipsychotic trials only 18 used a biomarker as an outcome measure. Several of these trials targeted plasma lipids as sentinel marker for metabolic adverse effects associated with the use of atypical antipsychotics, while only few studies were aimed to new disease specific biological markers. As an example of a mechanistic biomarker, we described the work done to progress the novel class of glycine transporter inhibitors as putative treatment for negative symptoms of schizophrenia. We also review how large-scale multiplex biological assays were applied to samples from tissues of psychiatric patients, so to learn from changes of numerous analytes (metabolic products, lipids, proteins, RNA transcripts) about the substrates involved in the disease. We concluded that a stringent implementation of these techniques could contribute to the endophenotypic characterization of patients, helping in the identification of key biomarkers to drive personalized medicine and new treatment development. PMID:23129338

  13. Project Link-Four: Pre-Vocational Education for Adults through Community Linkages.

    ERIC Educational Resources Information Center

    Stedman, Deborah S.

    The Texas adult performance level (APL) project LINK-FOUR implemented a curriculum based on functional competencies at four sites (Austin, Texarkana, Texas City, and Abilene) and formed linkages with local organizations involved in adult vocational education. The concept on which the project was based was that a set of prevocational skills, plus a…

  14. Applied Scholarship in the Community Service Link: From Classroom Texts to Classroom as Text.

    ERIC Educational Resources Information Center

    Fischer, Ruth Overman

    Students entering the university have to create a space for themselves, not only in the writing classroom, but in their relationships with faculty, other students, and their evolving selves. A curricular support mechanism helps students enlarge their educational process. Such a support system, the Linked Courses Program, has been in operation at…

  15. Service-Learning Linking Family Child Care Providers, Community Partners, and Preservice Professionals

    ERIC Educational Resources Information Center

    Garner, Pamela W.; Parker, Tameka S.

    2016-01-01

    This article describes the implementation of a service-learning project, which was infused into a child development course. The project linked family child care providers, their licensing agency, and 39 preservice teachers in a joint effort to develop a parent handbook to be used by the providers in their child care businesses and to support…

  16. Linking Faculty Development to Community College Student Achievement: A Mixed Methods Approach

    ERIC Educational Resources Information Center

    Elliott, Robert W.; Oliver, Diane E.

    2016-01-01

    Using a mixed methods, multilevel research design, this pilot inquiry explored the relationship between college faculty professional development and the academic achievement of diverse students by coupling two separate links: (a) the effects that professional development activities have on improving teaching strategies, and (b) the effects these…

  17. Linking Postdoctoral General Dentistry Programs with Community-Based Clinical Care Settings.

    ERIC Educational Resources Information Center

    Weaver, Richard G.; Gray, Carolyn F.; Demby, Neal A.; Cinotti, William R.; Clark, Nereyda P.; Hicks, Jeffrey L.

    1997-01-01

    Reports results of a working group convened by the American Association of Dental Schools to examine establishment of dental education programs with significant affiliations with community-based clinical care settings. Identifies factors and conditions believed to be critical to successful program linkages, including goals and objectives, support…

  18. Assessing the bias linked to DNA recovery from biofiltration woodchips for microbial community investigation by fingerprinting.

    PubMed

    Cabrol, Léa; Malhautier, Luc; Poly, Franck; Lepeuple, Anne-Sophie; Fanlo, Jean-Louis

    2010-01-01

    In this study, we explored methodological aspects of nucleic acid recovery from microbial communities involved in a gas biofilter filled with pine bark woodchips. DNA was recovered indirectly in two steps, comparing different methods: cell dispersion (crushing, shaking, and sonication) and DNA extraction (three commercial kits and a laboratory protocol). The objectives were (a) to optimize cell desorption from the packing material and (b) to compare the 12 combinations of desorption and extraction methods, according to three relevant criteria: DNA yield, DNA purity, and community structure representation by denaturing gradient gel electrophoresis (DGGE). Cell dispersion was not influenced by the operational parameters tested for shaking and blending, while it increased with time for sonication. DNA extraction by the laboratory protocol provided the highest DNA yields, whereas the best DNA purity was obtained by a commercial kit designed for DNA extraction from soil. After successful PCR amplification, the 12 methods did not generate the same bias in microbial community representation. Eight combinations led to high diversity estimation, independently of the experimental procedure. Among them, six provided highly similar DGGE profiles. Two protocols generated a significantly dissimilar community profile, with less diversity. This study highlighted the crucial importance of DNA recovery bias evaluation.

  19. Psychological Symptoms Linking Exposure to Community Violence and Academic Functioning in African American Adolescents

    ERIC Educational Resources Information Center

    Busby, Danielle R.; Lambert, Sharon F.; Ialongo, Nicholas S.

    2013-01-01

    African American adolescents are exposed disproportionately to community violence, increasing their risk for emotional and behavioral symptoms that can detract from learning and undermine academic outcomes. The present study examined whether aggressive behavior and depressive and anxious symptoms mediated the association between exposure to…

  20. Applying the Learning Community Model to Graduate Education: Linking Research and Teaching between Core Courses

    ERIC Educational Resources Information Center

    Romsdahl, Rebecca J.; Hill, Michael J.

    2012-01-01

    In graduate education, there is often a great divide between classroom learning and research endeavors. Using learning community (LC) values and strategies, our goal is to build stronger and more meaningful ties between these two aspects of graduate education so that students see them as complimentary learning rather than separate components. This…

  1. Roger Tory Peterson Institute Links Interdisciplinary Nature Studies to Increased Community Understanding. Rural Trust Featured Project.

    ERIC Educational Resources Information Center

    Null, Elizabeth Higgins

    The Roger Tory Peterson Institute (Jamestown, New York) has been sparking a regional revival in K-12 nature studies and attracting attention from educators across America. Through summer training sessions and workshops, the Institute introduces multidisciplinary teams of teachers and community members to empirical research techniques for observing…

  2. New Song Academy: Linking Education and Community Development To Build Stronger Families and Neighborhoods.

    ERIC Educational Resources Information Center

    Brown, Prudence; Fiester, Leila

    This report describes the New Song Academy, led by New Song Urban Ministries (NSUM), which serves preK-8 children in Baltimore, Maryland, and promotes quality education for urban students through partnerships with families and the community. It operates year-round in six 6-week sessions. Despite the often chaotic nature of children's lives outside…

  3. Natural Resource Service Learning to Link Students, Communities, and the Land

    ERIC Educational Resources Information Center

    Barlow, Rebecca J.

    2013-01-01

    University-based Extension specialists often face the dilemma of scheduling time for both teaching and outreach activities. Service learning projects that give hands-on experience in the application of classroom activities while giving back to the community can bridge this gap. A demonstration forest and service learning techniques were used to…

  4. The Link Between Hepatitis B and Liver Cancer: The Asian American Community

    Cancer.gov

    Dr. Moon Chen, Professor of the Department of Internal Medicine and Associate Director of Cancer Control at the University of California-Davis Comprehensive Cancer Center, speaks about Hepatitis B and Liver Cancer as a more prevalent problem in the Asian American community.

  5. Understanding Community College Students' Learning Styles and the Link to Academic Achievement

    ERIC Educational Resources Information Center

    Peters, Kathleen

    2012-01-01

    Learning styles have been an area of interest in educational psychology for many decades. However, community college students have been overlooked in learning styles research. To enhance teacher efficacy and student success, it is important to continue to evaluate the relationship between learning styles and academic achievement. The purpose of…

  6. MARINE-DERIVED DINOFLAGELLATES IN ANTARCTIC SALINE LAKES: COMMUNITY COMPOSITION AND ANNUAL DYNAMICS(1) *[link].

    PubMed

    Rengefors, Karin; Laybourn-Parry, Johanna; Logares, Ramiro; Marshall, William A; Hansen, Gert

    2008-06-01

    The saline lakes of the Vestfold Hills in Antarctica offer a remarkable natural laboratory where the adaptation of planktonic protists to a range of evolving physiochemical conditions can be investigated. This study illustrates how an ancestral marine community has undergone radical simplification leaving a small number of well-adapted species. Our objective was to investigate the species composition and annual dynamics of dinoflagellate communities in three saline Antarctic lakes. We observed that dinoflagellates occur year-round despite extremely low PAR during the southern winter, which suggests significant mixotrophic or heterotrophic activity. Only a small number of dominant dinoflagellate species were found in each lake, in contrast to the species-rich Southern Ocean from which the lake communities are believed to be derived. We verified that the lake species were representatives of the marine polar dinoflagellate community, and not freshwater species. Polarella glacialis Montresor, Procaccini et Stoecker, a bipolar marine species, was for the first time described in a lake habitat and was an important phototrophic component in the higher salinity lakes. In the brackish lakes, we found a new sibling species to the brackish-water species Scrippsiella hangoei (J. Schiller) J. Larsen, previously observed only in the Baltic Sea.

  7. Exploring Possible Links between Professional Learning Communities and Complex Adaptive Systems

    ERIC Educational Resources Information Center

    Johnson, Eric

    2013-01-01

    Implementation of Professional Learning Communities (PLC), as described by DuFour (2006), has depended upon a balance between teacher buy-in and administrative fiat. The tension between the "bottom-up" character of the former and the "top-down" character of the latter presents a leadership challenge: meeting students' learning…

  8. Linked hydrologic and social systems that support resilience of traditional irrigation communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Southwestern US irrigated landscapes are facing upheaval due to water scarcity and land use conversion associated with climate change, population growth, and changing economics. In the traditionally irrigated valleys of northern New Mexico, these stresses, as well as instances of community longevity...

  9. Linking Student Achievement to Professional Learning Communities in a Juvenile Court School Setting

    ERIC Educational Resources Information Center

    Wyatt, Scott

    2010-01-01

    Purpose: The purpose of the study was to provide verifiable data regarding the impact Professional Learning Communities (PLCs) have on student achievement in the Juvenile Court School (JCS) system. A second purpose was to measure staff perceptions regarding their support and beliefs about the use of PLCs in the JCS setting. Methodology: This…

  10. Experiential Learning in Higher Education: Linking Classroom and Community. ERIC Digest.

    ERIC Educational Resources Information Center

    Cantor, Jeffrey A.

    Based on a longer report with the same title, this digest summarizes research on the use of experiential learning in higher education, focusing on classroom-community linkages. While the literature suggests that experiential learning is a necessary and vital component of formal instruction in colleges and universities, controversy exists among…

  11. A 150-year record of ancient DNA, lipid biomarkers and hydrogen isotopes, tracing the microbial-planktonic community succession controlled by (hydro)climatic variability in a tropical lake

    NASA Astrophysics Data System (ADS)

    Smittenberg, Rienk; Yamoah, Kweku; Callac, Nolwenn; Fru, Ernest Chi; Chabangborn, Akkaneewut; Rattray, Jayne; Wohlfarth, Barbara

    2016-04-01

    We investigated the decadal variations in phytoplankton communities, and their response to environmental and climatic conditions, from a ˜150 year long sedimentary archive of Lake Nong Thale Prong (NTP), southern Thailand. We applied a combination of analyses: lipid biomarkers, compound-specific hydrogen isotopes, bulk carbon and nitrogen concentrations and isotopes, environmental SEM, and fossil DNA using qPCR targeted to specific taxa. Past hydrological conditions were reconstructed using the hydrogen isotopic composition of leaf wax n-alkanes. Temperatures were reconstructed using the tetraether-based MBT/CBT index, measured using a new and efficient reverse-phase HPLC-MS method. The climatological data compared well with meteorological data from the last decades. Reconstructed drier and warmer conditions from ˜1857-1916 Common Era (CE) coincided with oligotrophic lake water conditions and dominance of the green algae Botryococcus braunii - evidenced by a combination of both fossil DNA and the occurrence of characteristic botryococcene lipids. A change to higher silica (Si) input ˜1916 CE was related to increased rainfall and lower temperatures concurring with an abrupt takeover by diatom blooms lasting for 50 years - as evidenced by ancient DNA, characteristic highly branched isoprenoid lipids, and SEM. From the 1970s onwards, more eutrophic conditions prevailed, and these were likely caused by increased levels of anthropogenic phosphate (P), aided by stronger lake stratification caused by dryer and warmer conditions. The eutrophic conditions led to increased primary productivity in the lake, consisting again of a Botryococcus sp., although this time not producing botryococcene lipids. Moreover, Cyanobacteria became dominant - again evidenced by ancient DNA and the characteristic C19 alkane. Throughout the record, stratification and primary production could be linked to the intensity of methane cycling, by targeting and quantifying the mcrA gene that is used

  12. Shifts in deep-sea community structure linked to climate and food supply.

    PubMed

    Ruhl, Henry A; Smith, Kenneth L

    2004-07-23

    A major change in the community structure of the dominant epibenthic megafauna was observed at 4100 meters depth in the northeast Pacific and was synchronous to a major El Niño/La Niña event that occurred between 1997 and 1999. Photographic abundance estimates of epibenthic megafauna from 1989 to 2002 show that two taxa decreased in abundance after 1998 by 2 to 3 orders of magnitude, whereas several other species increased in abundance by 1 to 2 orders of magnitude. These faunal changes are correlated to climate fluctuations dominated by El Niño/La Niña. Megafauna even in remote marine areas appear to be affected by contemporary climatic fluctuations. Such faunal changes highlight the importance of an adequate temporal perspective in describing biodiversity, ecology, and anthropogenic impacts in deep-sea communities. PMID:15273392

  13. Student, Home, and School Socio-Demographic Factors: Links to School, Home, and Community Arts Participation

    ERIC Educational Resources Information Center

    Mansour, Marianne; Martin, Andrew J.; Anderson, Michael; Gibson, Robyn; Liem, Gregory Arief D.; Sudmalis, David

    2016-01-01

    This study explored the role of student (e.g., age, language background, gender), home (e.g., parent/caregiver education), and school (e.g., school type, size) socio-demographic factors in students' school (e.g., in-school arts tuition, arts engagement), home (e.g., parent/caregiver-child arts interaction), and community (e.g., arts attendance,…

  14. Linking Bacterial Endophytic Communities to Essential Oils: Clues from Lavandula angustifolia Mill.

    PubMed

    Emiliani, Giovanni; Mengoni, Alessio; Maida, Isabel; Perrin, Elena; Chiellini, Carolina; Fondi, Marco; Gallo, Eugenia; Gori, Luigi; Maggini, Valentina; Vannacci, Alfredo; Biffi, Sauro; Firenzuoli, Fabio; Fani, Renato

    2014-01-01

    Endophytic bacteria play a crucial role in plant life and are also drawing much attention for their capacity to produce bioactive compounds of relevant biotechnological interest. Here we present the characterisation of the cultivable endophytic bacteria of Lavandula angustifolia Mill.-a species used since antiquity for its therapeutic properties-since the production of bioactive metabolites from medical plants may reside also in the activity of bacterial endophytes through their direct production, PGPR activity on host, and/or elicitation of plant metabolism. Lavender tissues are inhabited by a tissue specific endophytic community dominated by Proteobacteria, highlighting also their difference from the rhizosphere environment where Actinobacteria and Firmicutes are also found. Leaves' endophytic community resulted as the most diverse from the other ecological niches. Overall, the findings reported here suggest: (i) the existence of different entry points for the endophytic community, (ii) its differentiation on the basis of the ecological niche variability, and (iii) a two-step colonization process for roots endophytes. Lastly, many isolates showed a strong inhibition potential against human pathogens and the molecular characterization demonstrated also the presence of not previously described isolates that may constitute a reservoir of bioactive compounds relevant in the field of pathogen control, phytoremediation, and human health. PMID:24971151

  15. Community-integrated omics links dominance of a microbial generalist to fine-tuned resource usage

    PubMed Central

    Muller, Emilie E. L.; Pinel, Nicolás; Laczny, Cédric C.; Hoopmann, Michael R.; Narayanasamy, Shaman; Lebrun, Laura A.; Roume, Hugo; Lin, Jake; May, Patrick; Hicks, Nathan D.; Heintz-Buschart, Anna; Wampach, Linda; Liu, Cindy M.; Price, Lance B.; Gillece, John D.; Guignard, Cédric; Schupp, James M.; Vlassis, Nikos; Baliga, Nitin S.; Moritz, Robert L.; Keim, Paul S.; Wilmes, Paul

    2014-01-01

    Microbial communities are complex and dynamic systems that are primarily structured according to their members’ ecological niches. To investigate how niche breadth (generalist versus specialist lifestyle strategies) relates to ecological success, we develop and apply an integrative workflow for the multi-omic analysis of oleaginous mixed microbial communities from a biological wastewater treatment plant. Time- and space-resolved coupled metabolomic and taxonomic analyses demonstrate that the community-wide lipid accumulation phenotype is associated with the dominance of the generalist bacterium Candidatus Microthrix spp. By integrating population-level genomic reconstructions (reflecting fundamental niches) with transcriptomic and proteomic data (realised niches), we identify finely tuned gene expression governing resource usage by Candidatus Microthrix parvicella over time. Moreover, our results indicate that the fluctuating environmental conditions constrain the accumulation of genetic variation in Candidatus Microthrix parvicella likely due to fitness trade-offs. Based on our observations, niche breadth has to be considered as an important factor for understanding the evolutionary processes governing (microbial) population sizes and structures in situ. PMID:25424998

  16. Analysis of links between groundwater recharge and discharge areas and wetland plant communities distribution in Middle Biebrza Basin, Poland

    NASA Astrophysics Data System (ADS)

    Grygoruk, Mateusz; Batelaan, Okke; Okruszko, Tomasz; Kotowski, Wiktor; Rycharski, Marek; Chormanski, Jaroslaw; Miroslaw-Swiatek, Dorota

    2010-05-01

    Natural evolution of wetlands is strongly dependent on groundwater dynamics, soil aeration and climate. These environmental factors determine the constant development of wetland plant communities and peat forming processes. Depending on spatial distribution of groundwater flow systems and recharge and discharge conditions, shallow groundwater can also be influenced by phreatophytic plants. Such feedback plays an important role in wetland development, especially when landuse or climate changes occur. Thus, understanding the links between dynamics of biotopic and biocenotic relations is crucial for wetland management aimed at the comprehensive set of conservation strategies. Main aim of this study was to review links between valuable wetland plant communities and the groundwater recharge/discharge conditions of particular habitats of Middle Biebrza Basin, Poland. The study area consists of various types of wetland landscapes, of which the dominant are fens. Organogenic top layer is intersected locally by sandy dunes and glaci-fluvial residual plateaus. The northern boundary of the study area is covered with an outwash plateau. A three-dimensional regional groundwater flow model was set up to quantify groundwater system and flow paths. Model calibration involved measured heads of the unconfined organogenic top layer and the underlaying, confined sandy aquifer. Measured thickness of unsaturated zone as well as physical parameters of organogenic layer were taken into account in interpretation of shallow groundwater dynamics. Recharge to groundwater was spatially distributed in accordance to analysis of measured precipitation-groundwater level relationships. Cell-by-cell flow analysis and groundwater exfiltration analysis were applied to map groundwater recharge and discharge areas within the modelled area. Results of groundwater modelling were validated with phytosociologic research combined with remote-sensing based spatial analysis of wetland habitats distribution

  17. [A comprehensive signature biomarker analysis of the in-situ viable biomass, community composition, and nutritional status attributes of deep subsurface microbiota]. Final report

    SciTech Connect

    1998-09-01

    The TAN sites contains subsurface sediment contaminated with trichloroethylene (TC). A suite of microbiological analyses, including ester-linked phospholipid fatty acid (PLFA) analysis, were performed to ascertain the microbial ecology associated with TCE degradation processes. The objective of the PLFA analyses were: (1) to determine the distribution of viable microbes throughout a vertical depth profile through the TCE plume, (2) determine the community composition of the viable extant microbiota and (3) relate the data derived from the PLFA analyses to other measures of the in situ microbiota as well as to the presence of TCE degradative products.

  18. A three-dimensional numerical model for linking community-wide vapour risks.

    PubMed

    Mustafa, Nizar; Mumford, Kevin G; Gerhard, Jason I; O'Carroll, Denis M

    2014-01-01

    A three-dimensional (3D) numerical model that couples contaminant transport in the saturated zone to vapour transport in the vadose zone and vapour intrusion into buildings was developed. Coupling these processes allows the simulation of vapour intrusion, arising from volatilization at the water table, associated with temporally and spatially variable groundwater plumes. In particular, the model was designed to permit, for the first time, 3D simulations of risk at receptors located in the wider community (i.e., kilometre scale) surrounding a contaminated site. The model can account for heterogeneous distributions of permeability, fraction organic carbon, sorption and biodegradation in the vadose and saturated zones. The model formulation, based upon integration of a number of widely accepted models, is presented along with verification and benchmarking tests. In addition, a number of exploratory simulations of benzene and naphthalene transport in a 1000 m long domain (aquifer cross-section: 500 m×14 m) are presented, which employed conservative assumptions consistent with the development of regulatory guidance. Under these conservative conditions, these simulations demonstrated, for example, that whether houses in the community were predicted to be impacted by groundwater and indoor air concentrations exceeding regulatory standards strongly depended on their distance downgradient from the source and lateral distance from the plume centreline. In addition, this study reveals that the degree of reduction in source concentration (i.e., remediation) required to achieve compliance with standards is less if the risk receptor is in the wider community than at the site boundary. However, these example scenarios suggest that, even considering community receptors, sources with initially high concentrations still required substantial remediation (i.e., >99% reductions in source concentration). Overall, this work provides insights and a new tool for considering the

  19. Links between community violence and the family system: evidence from children's feelings of relatedness and perceptions of parent behavior.

    PubMed

    Lynch, Michael; Cicchetti, Dante

    2002-01-01

    In this study, we examined some of the ways in which broader ecological systems may influence the organization of behavior within the family system. Specifically, links between exposure to community violence and children's relationships with maternal caregivers were investigated in a sample of 127 urban children between the ages of 7 and 13 years. Children were asked to indicate whether they had been exposed to a wide variety of violent events. In addition, their feelings of relatedness and separation anxiety, and their perceptions of maternal behavior were assessed. It was expected that exposure to community violence would be associated with feeling less secure with caregivers. Consistent with predictions from ecological-transactional theory, data supported this hypothesis. Children who reported that they had been exposed to high levels of community violence also indicated that they felt less positive affect when with their caregiver, were dissatisfied with how close they felt to her, felt more separation anxiety, and reported more negative maternal behavior than children exposed to less violence. Findings are discussed in terms of how violence may affect the family system and the protective function of human attachment.

  20. Unusually high food availability in Kaikoura Canyon linked to distinct deep-sea nematode community

    NASA Astrophysics Data System (ADS)

    Leduc, D.; Rowden, A. A.; Nodder, S. D.; Berkenbusch, K.; Probert, P. K.; Hadfield, M. G.

    2014-06-01

    Kaikoura Canyon, on the eastern New Zealand continental margin, is the most productive, non-chemosynthetic deep-sea habitat described to date, with megafaunal biomass 100-fold higher than those of other deep-sea habitats. The present study, which focused on free-living nematodes, provides the first comparison of faunal community structure and diversity between Kaikoura Canyon and nearby open slope habitats. Results show substantially higher food availability in the canyon relative to open slope sediments, which probably reflects greater levels of primary productivity above the canyon, coupled with downwelling and/or topographically-induced channelling, which serves to concentrate surface-derived organic matter along the canyon axis. This high food availability appears to be responsible for the elevated nematode biomass in Kaikoura Canyon, with values exceeding all published nematode biomass data from canyons elsewhere. There was also markedly lower local species diversity of nematodes inside the canyon relative to the open slope habitat, as well as a distinct community structure. The canyon community was dominated by species, such as Sabateria pulchra, which were absent from the open slope and are typically associated with highly eutrophic and/or disturbed environments. The presence of these taxa, as well as the low observed diversity, is likely to reflect the high food availability, and potentially the high levels of physically and biologically induced disturbance within the canyon. Kaikoura Canyon is a relatively small habitat characterised by different environmental conditions that makes a disproportionate contribution to deep-sea diversity in the region, despite its low species richness.

  1. Linking Sediment Microbial Communities to Carbon Cycling in High-Latitude Lakes

    NASA Astrophysics Data System (ADS)

    Emerson, J. B.; Varner, R. K.; Johnson, J. E.; Owusu-Dommey, A.; Binder, M.; Woodcroft, B. J.; Wik, M.; Freitas, N. L.; Boyd, J. A.; Crill, P. M.; Saleska, S. R.; Tyson, G. W.; Rich, V. I.

    2015-12-01

    It is well recognized that thawing permafrost peatlands are likely to provide a positive feedback to climate change via CH4 and CO2 emissions. High-latitude lakes in these landscapes have also been identified as sources of CH4 and CO2 loss to the atmosphere. To investigate microbial contributions to carbon loss from high-latitude lakes, we characterized sediment geochemistry and microbiota via cores collected from deep and shallow regions of two lakes (Inre Harrsjön and Mellersta Harrsjön) in Arctic Sweden in July, 2012. These lakes are within the Stordalen Mire long-term ecological area, a focal site for investigating the impacts of climate change-related permafrost thaw, and the lakes in this area are responsible for ~55% of the CH4 loss from this hydrologically interconnected system. Across 40 samples from 4 to 40 cm deep within four sediment cores, Illumina 16S rRNA gene sequencing revealed that the sedimentary microbiota was dominated by candidate phyla OP9 and OP8 (Atribacteria and Aminicenantes, respectively, including putative fermenters and anaerobic respirers), predicted methanotrophic Gammaproteobacteria, and predicted methanogenic archaea from the Thermoplasmata Group E2 clade. We observed some overlap in community structure with nearby peatlands, which tend to be dominated by methanogens and Acidobacteria. Sediment microbial communities differed significantly between lakes, by overlying lake depth (shallow vs. deep), and by depth within a core, with each trend corresponding to parallel differences in biogeochemical measurements. Overall, our results support the potential for significant microbial controls on carbon cycling in high-latitude lakes associated with thawing permafrost, and ongoing metagenomic analyses of focal samples will yield further insight into the functional potential of these microbial communities and their dominant members.

  2. Linking Attitudes, Policy, and Forest Cover Change in Buffer Zone Communities of Chitwan National Park, Nepal.

    PubMed

    Stapp, Jared R; Lilieholm, Robert J; Leahy, Jessica; Upadhaya, Suraj

    2016-06-01

    Deforestation in Nepal threatens the functioning of complex social-ecological systems, including rural populations that depend on forests for subsistence, as well as Nepal's biodiversity and other ecosystem services. Nepal's forests are particularly important to the nation's poorest inhabitants, as many depend upon them for daily survival. Two-thirds of Nepal's population relies on forests for sustenance, and these pressures are likely to increase in the future. This, coupled with high population densities and growth rates, highlights the importance of studying the relationship between human communities, forest cover trends through time, and forest management institutions. Here, we used surveys to explore how household attitudes associated with conservation-related behaviors in two rural communities-one that has experienced significant forest loss, and the other forest gain-compare with forest cover trends as indicated by satellite-derived forest-loss and -regeneration estimates between 2005 and 2013. Results found a significant difference in attitudes in the two areas, perhaps contributing to and reacting from current forest conditions. In both study sites, participation in community forestry strengthened support for conservation, forest conservation-related attitudes aligned with forest cover trends, and a negative relationship was found between economic status and having supportive forest conservation-related attitudes. In addition, on average, respondents were not satisfied with their district forest officers and did not feel that the current political climate in Nepal supported sustainable forestry. These findings are important as Nepal's Master Plan for the Forestry Sector has expired and the country is in the process of structuring a new Forestry Sector Strategy. PMID:26920157

  3. Microbial Community Dynamics and Activity Link to Indigo Production from Indole in Bioaugmented Activated Sludge Systems

    PubMed Central

    Deng, Jie; Deng, Ye; Van Nostrand, Joy D.; Wu, Liyou; He, Zhili; Qin, Yujia; Zhou, Jiti; Zhou, Jizhong

    2015-01-01

    Biosynthesis of the popular dyestuff indigo from indole has been comprehensively studied using pure cultures, but less has been done to characterize the indigo production by microbial communities. In our previous studies, a wild strain Comamonas sp. MQ was isolated from activated sludge and the recombinant Escherichia coli nagAc carrying the naphthalene dioxygenase gene (nag) from strain MQ was constructed, both of which were capable of producing indigo from indole. Herein, three activated sludge systems, G1 (non-augmented control), G2 (augmented with Comamonas sp. MQ), and G3 (augmented with recombinant E. coli nagAc), were constructed to investigate indigo production. After 132-day operation, G3 produced the highest yields of indigo (99.5 ± 3.0 mg/l), followed by G2 (27.3 ± 1.3 mg/l) and G1 (19.2 ± 1.2 mg/l). The microbial community dynamics and activities associated with indigo production were analyzed by Illumina Miseq sequencing of 16S rRNA gene amplicons. The inoculated strain MQ survived for at least 30 days, whereas E. coli nagAc was undetectable shortly after inoculation. Quantitative real-time PCR analysis suggested the abundance of naphthalene dioxygenase gene (nagAc) from both inoculated strains was strongly correlated with indigo yields in early stages (0–30 days) (P < 0.001) but not in later stages (30–132 days) (P > 0.10) of operation. Based on detrended correspondence analysis (DCA) and dissimilarity test results, the communities underwent a noticeable shift during the operation. Among the four major genera (> 1% on average), the commonly reported indigo-producing populations Comamonas and Pseudomonas showed no positive relationship with indigo yields (P > 0.05) based on Pearson correlation test, while Alcaligenes and Aquamicrobium, rarely reported for indigo production, were positively correlated with indigo yields (P < 0.05). This study should provide new insights into our understanding of indigo bio-production by microbial communities

  4. Link between microbial composition and carbon substrate-uptake preferences in a PHA-storing community

    PubMed Central

    Albuquerque, Maria G E; Carvalho, Gilda; Kragelund, Caroline; Silva, Ana F; Barreto Crespo, Maria T; Reis, Maria A M; Nielsen, Per H

    2013-01-01

    The microbial community of a fermented molasses-fed sequencing batch reactor (SBR) operated under feast and famine conditions for production of polyhydroxyalkanoates (PHAs) was identified and quantified through a 16 S rRNA gene clone library and fluorescence in situ hybridization (FISH). The microbial enrichment was found to be composed of PHA-storing populations (84% of the microbial community), comprising members of the genera Azoarcus, Thauera and Paracoccus. The dominant PHA-storing populations ensured the high functional stability of the system (characterized by high PHA-storage efficiency, up to 60% PHA content). The fermented molasses contained primarily acetate, propionate, butyrate and valerate. The substrate preferences were determined by microautoradiography-FISH and differences in the substrate-uptake capabilities for the various probe-defined populations were found. The results showed that in the presence of multiple substrates, microbial populations specialized in different substrates were selected, thereby co-existing in the SBR by adapting to different niches. Azoarcus and Thauera, primarily consumed acetate and butyrate, respectively. Paracoccus consumed a broader range of substrates and had a higher cell-specific substrate uptake. The relative species composition and their substrate specialization were reflected in the substrate removal rates of different volatile fatty acids in the SBR reactor. PMID:22810062

  5. Links among nitrification, nitrifier communities, and edaphic properties in contrasting soils receiving dairy slurry.

    PubMed

    Fortuna, Ann-Marie; Honeycutt, C Wayne; Vandemark, George; Griffin, Timothy S; Larkin, Robert P; He, Zhongqi; Wienhold, Brian J; Sistani, Karamat R; Albrecht, Stephan L; Woodbury, Bryan L; Torbert, Henry A; Powell, J Mark; Hubbard, Robert K; Eigenberg, Roger A; Wright, Robert J; Alldredge, J Richard; Harsh, James B

    2012-01-01

    Soil biotic and abiotic factors strongly influence nitrogen (N) availability and increases in nitrification rates associated with the application of manure. In this study, we examine the effects of edaphic properties and a dairy (Bos taurus) slurry amendment on N availability, nitrification rates and nitrifier communities. Soils of variable texture and clay mineralogy were collected from six USDA-ARS research sites and incubated for 28 d with and without dairy slurry applied at a rate of ~300 kg N ha(-1). Periodically, subsamples were removed for analyses of 2 M KCl extractable N and nitrification potential, as well as gene copy numbers of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Spearman coefficients for nitrification potentials and AOB copy number were positively correlated with total soil C, total soil N, cation exchange capacity, and clay mineralogy in treatments with and without slurry application. Our data show that the quantity and type of clay minerals present in a soil affect nitrifier populations, nitrification rates, and the release of inorganic N. Nitrogen mineralization, nitrification potentials, and edaphic properties were positively correlated with AOB gene copy numbers. On average, AOA gene copy numbers were an order of magnitude lower than those of AOB across the six soils and did not increase with slurry application. Our research suggests that the two nitrifier communities overlap but have different optimum environmental conditions for growth and activity that are partly determined by the interaction of manure-derived ammonium with soil properties. PMID:22218194

  6. Links among nitrification, nitrifier communities, and edaphic properties in contrasting soils receiving dairy slurry.

    PubMed

    Fortuna, Ann-Marie; Honeycutt, C Wayne; Vandemark, George; Griffin, Timothy S; Larkin, Robert P; He, Zhongqi; Wienhold, Brian J; Sistani, Karamat R; Albrecht, Stephan L; Woodbury, Bryan L; Torbert, Henry A; Powell, J Mark; Hubbard, Robert K; Eigenberg, Roger A; Wright, Robert J; Alldredge, J Richard; Harsh, James B

    2012-01-01

    Soil biotic and abiotic factors strongly influence nitrogen (N) availability and increases in nitrification rates associated with the application of manure. In this study, we examine the effects of edaphic properties and a dairy (Bos taurus) slurry amendment on N availability, nitrification rates and nitrifier communities. Soils of variable texture and clay mineralogy were collected from six USDA-ARS research sites and incubated for 28 d with and without dairy slurry applied at a rate of ~300 kg N ha(-1). Periodically, subsamples were removed for analyses of 2 M KCl extractable N and nitrification potential, as well as gene copy numbers of ammonia-oxidizing bacteria (AOB) and archaea (AOA). Spearman coefficients for nitrification potentials and AOB copy number were positively correlated with total soil C, total soil N, cation exchange capacity, and clay mineralogy in treatments with and without slurry application. Our data show that the quantity and type of clay minerals present in a soil affect nitrifier populations, nitrification rates, and the release of inorganic N. Nitrogen mineralization, nitrification potentials, and edaphic properties were positively correlated with AOB gene copy numbers. On average, AOA gene copy numbers were an order of magnitude lower than those of AOB across the six soils and did not increase with slurry application. Our research suggests that the two nitrifier communities overlap but have different optimum environmental conditions for growth and activity that are partly determined by the interaction of manure-derived ammonium with soil properties.

  7. Link between microbial composition and carbon substrate-uptake preferences in a PHA-storing community.

    PubMed

    Albuquerque, Maria G E; Carvalho, Gilda; Kragelund, Caroline; Silva, Ana F; Barreto Crespo, Maria T; Reis, Maria A M; Nielsen, Per H

    2013-01-01

    The microbial community of a fermented molasses-fed sequencing batch reactor (SBR) operated under feast and famine conditions for production of polyhydroxyalkanoates (PHAs) was identified and quantified through a 16 S rRNA gene clone library and fluorescence in situ hybridization (FISH). The microbial enrichment was found to be composed of PHA-storing populations (84% of the microbial community), comprising members of the genera Azoarcus, Thauera and Paracoccus. The dominant PHA-storing populations ensured the high functional stability of the system (characterized by high PHA-storage efficiency, up to 60% PHA content). The fermented molasses contained primarily acetate, propionate, butyrate and valerate. The substrate preferences were determined by microautoradiography-FISH and differences in the substrate-uptake capabilities for the various probe-defined populations were found. The results showed that in the presence of multiple substrates, microbial populations specialized in different substrates were selected, thereby co-existing in the SBR by adapting to different niches. Azoarcus and Thauera, primarily consumed acetate and butyrate, respectively. Paracoccus consumed a broader range of substrates and had a higher cell-specific substrate uptake. The relative species composition and their substrate specialization were reflected in the substrate removal rates of different volatile fatty acids in the SBR reactor.

  8. Community-based carbon sequestration in East Africa: Linking science and sustainability

    NASA Astrophysics Data System (ADS)

    Hultman, N. E.

    2004-12-01

    International agreements on climate change have set the stage for an expanding market for greenhouse gas emissions reduction credits. Projects that can generate credits for trading are diverse, but one of the more controversial types involve biological carbon sequestration. For several reasons, most of the activity on these "sinks" projects has been in Latin America and Southeast Asia. Yet people in sub-saharan Africa could benefit from properly implemented projects. This poster will discuss estimates of the potential and risks of such projects in East Africa, and will describe in detail a case study located in central Tanzania and now part of the World Bank's BioCarbon Fund portfolio. Understanding climate variability and risk can effectively link international agreements on climate change, local realities of individual projects, and the characteristics of targeted ecosystems.

  9. Linking environmental forcing and trophic supply to benthic communities in the Vercelli Seamount area (Tyrrhenian Sea).

    PubMed

    Covazzi Harriague, Anabella; Bavestrello, Giorgio; Bo, Marzia; Borghini, Mireno; Castellano, Michela; Majorana, Margherita; Massa, Francesco; Montella, Alessandro; Povero, Paolo; Misic, Cristina

    2014-01-01

    Seamounts and their influence on the surrounding environment are currently being extensively debated but, surprisingly, scant information is available for the Mediterranean area. Furthermore, although the deep Tyrrhenian Sea is characterised by a complex bottom morphology and peculiar hydrodynamic features, which would suggest a variable influence on the benthic domain, few studies have been carried out there, especially for soft-bottom macrofaunal assemblages. In order to fill this gap, the structure of the meio-and macrofaunal assemblages of the Vercelli Seamount and the surrounding deep area (northern Tyrrhenian Sea - western Mediterranean) were studied in relation to environmental features. Sediment was collected with a box-corer from the seamount summit and flanks and at two far-field sites in spring 2009, in order to analyse the metazoan communities, the sediment texture and the sedimentary organic matter. At the summit station, the heterogeneity of the habitat, the shallowness of the site and the higher trophic supply (water column phytopigments and macroalgal detritus, for instance) supported a very rich macrofaunal community, with high abundance, biomass and diversity. In fact, its trophic features resembled those observed in coastal environments next to seagrass meadows. At the flank and far-field stations, sediment heterogeneity and depth especially influenced the meiofaunal distribution. From a trophic point of view, the low content of the valuable sedimentary proteins that was found confirmed the general oligotrophy of the Tyrrhenian Sea, and exerted a limiting influence on the abundance and biomass of the assemblages. In this scenario, the rather refractory sedimentary carbohydrates became a food source for metazoans, which increased their abundance and biomass at the stations where the hydrolytic-enzyme-mediated turnover of carbohydrates was faster, highlighting high lability. PMID:25343621

  10. Effects of wetland vs. landscape variables on parasite communities of Rana pipiens: links to anthropogenic factors

    USGS Publications Warehouse

    Schotthoefer, Anna M.; Rohr, Jason R.; Cole, Rebecca A.; Koehler, Anson V.; Johnson, Catherine M.; Johnson, Lucinda B.; Beasley, Val R.

    2011-01-01

    The emergence of several diseases affecting amphibian populations worldwide has prompted investigations into determinants of the occurrence and abundance of parasites in frogs. To understand the spatial scales and identify specific environmental factors that determine risks of parasitism in frogs, helminth communities in metamorphic frogs of the northern leopard frog (Rana pipiens) were examined in relation to wetland and landscape factors at local (1 km) and regional (10 km) spatial extents in an agricultural region of Minnesota (USA) using regression analyses, ordination, and variance partitioning techniques. Greater amounts of forested and woody wetland habitats, shorter distances between woody wetlands, and smaller-sized open water patches in surrounding landscapes were the most consistently positive correlates with the abundances, richness, and diversity of helminths found in the frogs. Wetland and local landscape variables were suggested as most important for larval trematode abundances, whereas local and regional landscape variables appeared most important for adult helminths. As previously reported, the sum concentration of atrazine and its metabolite desethylatrazine, was the strongest predictor of larval trematode communities. In this report, we highlight the additional influences of landscape factors. In particular, our data suggest that anthropogenic activities that have resulted in the loss of the availability and connectivity of suitable habitats in the surrounding landscapes of wetlands are associated with declines in helminth richness and abundance, but that alteration of wetland water quality through eutrophication or pesticide contamination may facilitate the transmission of certain parasite taxa when they are present at wetlands. Although additional research is needed to quantify the negative effects of parasitism on frog populations, efforts to reduce inputs of agrochemicals into wetlands to limit larval trematode infections may be warranted

  11. Linking environmental forcing and trophic supply to benthic communities in the Vercelli Seamount area (Tyrrhenian Sea).

    PubMed

    Covazzi Harriague, Anabella; Bavestrello, Giorgio; Bo, Marzia; Borghini, Mireno; Castellano, Michela; Majorana, Margherita; Massa, Francesco; Montella, Alessandro; Povero, Paolo; Misic, Cristina

    2014-01-01

    Seamounts and their influence on the surrounding environment are currently being extensively debated but, surprisingly, scant information is available for the Mediterranean area. Furthermore, although the deep Tyrrhenian Sea is characterised by a complex bottom morphology and peculiar hydrodynamic features, which would suggest a variable influence on the benthic domain, few studies have been carried out there, especially for soft-bottom macrofaunal assemblages. In order to fill this gap, the structure of the meio-and macrofaunal assemblages of the Vercelli Seamount and the surrounding deep area (northern Tyrrhenian Sea - western Mediterranean) were studied in relation to environmental features. Sediment was collected with a box-corer from the seamount summit and flanks and at two far-field sites in spring 2009, in order to analyse the metazoan communities, the sediment texture and the sedimentary organic matter. At the summit station, the heterogeneity of the habitat, the shallowness of the site and the higher trophic supply (water column phytopigments and macroalgal detritus, for instance) supported a very rich macrofaunal community, with high abundance, biomass and diversity. In fact, its trophic features resembled those observed in coastal environments next to seagrass meadows. At the flank and far-field stations, sediment heterogeneity and depth especially influenced the meiofaunal distribution. From a trophic point of view, the low content of the valuable sedimentary proteins that was found confirmed the general oligotrophy of the Tyrrhenian Sea, and exerted a limiting influence on the abundance and biomass of the assemblages. In this scenario, the rather refractory sedimentary carbohydrates became a food source for metazoans, which increased their abundance and biomass at the stations where the hydrolytic-enzyme-mediated turnover of carbohydrates was faster, highlighting high lability.

  12. Effects of wetland vs. landscape variables on parasite communities of Rana pipiens: links to anthropogenic factors.

    PubMed

    Schotthoefer, Anna M; Rohr, Jason R; Cole, Rebecca A; Koehler, Anson V; Johnson, Catherine M; Johnson, Lucinda B; Beasley, Val R

    2011-06-01

    The emergence of several diseases affecting amphibian populations worldwide has prompted investigations into determinants of the occurrence and abundance of parasites in frogs. To understand the spatial scales and identify specific environmental factors that determine risks of parasitism in frogs, helminth communities in metamorphic frogs of the northern leopard frog (Rana pipiens) were examined in relation to wetland and landscape factors at local (1 km) and regional (10 km) spatial extents in an agricultural region of Minnesota (USA) using regression analyses, ordination, and variance partitioning techniques. Greater amounts of forested and woody wetland habitats, shorter distances between woody wetlands, and smaller-sized open water patches in surrounding landscapes were the most consistently positive correlates with the abundances, richness, and diversity of helminths found in the frogs. Wetland and local landscape variables were suggested as most important for larval trematode abundances, whereas local and regional landscape variables appeared most important for adult helminths. As previously reported, the sum concentration of atrazine and its metabolite desethylatrazine, was the strongest predictor of larval trematode communities. In this report, we highlight the additional influences of landscape factors. In particular, our data suggest that anthropogenic activities that have resulted in the loss of the availability and connectivity of suitable habitats in the surrounding landscapes of wetlands are associated with declines in helminth richness and abundance, but that alteration of wetland water quality through eutrophication or pesticide contamination may facilitate the transmission of certain parasite taxa when they are present at wetlands. Although additional research is needed to quantify the negative effects of parasitism on frog populations, efforts to reduce inputs of agrochemicals into wetlands to limit larval trematode infections may be warranted

  13. Linking Environmental Forcing and Trophic Supply to Benthic Communities in the Vercelli Seamount Area (Tyrrhenian Sea)

    PubMed Central

    Covazzi Harriague, Anabella; Bavestrello, Giorgio; Bo, Marzia; Borghini, Mireno; Castellano, Michela; Majorana, Margherita; Massa, Francesco; Montella, Alessandro; Povero, Paolo; Misic, Cristina

    2014-01-01

    Seamounts and their influence on the surrounding environment are currently being extensively debated but, surprisingly, scant information is available for the Mediterranean area. Furthermore, although the deep Tyrrhenian Sea is characterised by a complex bottom morphology and peculiar hydrodynamic features, which would suggest a variable influence on the benthic domain, few studies have been carried out there, especially for soft-bottom macrofaunal assemblages. In order to fill this gap, the structure of the meio-and macrofaunal assemblages of the Vercelli Seamount and the surrounding deep area (northern Tyrrhenian Sea – western Mediterranean) were studied in relation to environmental features. Sediment was collected with a box-corer from the seamount summit and flanks and at two far-field sites in spring 2009, in order to analyse the metazoan communities, the sediment texture and the sedimentary organic matter. At the summit station, the heterogeneity of the habitat, the shallowness of the site and the higher trophic supply (water column phytopigments and macroalgal detritus, for instance) supported a very rich macrofaunal community, with high abundance, biomass and diversity. In fact, its trophic features resembled those observed in coastal environments next to seagrass meadows. At the flank and far-field stations, sediment heterogeneity and depth especially influenced the meiofaunal distribution. From a trophic point of view, the low content of the valuable sedimentary proteins that was found confirmed the general oligotrophy of the Tyrrhenian Sea, and exerted a limiting influence on the abundance and biomass of the assemblages. In this scenario, the rather refractory sedimentary carbohydrates became a food source for metazoans, which increased their abundance and biomass at the stations where the hydrolytic-enzyme-mediated turnover of carbohydrates was faster, highlighting high lability. PMID:25343621

  14. Linking Attitudes, Policy, and Forest Cover Change in Buffer Zone Communities of Chitwan National Park, Nepal

    NASA Astrophysics Data System (ADS)

    Stapp, Jared R.; Lilieholm, Robert J.; Leahy, Jessica; Upadhaya, Suraj

    2016-06-01

    Deforestation in Nepal threatens the functioning of complex social-ecological systems, including rural populations that depend on forests for subsistence, as well as Nepal's biodiversity and other ecosystem services. Nepal's forests are particularly important to the nation's poorest inhabitants, as many depend upon them for daily survival. Two-thirds of Nepal's population relies on forests for sustenance, and these pressures are likely to increase in the future. This, coupled with high population densities and growth rates, highlights the importance of studying the relationship between human communities, forest cover trends through time, and forest management institutions. Here, we used surveys to explore how household attitudes associated with conservation-related behaviors in two rural communities—one that has experienced significant forest loss, and the other forest gain—compare with forest cover trends as indicated by satellite-derived forest-loss and -regeneration estimates between 2005 and 2013. Results found a significant difference in attitudes in the two areas, perhaps contributing to and reacting from current forest conditions. In both study sites, participation in community forestry strengthened support for conservation, forest conservation-related attitudes aligned with forest cover trends, and a negative relationship was found between economic status and having supportive forest conservation-related attitudes. In addition, on average, respondents were not satisfied with their district forest officers and did not feel that the current political climate in Nepal supported sustainable forestry. These findings are important as Nepal's Master Plan for the Forestry Sector has expired and the country is in the process of structuring a new Forestry Sector Strategy.

  15. Demographic and Behavioral Factors Linked to Obesity Among Inner-City Latino New Yorkers in the Bronx Community.

    PubMed

    Kanna, Balavenkatesh; Boutin-Foster, Carla

    2016-10-01

    New York City (NYC) Latinos are disproportionately affected by obesity. However, little information is available on demographic and behavioral factors linked to body mass index (BMI) in this population. A community-based survey was conducted in the inner-city Bronx community of NYC to evaluate these factors among Latino New Yorkers. 738 Latinos completed the survey. 241 (32.7 %) participants were obese (BMI > 30 kg/m(2)) and 302 (41 %) individuals were overweight (BMI 25-30 kg/m(2)). Adjusted regression analyses show that Latinos who are overweight or obese were found at greater odds of being men, residing in the US for >10 years, in early stages 1-3 of change of physical activity behavior, and at lower odds of being young adults aged <35 years or with college education. Analysis of factors associated stages of change (SOC) revealed that subjects in these preliminary SOC related to physical activity were at greater odds of speaking Spanish alone, in the same SOC with respect to diet, and at lower odds of living >10 years in the US. With respect to diet, subjects in preliminary stages were at greater odds of being young adults <35 years of age or in early SOC of physical activity and at lower odds of low income <20  dollars per year. The survey shows that Latino New-Yorkers in the Bronx with high prevalence of overweight status and obesity have unique demographic, socio-economic, behavioral and cultural factors that can be linked to excessive body weight.

  16. Community Theories of Change: Linking Environmental Justice to Sustainability through Stakeholder Perceptions in Milwaukee (WI, USA)

    PubMed Central

    Hornik, Kaitlyn; Cutts, Bethany; Greenlee, Andrew

    2016-01-01

    Environmental justice and sustainability are compatible lenses, yet action toward equity is often missing from urban sustainability initiatives. This study aims to assess the cohesion of these frameworks in practice. To do this, we parse individuals’ theories of change, or how they identify and propose to resolve environmental injustices in the pursuit of sustainability. We posit that these theories of change are comprised of three main components: (1) perceived environmental benefits and burdens; (2) the causal pathways of environmental and social injustice; and (3) visions for positive change. Drawing from 35 stakeholder interviews in Milwaukee (WI, USA) we examine individual and institutional perspectives on environmental and social change and their links to the production of injustice. Our findings reveal that participants do not distinguish between environmental and social injustices. Instead, both social and environmental factors are implicated in injustice. Furthermore, we identify two mental maps for how social and economic change reproduce injustice. These findings suggest the need to reorient how urban injustice is considered and make efforts to acknowledge how a diversity of operational theories of change could either be divisive or could bring environmental justice and sustainability initiatives together. PMID:27706068

  17. A tale of two chitons: is habitat specialisation linked to distinct associated bacterial communities?

    PubMed

    Duperron, Sébastien; Pottier, Marie-Anne; Léger, Nelly; Gaudron, Sylvie M; Puillandre, Nicolas; Le Prieur, Stéphanie; Sigwart, Julia D; Ravaux, Juliette; Zbinden, Magali

    2013-03-01

    Although most chitons (Mollusca: Polyplacophora) are shallow-water molluscs, diverse species also occur in deep-sea habitats. We investigated the feeding strategies of two species, Leptochiton boucheti and Nierstraszella lineata, recovered on sunken wood sampled in the western Pacific, close to the Vanuatu Islands. The two species display distinctly different associations with bacterial partners. Leptochiton boucheti harbours Mollicutes in regions of its gut epithelium and has no abundant bacterium associated with its gill. Nierstraszella lineata displays no dense gut-associated bacteria, but harbours bacterial filaments attached to its gill epithelium, related to the Deltaproteobacteria symbionts found in gills of the wood-eating limpet Pectinodonta sp. Stable carbon and nitrogen isotope signatures and an absence of cellulolytic activity give evidence against a direct wood-feeding diet; both species are secondary consumers within the wood food web. We suggest that the distinct associations with bacterial partners are linked to niche specialisations of the two species. Nierstraszella lineata is in a taxonomic family restricted to sunken wood and is possibly adapted to more anoxic conditions thanks to its gill-associated bacteria. Leptochiton boucheti is phylogenetically more proximate to an ancestral form not specialised on wood and may itself be more of a generalist; this observation is congruent with its association with Mollicutes, a bacterial clade comprising gut-associated bacteria occurring in several metazoan phyla.

  18. A tale of two chitons: is habitat specialisation linked to distinct associated bacterial communities?

    PubMed

    Duperron, Sébastien; Pottier, Marie-Anne; Léger, Nelly; Gaudron, Sylvie M; Puillandre, Nicolas; Le Prieur, Stéphanie; Sigwart, Julia D; Ravaux, Juliette; Zbinden, Magali

    2013-03-01

    Although most chitons (Mollusca: Polyplacophora) are shallow-water molluscs, diverse species also occur in deep-sea habitats. We investigated the feeding strategies of two species, Leptochiton boucheti and Nierstraszella lineata, recovered on sunken wood sampled in the western Pacific, close to the Vanuatu Islands. The two species display distinctly different associations with bacterial partners. Leptochiton boucheti harbours Mollicutes in regions of its gut epithelium and has no abundant bacterium associated with its gill. Nierstraszella lineata displays no dense gut-associated bacteria, but harbours bacterial filaments attached to its gill epithelium, related to the Deltaproteobacteria symbionts found in gills of the wood-eating limpet Pectinodonta sp. Stable carbon and nitrogen isotope signatures and an absence of cellulolytic activity give evidence against a direct wood-feeding diet; both species are secondary consumers within the wood food web. We suggest that the distinct associations with bacterial partners are linked to niche specialisations of the two species. Nierstraszella lineata is in a taxonomic family restricted to sunken wood and is possibly adapted to more anoxic conditions thanks to its gill-associated bacteria. Leptochiton boucheti is phylogenetically more proximate to an ancestral form not specialised on wood and may itself be more of a generalist; this observation is congruent with its association with Mollicutes, a bacterial clade comprising gut-associated bacteria occurring in several metazoan phyla. PMID:22988940

  19. Determination of neutrophil CD64 expression as a prognostic biomarker in patients with community-acquired pneumonia.

    PubMed

    Burgos, J; Los-Arcos, I; Álvarez de la Sierra, D; Falcó, V; Aguiló, A; Sánchez, I; Almirante, B; Martinez-Gallo, M

    2016-09-01

    The expression of CD64 in neutrophils (nCD64) has shown utility in the diagnosis of sepsis. The aim of this study was to assess the usefulness of nCD64 expression to identify patients with community-acquired pneumonia (CAP) at risk of a poor outcome. A prospective study of nCD64 expression (determined by flow cytometry) in patients with CAP was performed. The sensitivity/specificity of nCD64 in predicting poor outcome [defined as intensive care unit (ICU) admission and/or clinical deterioration after arrival at the emergency department] was calculated. Eighty-three adults with CAP were included; 14.5 % had septic shock, 19.3 % required ICU admission, and 10.8 % presented clinical deterioration after admission. The mean of the median fluorescence intensity (MFI) of nCD64 expression was 1140 (±1097). Patients with nCD64 expression ≥2700 MFI had more clinical deterioration (36.4 vs. 7.2 %, p = 0.015) and more ICU admission (45.5 vs. 14.5 %, p = 0.028). To identify clinical deterioration and ICU admission, nCD64 expression showed a sensitivity of 44.4 and 33.3 % and a specificity of 90.1 and 90.8 %, respectively. The addition of nCD64 expression to the Pneumonia Severity Index and CURB-65 severity scores did not improve the accuracy of predicting these outcomes. Although nCD64 expression is associated with an increased risk of ICU admission or clinical deterioration after admission, its accuracy in predicting these poor outcomes is modest and does not significantly improve the predictive ability of the PSI and CURB-65 severity scores. PMID:27240938

  20. Linking avian communities and avian influenza ecology in southern Africa using epidemiological functional groups.

    PubMed

    Caron, Alexandre; de Garine-Wichatitsky, Michel; Ndlovu, Mduduzi; Cumming, Graeme S

    2012-01-01

    The ecology of pathogens, and particularly their emergence in multi-host systems, is complex. New approaches are needed to reduce superficial complexities to a level that still allows scientists to analyse underlying and more fundamental processes. One promising approach for simplification is to use an epidemiological-function classification to describe ecological diversity in a way that relates directly to pathogen dynamics. In this article, we develop and apply the epidemiological functional group (EFG) concept to explore the relationships between wild bird communities and avian influenza virus (AIV) in three ecosystems in southern Africa. Using a two year dataset that combined bird counts and bimonthly sampling for AIV, we allocated each bird species to a set of EFGs that captured two overarching epidemiological functions: the capacity of species to maintain AIV in the system, and their potential to introduce the virus. Comparing AIV prevalence between EFGs suggested that the hypothesis that anseriforms (ducks) and charadriiforms (waders) drive AIV epidemiology cannot entirely explain the high prevalence observed in some EFGs. If anseriforms do play an important role in AIV dynamics in each of the three ecosystems, the role of other species in the local maintenance of AIV cannot be ruled out. The EFG concept thus helped us to identify gaps in knowledge and to highlight understudied bird groups that might play a role in AIV epidemiology. In general, the use of EFGs has potential for generating a range of valuable insights in epidemiology, just as functional group approaches have done in ecology. PMID:23101696

  1. Meeting Report--NASA Radiation Biomarker Workshop

    SciTech Connect

    Straume, Tore; Amundson, Sally A,; Blakely, William F.; Burns, Frederic J.; Chen, Allen; Dainiak, Nicholas; Franklin, Stephen; Leary, Julie A.; Loftus, David J.; Morgan, William F.; Pellmar, Terry C.; Stolc, Viktor; Turteltaub, Kenneth W.; Vaughan, Andrew T.; Vijayakumar, Srinivasan; Wyrobek, Andrew J.

    2008-05-01

    A summary is provided of presentations and discussions from the NASA Radiation Biomarker Workshop held September 27-28, 2007, at NASA Ames Research Center in Mountain View, California. Invited speakers were distinguished scientists representing key sectors of the radiation research community. Speakers addressed recent developments in the biomarker and biotechnology fields that may provide new opportunities for health-related assessment of radiation-exposed individuals, including for long-duration space travel. Topics discussed include the space radiation environment, biomarkers of radiation sensitivity and individual susceptibility, molecular signatures of low-dose responses, multivariate analysis of gene expression, biomarkers in biodefense, biomarkers in radiation oncology, biomarkers and triage following large-scale radiological incidents, integrated and multiple biomarker approaches, advances in whole-genome tiling arrays, advances in mass-spectrometry proteomics, radiation biodosimetry for estimation of cancer risk in a rat skin model, and confounding factors. Summary conclusions are provided at the end of the report.

  2. Spatial and temporal variability of biomarkers and microbial diversity reveal metabolic and community flexibility in Streamer Biofilm Communities in the Lower Geyser Basin, Yellowstone National Park.

    PubMed

    Schubotz, F; Meyer-Dombard, D R; Bradley, A S; Fredricks, H F; Hinrichs, K-U; Shock, E L; Summons, R E

    2013-11-01

    Detailed analysis of 16S rRNA and intact polar lipids (IPLs) from streamer biofilm communities (SBCs), collected from geochemically similar hot springs in the Lower Geyser Basin, Yellowstone National Park, shows good agreement and affirm that IPLs can be used as reliable markers for the microbial constituents of SBCs. Uncultured Crenarchaea are prominent in SBS, and their IPLs contain both glycosidic and mixed glyco-phospho head groups with tetraether cores, having 0-4 rings. Archaeal IPL contributions increase with increasing temperature and comprise up to one-fourth of the total IPL inventory at >84 °C. At elevated temperatures, bacterial IPLs contain abundant glycosidic glycerol diether lipids. Diether and diacylglycerol (DAG) lipids with aminopentanetetrol and phosphatidylinositol head groups were identified as lipids diagnostic of Aquificales, while DAG glycolipids and glyco-phospholipids containing N-acetylgycosamine as head group were assigned to members of the Thermales. With decreasing temperature and concomitant changes in water chemistry, IPLs typical of phototrophic bacteria, such as mono-, diglycosyl, and sulfoquinovosyl DAG, which are specific for cyanobacteria, increase in abundance, consistent with genomic data from the same samples. Compound-specific stable carbon isotope analysis of IPL breakdown products reveals a large isotopic diversity among SBCs in different hot springs. At two of the hot springs, 'Bison Pool' and Flat Cone, lipids derived from Aquificales are enriched in (13) C relative to biomass and approach values close to dissolved inorganic carbon (DIC) (approximately 0‰), consistent with fractionation during autotrophic carbon fixation via the reversed tricarboxylic acid pathway. At a third site, Octopus Spring, the same Aquificales-diagnostic lipids are 10‰ depleted relative to biomass and resemble stable carbon isotope values of dissolved organic carbon (DOC), indicative of heterotrophy. Other bacterial and archaeal lipids show

  3. Spatial and temporal variability of biomarkers and microbial diversity reveal metabolic and community flexibility in Streamer Biofilm Communities in the Lower Geyser Basin, Yellowstone National Park.

    PubMed

    Schubotz, F; Meyer-Dombard, D R; Bradley, A S; Fredricks, H F; Hinrichs, K-U; Shock, E L; Summons, R E

    2013-11-01

    Detailed analysis of 16S rRNA and intact polar lipids (IPLs) from streamer biofilm communities (SBCs), collected from geochemically similar hot springs in the Lower Geyser Basin, Yellowstone National Park, shows good agreement and affirm that IPLs can be used as reliable markers for the microbial constituents of SBCs. Uncultured Crenarchaea are prominent in SBS, and their IPLs contain both glycosidic and mixed glyco-phospho head groups with tetraether cores, having 0-4 rings. Archaeal IPL contributions increase with increasing temperature and comprise up to one-fourth of the total IPL inventory at >84 °C. At elevated temperatures, bacterial IPLs contain abundant glycosidic glycerol diether lipids. Diether and diacylglycerol (DAG) lipids with aminopentanetetrol and phosphatidylinositol head groups were identified as lipids diagnostic of Aquificales, while DAG glycolipids and glyco-phospholipids containing N-acetylgycosamine as head group were assigned to members of the Thermales. With decreasing temperature and concomitant changes in water chemistry, IPLs typical of phototrophic bacteria, such as mono-, diglycosyl, and sulfoquinovosyl DAG, which are specific for cyanobacteria, increase in abundance, consistent with genomic data from the same samples. Compound-specific stable carbon isotope analysis of IPL breakdown products reveals a large isotopic diversity among SBCs in different hot springs. At two of the hot springs, 'Bison Pool' and Flat Cone, lipids derived from Aquificales are enriched in (13) C relative to biomass and approach values close to dissolved inorganic carbon (DIC) (approximately 0‰), consistent with fractionation during autotrophic carbon fixation via the reversed tricarboxylic acid pathway. At a third site, Octopus Spring, the same Aquificales-diagnostic lipids are 10‰ depleted relative to biomass and resemble stable carbon isotope values of dissolved organic carbon (DOC), indicative of heterotrophy. Other bacterial and archaeal lipids show

  4. ISOGENIE: Linking geochemistry, isotopic chemistry and microbial dynamics & community composition in a thawing permafrost peatland, Stordalen Mire, Abisco, Sweden.

    NASA Astrophysics Data System (ADS)

    Chanton, J.; Crill, P. M.; Rich, V.; McCalley, C. K.; Hodgkins, S. B.; Tyson, G.; Logan, T.; Wehr, R.; Mondav, R.; Li, C.; Frolking, S.; Saleska, S. R.

    2011-12-01

    As permafrost thaws, increasing CH4 emissions from northern wetlands are likely to cause positive feedback to atmospheric warming. One of the over-arching goals of this project is to connect geochemical processes, particularly focusing on methane production, to underlying microbial population dynamics and genomics. Recent transformative technical advances in both high throughput investigations of microbial communities and high temporal resolution biogeochemical isotope measurements now permit a uniquely comprehensive approach to opening the microbial "black boxes" that impact carbon cycling on global scales. This project links detailed microbial sampling with detailed geochemical and isotopic sampling on seasonal and diel timescales and has an extensive modeling component. Gas exchange is monitored across the wetland gradients in a series of automated chambers and isotopes of emitted and belowground methane and carbon dioxide are measured with a QC laser system. The mire is in a state of partial thaw. With this thaw is an apparent ecological session in wetland community structure and associated changes in organic matter lability, rates of methane production and microbial community. Our group's study sites range from palsa with underlying permanently frozen peat, to recently collapsed and flooded palsa, to flooded palsa colonized by Sphagnum, to flooded eriophorum sites, to sites populated by Carex, to open water lakes. Across this environmental gradient pH ranges from 4 to 6.5. This change is driven by changes in hydrology as the surface of the thawing permafrost subsides and an adjacent lake drains into the mire. Along this environmental gradient, from palsa to Carex, the lability of the peat increases significantly as determined in incubations of peat material and monitoring of methane and carbon dioxide production rates. Coincident with this environmental gradient is a decrease in the apparent fractionation factor between methane and carbon dioxide and methane

  5. Linked Learning in Porterville: Creating Capacity for Innovation and Change through Collaborative Leadership and Community Engagement. Linked Learning Case Study Series

    ERIC Educational Resources Information Center

    Rustique, Elle; Rutherford-Quach, Sara

    2012-01-01

    This case study describes how Porterville Unified School District (PUSD), a rural school district in California's Central Valley, began to fulfill its vision to transform high school and career education through the implementation of Linked Learning. Linked Learning is a state-wide initiative for redesigning large comprehensive high schools into…

  6. Traditional uses of plants in a rural community of Mozambique and possible links with Miombo degradation and harvesting sustainability

    PubMed Central

    2014-01-01

    Background Miombo woodlands play an important role in the livelihood of people living in sub-equatorial African countries, contributing to satisfy basic human needs such as food, medicine, fuelwood and building materials. However, over-exploitation of plant resources and unsustainable harvest practices can potentially degrade forests. The aim of this study was to document the use of Miombo plant products, other than medicinal plants, in local communities, within a wider framework in which we discussed possible links between traditional uses and conservation status of the used species and of the whole Miombo environment. Methods Fieldwork took place in four communities of Muda-Serração, central Mozambique. We conducted semi-structured interviews with 52 informants about their knowledge, use and harvesting practices of useful plants. A survey on local Miombo vegetation was also carried out in order to assess abundance and distribution of useful woody plants cited in the interviews in areas exposed to different exploitation rates. A Conservation Priority index was also applied to rank conservation values of each used woody species. Results Ninety-eight plants cited by the informants were botanically identified. The most relevant general category was represented by food plants (45 species), followed by handicraft plants (38 species) and domestic plants (37 species). Among the 54 woody species observed in vegetation plots, 52% were cited as useful in the interviews. Twenty-six woody species found in ‘natural’ Miombo areas were not found in ‘degraded’ ones: of these, 46% were cited in the interviews (58% in the food category, 50% in the handicraft category, 25% in the domestic category and 8% in the fishing category). Results of conservation ranking showed that 7 woody species deserve conservation priority in the investigated area. Conclusions This study shows that the communities investigated rely heavily on local forest products for their daily subsistence

  7. Linking International Development Actors to Geophysical Infrastructure: Exploring an IRIS Community Role in Bridging a Communications Gap

    NASA Astrophysics Data System (ADS)

    Lerner-Lam, A.; Aster, R.; Beck, S.; Ekstrom, G.; Fisher, K.; Meltzer, A.; Nyblade, A.; Sandvol, E.; Willemann, R.

    2008-12-01

    Over the past quarter century, national investments in high-fidelity digital seismograph networks have resulted in a global infrastructure for real-time in situ earthquake monitoring. Many network operators adhere to community-developed standards, with the result that there are few technical impediments to data sharing and real-time information exchange. Two unanswered questions, however, are whether the existing models of international collaboration will ensure the stability and sustainability of global earthquake monitoring, and whether the participating institutions can work with international development agencies and non- governmental organizations in meeting linked development and natural hazard risk reduction goals. Since the 2004 Indian Ocean tsunami, many of these actors are enlarging their commitments to natural hazard risk reduction and building national technical capacities, among broader programs in poverty alleviation and adaptation to environmental stress. Despite this renewed commitment, international development organizations, with notable exceptions, have been relatively passive in discussions of how the existing earthquake monitoring infrastructure could be leveraged to support risk-reduction programs and meet sustainable development goals. At the same time, the international seismological community - comprising universities and government seismological surveys - has built research and education initiatives such as EarthScope, AfricaArray, and similar programs in China, Europe and South America, that use innovative instrumentation technologies and deployment strategies to enable new science and applications, and promote education and training in critical sectors. Can these developments be combined? Recognizing this communication or knowledge gap, the IRIS International Working Group (IWG) explores the link between the activities of IRIS Members using IRIS facilities and the missions of international development agencies, such as US AID, the World

  8. Regional Approach for Linking Ecosystem Services and Livelihood Strategies Under Climate Change of Pastoral Communities in the Mongolian Steppe Ecosystem

    NASA Astrophysics Data System (ADS)

    Ojima, D. S.; Galvin, K.; Togtohyn, C.

    2012-12-01

    Dramatic changes due to climate and land use dynamics in the Mongolian Plateau affecting ecosystem services and agro-pastoral systems in Mongolia. Recently, market forces and development strategies are affecting land and water resources of the pastoral communities which are being further stressed due to climatic changes. Evaluation of pastoral systems, where humans depend on livestock and grassland ecosystem services, have demonstrated the vulnerability of the social-ecological system to climate change. Current social-ecological changes in ecosystem services are affecting land productivity and carrying capacity, land-atmosphere interactions, water resources, and livelihood strategies. The general trend involves greater intensification of resource exploitation at the expense of traditional patterns of extensive range utilization. Thus we expect climate-land use-land cover relationships to be crucially modified by the social-economic forces. The analysis incorporates information about the social-economic transitions taking place in the region which affect land-use, food security, and ecosystem dynamics. The region of study extends from the Mongolian plateau in Mongolia. Our research indicate that sustainability of pastoral systems in the region needs to integrate the impact of climate change on ecosystem services with socio-economic changes shaping the livelihood strategies of pastoral systems in the region. Adaptation strategies which incorporate integrated analysis of landscape management and livelihood strategies provides a framework which links ecosystem services to critical resource assets. Analysis of the available livelihood assets provides insights to the adaptive capacity of various agents in a region or in a community. Sustainable development pathways which enable the development of these adaptive capacity elements will lead to more effective adaptive management strategies for pastoral land use and herder's living standards. Pastoralists will have the

  9. Partnerships in Education: Home, School and Community Links in the Asia-Pacific Region, Report of a Regional Seminar June 17-28, 1996.

    ERIC Educational Resources Information Center

    National Inst. for Educational Research, Tokyo (Japan).

    This report comes from a regional seminar on Improving the Links between School, Home and Community in the Asia-Pacific Region in June 1996. Twenty-four participants from Australia, China, Indonesia, Japan, Malaysia, New Zealand, Philippines, Republic of Korea, and Thailand took part in the meeting. Country reports comprised the first two days of…

  10. Aggregated silver nanoparticles based surface-enhanced Raman scattering enzyme-linked immunosorbent assay for ultrasensitive detection of protein biomarkers and small molecules.

    PubMed

    Liang, Jiajie; Liu, Hongwu; Huang, Caihong; Yao, Cuize; Fu, Qiangqiang; Li, Xiuqing; Cao, Donglin; Luo, Zhi; Tang, Yong

    2015-06-01

    Lowering the detection limit is critical to the design of bioassays required for medical diagnostics, environmental monitoring, and food safety regulations. The current sensitivity of standard color-based analyte detection limits the further use of enzyme-linked immunosorbent assays (ELISAs) in research and clinical diagnoses. Here, we demonstrate a novel method that uses the Raman signal as the signal-generating system of an ELISA and combines surface-enhanced Raman scattering (SERS) with silver nanoparticles aggregation for ultrasensitive analyte detection. The enzyme label of the ELISA controls the dissolution of Raman reporter-labeled silver nanoparticles through hydrogen peroxide and generates a strong Raman signal when the analyte is present. Using this assay, prostate-specific antigen (PSA) and the adrenal stimulant ractopamine (Rac) were detected in whole serum and urine at the ultralow concentrations of 10(-9) and 10(-6) ng/mL, respectively. The methodology proposed here could potentially be applied to other molecules detection as well as PSA and Rac.

  11. Analysis of bacterial core communities in the central Baltic by comparative RNA-DNA-based fingerprinting provides links to structure-function relationships.

    PubMed

    Brettar, Ingrid; Christen, Richard; Höfle, Manfred G

    2012-01-01

    Understanding structure-function links of microbial communities is a central theme of microbial ecology since its beginning. To this end, we studied the spatial variability of the bacterioplankton community structure and composition across the central Baltic Sea at four stations, which were up to 450 km apart and at a depth profile representative for the central part (Gotland Deep, 235 m). Bacterial community structure was followed by 16S ribosomal RNA (rRNA)- and 16S rRNA gene-based fingerprints using single-strand conformation polymorphism (SSCP) electrophoresis. Species composition was determined by sequence analysis of SSCP bands. High similarities of the bacterioplankton communities across several hundred kilometers were observed in the surface water using RNA- and DNA-based fingerprints. In these surface communities, the RNA- and DNA-based fingerprints resulted in very different pattern, presumably indicating large difference between the active members of the community as represented by RNA-based fingerprints and the present members represented by the DNA-based fingerprints. This large discrepancy changed gradually over depth, resulting in highly similar RNA- and DNA-based fingerprints in the anoxic part of the water column below 130 m depth. A conceivable mechanism explaining this high similarity could be the reduced oxidative stress in the anoxic zone. The stable communities on the surface and in the anoxic zone indicate the strong influence of the hydrography on the bacterioplankton community structure. Comparative analysis of RNA- and DNA-based community structure provided criteria for the identification of the core community, its key members and their links to biogeochemical functions.

  12. Combined use of Daphnia magna in situ bioassays, biomarkers and biological indices to diagnose and identify environmental pressures on invertebrate communities in two Mediterranean urbanized and industrialized rivers (NE Spain).

    PubMed

    Damásio, Joana; Tauler, Romà; Teixidó, Elisabeth; Rieradevall, Maria; Prat, Narcis; Riva, Maria Carmen; Soares, Amadeu M V M; Barata, Carlos

    2008-05-30

    Environmental factors affecting aquatic invertebrate communities were assessed using Daphnia magna in situ bioassays and biological indices based on community assemblages of benthic macroinvertebrates. Investigations were carried out in two heavily industrialized and urbanized river basins from the NE of Spain (Llobregat and Besós). Measures of energy consumption (i.e. algal grazing), and of specific biochemical responses (biomarkers) were conducted on individuals transplanted upstream and downstream from effluent discharges of sewage treatment plants. In both rivers there was a clear deterioration of the ecological water quality parameters and benthic communities towards downstream reaches. In all but one of the 19 locations studied, transplanted organisms were affected in at least one of the five measured responses. In three of them, significant effects were detected in most of the traits considered. Principal Component and Partial Least Square Projections to Latent Structures regression analyses indicated that the measured responses in D. magna in situ bioassays and those of macroinvertebrate assemblages were affected by distinct environmental factors. From up to 20 environmental variables considered, seven of them including habitat degradation, suspended solids, nitrogenous and conductivity related parameters affected macroinvertebrate assemblages. On the other hand, levels of organophosphorus compounds and polycyclic aromatic hydrocarbons were high enough to trigger the responses of D. magna in situ bioassays. These results emphasize the importance of combining biological indices with biomarkers and more generalized and ecologically relevant (grazing) in situ responses to identify ecological effects of effluent discharges from sewage treatment plants in surface waters.

  13. Ectomycorrhizal fungal diversity and saprotrophic fungal diversity are linked to different tree community attributes in a field-based tree experiment.

    PubMed

    Nguyen, Nhu H; Williams, Laura J; Vincent, John B; Stefanski, Artur; Cavender-Bares, Jeannine; Messier, Christian; Paquette, Alain; Gravel, Dominique; Reich, Peter B; Kennedy, Peter G

    2016-08-01

    Exploring the link between above- and belowground biodiversity has been a major theme of recent ecological research, due in large part to the increasingly well-recognized role that soil microorganisms play in driving plant community processes. In this study, we utilized a field-based tree experiment in Minnesota, USA, to assess the effect of changes in plant species richness and phylogenetic diversity on the richness and composition of both ectomycorrhizal and saprotrophic fungal communities. We found that ectomycorrhizal fungal species richness was significantly positively influenced by increasing plant phylogenetic diversity, while saprotrophic fungal species richness was significantly affected by plant leaf nitrogen content, specific root length and standing biomass. The increasing ectomycorrhizal fungal richness associated with increasing plant phylogenetic diversity was driven by the combined presence of ectomycorrhizal fungal specialists in plots with both gymnosperm and angiosperm hosts. Although the species composition of both the ectomycorrhizal and saprotrophic fungal communities changed significantly in response to changes in plant species composition, the effect was much greater for ectomycorrhizal fungi. In addition, ectomycorrhizal but not saprotrophic fungal species composition was significantly influenced by both plant phylum (angiosperm, gymnosperm, both) and origin (Europe, America, both). The phylum effect was caused by differences in ectomycorrhizal fungal community composition, while the origin effect was attributable to differences in community heterogeneity. Taken together, this study emphasizes that plant-associated effects on soil fungal communities are largely guild-specific and provides a mechanistic basis for the positive link between plant phylogenetic diversity and ectomycorrhizal fungal richness. PMID:27284759

  14. How Can We Work Sectorally in a Province? Building Links between the Nova Scotia Community College and the Nova Scotia Industry Sector Councils. An Association of Canadian Community Colleges Sponsored Sectoral Case Study.

    ERIC Educational Resources Information Center

    Kenny, Mary; Shaw, Robbie

    This paper focuses on the links between Nova Scotia Community College (NSCC) and the Nova Scotia Regional Industry Training Councils (RITCs). It discusses a 1999 evaluation of the RITCs, and provides major findings and implications for future cooperation between RITCs and NSCC. The evaluation study, on a general level, provided substantial…

  15. Adapting to Community-Based Learning. (Benefits)[Squared]: The Exponential Results of Linking School Improvement and Community Development, Issue Number Four.

    ERIC Educational Resources Information Center

    Boethel, Martha

    Building a rural community-school development project where students engage in community-based learning experiences requires changes in the way schools prepare rural youth for the future. This publication examines the kinds of changes a school system must make before planning and implementing community-based learning strategies. Changes in…

  16. Sepsis biomarkers.

    PubMed

    Prucha, Miroslav; Bellingan, Geoff; Zazula, Roman

    2015-02-01

    Sepsis is the most frequent cause of death in non-coronary intensive care units (ICUs). In the past 10 years, progress has been made in the early identification of septic patients and in their treatment and these improvements in support and therapy mean that the mortality is gradually decreasing but it still remains unacceptably high. Leaving clinical diagnosis aside, the laboratory diagnostics represent a complex range of investigations that can place significant demands on the system given the speed of response required. There are hundreds of biomarkers which could be potentially used for diagnosis and prognosis in septic patients. The main attributes of successful markers would be high sensitivity, specificity, possibility of bed-side monitoring, and financial accessibility. Only a fraction is used in routine clinical practice because many lack sufficient sensitivity or specificity. The following review gives a short overview of the current epidemiology of sepsis, its pathogenesis and state-of-the-art knowledge on the use of specific biochemical, hematological and immunological parameters in its diagnostics. Prospective approaches towards discovery of new diagnostic biomarkers have been shortly mentioned.

  17. Potential link between plant and fungal distributions in a dipterocarp rainforest: community and phylogenetic structure of tropical ectomycorrhizal fungi across a plant and soil ecotone.

    PubMed

    Peay, Kabir G; Kennedy, Peter G; Davies, Stuart J; Tan, Sylvester; Bruns, Thomas D

    2010-01-01

    *Relatively little is known about diversity or structure of tropical ectomycorrhizal communities or their roles in tropical ecosystem dynamics. In this study, we present one of the largest molecular studies to date of an ectomycorrhizal community in lowland dipterocarp rainforest. *We sampled roots from two 0.4 ha sites located across an ecotone within a 52 ha forest dynamics plot. Our plots contained > 500 tree species and > 40 species of ectomycorrhizal host plants. Fungi were identified by sequencing ribosomal RNA genes. *The community was dominated by the Russulales (30 species), Boletales (17), Agaricales (18), Thelephorales (13) and Cantharellales (12). Total species richness appeared comparable to molecular studies of temperate forests. Community structure changed across the ecotone, although it was not possible to separate the role of environmental factors vs host plant preferences. Phylogenetic analyses were consistent with a model of community assembly where habitat associations are influenced by evolutionary conservatism of functional traits within ectomycorrhizal lineages. *Because changes in the ectomycorrhizal fungal community parallel those of the tree community at this site, this study demonstrates the potential link between the distribution of tropical tree diversity and the distribution of tropical ectomycorrhizal diversity in relation to local-scale edaphic variation.

  18. The 2011 Bioinformatics Links Directory update: more resources, tools and databases and features to empower the bioinformatics community.

    PubMed

    Brazas, Michelle D; Yim, David S; Yamada, Joseph T; Ouellette, B F Francis

    2011-07-01

    The Bioinformatics Links Directory continues its collaboration with Nucleic Acids Research to collaboratively publish and compile a freely accessible, online collection of tools, databases and resource materials for bioinformatics and molecular biology research. The July 2011 Web Server issue of Nucleic Acids Research adds an additional 78 web server tools and 14 updates to the directory at http://bioinformatics.ca/links_directory/.

  19. Parasites of flounder (Platichthys flesus L.) from the German Bight, North Sea, and their potential use in biological effects monitoring. C. Pollution effects on the parasite community and a comparison to biomarker responses

    NASA Astrophysics Data System (ADS)

    Schmidt, V.; Zander, S.; Körting, W.; Broeg, K.; von Westernhagen, H.; Dizer, H.; Hansen, P. D.; Skouras, A.; Steinhagen, D.

    2003-10-01

    In the frame of an integrated biological effect monitoring programme, the parasite community of flounder (Platichthys flesus) was investigated at different locations in the German Bight from 1995 to 2000. In order to assess the impact of environmental contamination caused by anthropogenic activities on the parasite community, selected parasitological parameters that displayed significant differences between the sampling sites were subjected to correlation analyses with site-specific contamination and individual pollution loads of their fish hosts. In addition, correlation analyses were conducted with the responses of selected genetic, biochemical, histopathological, physiological and immunological parameters of fish, used as potential biomarkers. In total, 802 flounder were analysed for these parameters. Information on the chemical background at the sampling sites was derived from sediment samples and from 120 samples of blue mussel (Mytilus edulis) tissue, collected at each of the sampling sites. Based on chemical data available from the sediment and blue mussel samples, a pollution gradient could be established between the sampling sites for individual contaminants. The relative abundance of Acanthochondria cornuta, Cucullanus heterochrous and Zoogonoides viviparus, and the community measures species richness and number of heteroxenous species decreased with increasing concentrations of individual heavy metals or hydrocarbons in sediment and blue mussel samples. Most of the parasitological parameters significantly reflected the established site-specific contamination gradient, when data were pooled over all sampling campaigns. Significant correlations were also found with the contamination level of individual flounder. The parasitological parameters included the parasite species Lepeophtheirus pectoralis and Lernaeocera branchialis, which were not correlated to site-specific contamination. Several biomarkers were significantly correlated to the abundance of

  20. Broadening and Deepening the Definition of Outreach Scholarship: Linking Popular Education and Community-Based Participatory Action Research

    ERIC Educational Resources Information Center

    Rai, Kalyani

    2003-01-01

    This paper outlines a Community-based Participatory Action Research model designed and implemented by the University of Wisconsin-Milwaukee School of Continuing Education with two community-based agencies in Milwaukee. In two participatory action learning seminars, research was combined with action to improve the educational experience of…

  1. Improving community development by linking agriculture, nutrition and education: design of a randomised trial of “home-grown” school feeding in Mali

    PubMed Central

    2013-01-01

    Background Providing food through schools has well documented effects in terms of the education, health and nutrition of school children. However, there is limited evidence in terms of the benefits of providing a reliable market for small-holder farmers through “home-grown” school feeding approaches. This study aims to evaluate the impact of school feeding programmes sourced from small-holder farmers on small-holder food security, as well as on school children’s education, health and nutrition in Mali. In addition, this study will examine the links between social accountability and programme performance. Design This is a field experiment planned around the scale-up of the national school feeding programme, involving 116 primary schools in 58 communities in food insecure areas of Mali. The randomly assigned interventions are: 1) a school feeding programme group, including schools and villages where the standard government programme is implemented; 2) a “home-grown” school feeding and social accountability group, including schools and villages where the programme is implemented in addition to training of community based organisations and local government; and 3) the control group, including schools and household from villages where the intervention will be delayed by at least two years, preferably without informing schools and households. Primary outcomes include small-holder farmer income, school participation and learning, and community involvement in the programme. Other outcomes include nutritional status and diet-diversity. The evaluation will follow a mixed method approach, including household, school and village level surveys as well as focus group discussions with small-holder farmers, school children, parents and community members. The impact evaluation will be incorporated within the national monitoring and evaluation (M&E) system strengthening activities that are currently underway in Mali. Baselines surveys are planned for 2012. A monthly

  2. Achieving Synergy: Linking an Internet-Based Inflammatory Bowel Disease Cohort to a Community-Based Inception Cohort and Multicentered Cohort in Inflammatory Bowel Disease

    PubMed Central

    Aldridge, Molly; Cook, Suzanne Follan; Bright, Renee; Mallette, Meaghan; Moniz, Heather; Shah, Samir A; LeLeiko, Neal S; Shapiro, Jason; Sands, Bruce E; Chen, Wenli; Jaeger, Elizabeth; Galanko, Joseph; Long, Millie D; Martin, Christopher F; Sandler, Robert S; Kappelman, Michael D

    2016-01-01

    doctoral degrees, P=.01). In the SHARE cohort, 436 participants enrolled and linked to the Partners cohort. More women (60% vs 50%) linked and those who linked were predominantly white (96%; P<.01). Crohn’s disease patients who linked had lower mean scores on the Harvey-Bradshaw Index (3.6 vs 4.4, P<.01). Ulcerative colitis patients who linked had less extensive disease than those who did not link (45% vs 60%, P<.01). Conclusions Linkage of CCFA Partners with cohorts such as OSCCAR and SHARE may be a cost-effective way to expand the infrastructure for clinical outcomes and translational research. Although linkage is feasible from a technical, legal, and regulatory perspective, participant willingness appears to be a limiting factor. Overcoming this barrier will be needed to generate meaningful sample sizes to conduct studies of biomarkers, natural history, and clinical effectiveness using linked data. PMID:27261008

  3. Closing the gap in HIV prevention and care for children: early insights from a model that links communities and health care facilities in Uganda

    PubMed Central

    ‘t Hart, Doortje; Musinguzi, Merian; Ochen, Richard; Katushabe, Juliet; Rujumba, Joseph

    2016-01-01

    ABSTRACT Inequities in access to HIV prevention and treatment for children remain a global challenge and a black spot to effective HIV prevention and response especially in many HIV endemic countries like Uganda. In Uganda while about 51% of the adults living with HIV are on antiretrovirals, only 39% of the children aged 0–14 years accessed the needed HIV care in 2014. In this article, it is argued that much focus on health system interventions with little regard to bridging the gap between health facilities, where much of the care is provided, and the communities, where children are conceived, born and cared for, contributes to and sustains this inequality. Investments need to be made in building and implementing models that create and enhance linkages between communities and health care facilities. Success factors from the Towards an AIDS Free Generation in Uganda project model in creating these linkages are bringing all actors together in one approach, building on existing community structures and enabling community health workers to be the linking pin between communities and facilities. Only with models like this, full elimination of mother-to-child transmission and paediatric HIV care coverage (0–14 years) can be reached in Uganda and other HIV endemic countries.

  4. Final Report for Award #0006731. Modeling, Patterning and Evolving Syntrophic Communities that Link Fermentation to Metal Reduction

    SciTech Connect

    Marx, Christopher J.

    2015-07-17

    This project has developed and combined mathematical models, multi-species consortia, and spatially structured environments as an approach for studying metabolic exchange in communities like the ones between fermenters and metal reducers. We have developed novel, broadly-applicable tools for following community dynamics, come to a better understanding of both sugar and lactate-utilization in S. oneidensis, the interactions between carbon and mineral availability, and have a methodology for cell printing to match with spatiotemporal models of consortia metabolism.

  5. Community.

    ERIC Educational Resources Information Center

    Grauer, Kit, Ed.

    1995-01-01

    Art in context of community is the theme of this newsletter. The theme is introduced in an editorial "Community-Enlarging the Definition" (Kit Grauer). Related articles include: (1) "The Children's Bridge is not Destroyed: Heart in the Middle of the World" (Emil Robert Tanay); (2) "Making Bridges: The Sock Doll Project" (Anami Naths); (3)…

  6. BIOMARKERS OF REPRODUCTIVE TOXICITY

    EPA Science Inventory

    Identification and verification of anatomical, endocrine, cellular and molecular biomarkers is crucial for successful clinical diagnosis and treatment of toxicity and disease, as well as basic toxicological, epidemiological and other research. Various in situ biomarkers of repro...

  7. Biomarkers in Computational Toxicology

    EPA Science Inventory

    Biomarkers are a means to evaluate chemical exposure and/or the subsequent impacts on toxicity pathways that lead to adverse health outcomes. Computational toxicology can integrate biomarker data with knowledge of exposure, chemistry, biology, pharmacokinetics, toxicology, and e...

  8. Is reporting on interventions a weak link in understanding how and why they work? A preliminary exploration using community heart health exemplars

    PubMed Central

    Riley, Barbara L; MacDonald, JoAnne; Mansi, Omaima; Kothari, Anita; Kurtz, Donna; vonTettenborn, Linda I; Edwards, Nancy C

    2008-01-01

    Background The persistent gap between research and practice compromises the impact of multi-level and multi-strategy community health interventions. Part of the problem is a limited understanding of how and why interventions produce change in population health outcomes. Systematic investigation of these intervention processes across studies requires sufficient reporting about interventions. Guided by a set of best processes related to the design, implementation, and evaluation of community health interventions, this article presents preliminary findings of intervention reporting in the published literature using community heart health exemplars as case examples. Methods The process to assess intervention reporting involved three steps: selection of a sample of community health intervention studies and their publications; development of a data extraction tool; and data extraction from the publications. Publications from three well-resourced community heart health exemplars were included in the study: the North Karelia Project, the Minnesota Heart Health Program, and Heartbeat Wales. Results Results are organized according to six themes that reflect best intervention processes: integrating theory, creating synergy, achieving adequate implementation, creating enabling structures and conditions, modifying interventions during implementation, and facilitating sustainability. In the publications for the three heart health programs, reporting on the intervention processes was variable across studies and across processes. Conclusion Study findings suggest that limited reporting on intervention processes is a weak link in research on multiple intervention programs in community health. While it would be premature to generalize these results to other programs, important next steps will be to develop a standard tool to guide systematic reporting of multiple intervention programs, and to explore reasons for limited reporting on intervention processes. It is our contention that

  9. What Can Funders Do to Better Link Science with Decisions? Case Studies of Coastal Communities and Climate Change

    NASA Astrophysics Data System (ADS)

    Matso, Kalle E.; Becker, Mimi L.

    2014-12-01

    Many reports and studies have noted that a significant portion of problem-oriented coastal science does not actually link to decisions. Here, three competitively funded project case studies are studied to determine what funders can and should do to better link science with decisions. The qualitative analysis used for this study indicates that the studied program was seen as being unusually attentive to the issue of linking science to decisions, as opposed to simply generating new knowledge. Nevertheless, much of the data indicate that funders can and should do more. Three ideas figured most prominently in the qualitative data: (1) funders should do more to ensure that the problem itself is defined more thoroughly with people who are envisioned as potential users of the science; (2) funders need to allocate more resources and attention to communicating effectively (with users) throughout the project; and (3) funders need to demand more engagement of users throughout the project. These findings have important implications for how funders review and support science, especially when competitive processes are used. Most importantly, funders should adjust what kind of science they ask for. Secondly, funders need to change who is involved in the review process. Currently, review processes focus on knowledge generation, which means that the reviewers themselves have expertise in that area. Instead, review panels should be balanced between those who focus on knowledge generation and those who focus on linking knowledge to decisions; this is a separate but critical discipline currently left out of the review process.

  10. NASA Radiation Biomarker Workshop, September 27-28, 2007.

    PubMed

    Straume, Tore; Amundson, Sally A; Blakely, William F; Burns, Fredric J; Chen, Allen; Dainiak, Nicholas; Franklin, Stephen; Leary, Julie A; Loftus, David J; Morgan, William F; Pellmar, Terry C; Stolc, Viktor; Turteltaub, Kenneth W; Vaughan, Andrew T; Vijayakumar, Srinivasan; Wyrobek, Andrew J

    2008-09-01

    A summary is provided of presentations and discussions at the NASA Radiation Biomarker Workshop held September 27-28, 2007 at NASA Ames Research Center in Mountain View, CA. Invited speakers were distinguished scientists representing key sectors of the radiation research community. Speakers addressed recent developments in the biomarker and biotechnology fields that may provide new opportunities for health-related assessment of radiation-exposed individuals, including those exposed during long-duration space travel. Topics discussed included the space radiation environment, biomarkers of radiation sensitivity and individual susceptibility, molecular signatures of low-dose responses, multivariate analysis of gene expression, biomarkers in biodefense, biomarkers in radiation oncology, biomarkers and triage after large-scale radiological incidents, integrated and multiple biomarker approaches, advances in whole-genome tiling arrays, advances in mass spectrometry proteomics, radiation biodosimetry for estimation of cancer risk in a rat skin model, and confounding factors. A summary of conclusions is provided at the end of the report.

  11. Cyanobacterial ecotypes in the microbial mat community of Mushroom Spring (Yellowstone National Park, Wyoming) as species-like units linking microbial community composition, structure and function.

    PubMed

    Ward, David M; Bateson, Mary M; Ferris, Michael J; Kühl, Michael; Wieland, Andrea; Koeppel, Alex; Cohan, Frederick M

    2006-11-29

    We have investigated microbial mats of alkaline siliceous hot springs in Yellowstone National Park as natural model communities to learn how microbial populations group into species-like fundamental units. Here, we bring together empirical patterns of the distribution of molecular variation in predominant mat cyanobacterial populations, theory-based modelling of how to demarcate phylogenetic clusters that correspond to ecological species and the dynamic patterns of the physical and chemical microenvironments these populations inhabit and towards which they have evolved adaptations. We show that putative ecotypes predicted by the theory-based model correspond well with distribution patterns, suggesting populations with distinct ecologies, as expected of ecological species. Further, we show that increased molecular resolution enhances our ability to detect ecotypes in this way, though yet higher molecular resolution is probably needed to detect all ecotypes in this microbial community.

  12. Improving the coordination of care for low back pain patients by creating better links between acute and community services.

    PubMed

    Staiger, Petra K; Serlachius, Anna; Macfarlane, Susie; Anderson, Sharron; Chan, Thomas; Young, Greg

    2010-05-01

    This paper reports on the development of a care-pathway to improve service linkages between the acute setting and community health services in the treatment of low back pain. The pathway was informed by two processes: (1) a literature review based on best-practice guidelines in the assessment, treatment and continuity of care for low back pain patients; and (2) consultation with staff and key stakeholders. Stakeholders from both the acute and community sectors comprised the Working Group, who identified central areas of concern to be addressed in the care-pathway, with the goal of preventing chronicity of low back pain and reducing emergency department presentations. The main outcomes achieved include: the development of a new care-coordinator role, which would support a greater focus on integration between acute and community sectors for low back pain patients; identifying the need to screen at-risk patients; implementation of the SCTT (Service Coordination Tool Templates) tool as a system of referral across the acute and community settings; and agreement on the need to develop an evidence-based self-management program to be offered to low back pain patients. The benefits and challenges of implementing this care pathway are discussed. PMID:20497725

  13. Testing the link between community structure and function for ectomycorrhizal fungi involved in a global tripartite symbiosis.

    PubMed

    Walker, Jennifer K M; Cohen, Hannah; Higgins, Logan M; Kennedy, Peter G

    2014-04-01

    Alnus trees associate with ectomycorrhizal (ECM) fungi and nitrogen-fixing Frankia bacteria and, although their ECM fungal communities are uncommonly host specific and species poor, it is unclear whether the functioning of Alnus ECM fungal symbionts differs from that of other ECM hosts. We used exoenzyme root tip assays and molecular identification to test whether ECM fungi on Alnus rubra differed in their ability to access organic phosphorus (P) and nitrogen (N) when compared with ECM fungi on the non-Frankia host Pseudotsuga menziesii. At the community level, potential acid phosphatase (AP) activity of ECM fungal root tips from A. rubra was significantly higher than that from P. menziesii, whereas potential leucine aminopeptidase (LA) activity was significantly lower for A. rubra root tips at one of the two sites. At the individual species level, there was no clear relationship between ECM fungal relative root tip abundance and relative AP or LA enzyme activities on either host. Our results are consistent with the hypothesis that ECM fungal communities associated with Alnus trees have enhanced organic P acquisition abilities relative to non-Frankia ECM hosts. This shift, in combination with the chemical conditions present in Alnus forest soils, may drive the atypical structure of Alnus ECM fungal communities. PMID:24320607

  14. Structures and Strategies for Linking the Higher Education and Employment Communities. Higher Education/CETA Project Monograph.

    ERIC Educational Resources Information Center

    Clark, Donald M.; Rinehart, Richard L.

    A model is presented for establishing or improving cooperative relationships between higher education and the employment community, as part of the American Council on Education's Higher Education/Comprehensive Employment and Training Act (CETA) Project, which was supported by the Fund for the Improvement of Postsecondary Education. Attention is…

  15. SIMULATION COASTAL PLAIN STREAM FISH COMMUNITY RESPONSE TO NONPOINT SOURCE POLLUTION USING LINKED HYDROLOGIC-ECOLOGICAL MODELS

    EPA Science Inventory

    Nonpoint source pollution is the primary stress in many streams. Characteristic declines in stream fish communities are recognized in streams influenced by nonpoint source pollution, but the processes by which these declines occur are not well understood. Here, predicted time s...

  16. Experiential Learning in Higher Education: Linking Classroom and Community. ASHE-ERIC Higher Education Report No. 7.

    ERIC Educational Resources Information Center

    Cantor, Jeffrey A.

    This report reviews the literature and research on the use of experiential learning in higher education, focusing on classroom-community linkages. It defines experiential learning and reviews the current employment of experiential learning in higher education. An introductory section explains the politics and policy issues of experiential learning…

  17. Linking macrobenthic communities structure and zonation patterns on sandy shores: Mapping tool toward management and conservation perspectives in Northern France

    NASA Astrophysics Data System (ADS)

    Rolet, Céline; Spilmont, Nicolas; Dewarumez, Jean-Marie; Luczak, Christophe

    2015-05-01

    In a context of intensifying anthropogenic pressures on sandy shores, the mapping of benthic habitat appears as an essential first step and a fundamental baseline for marine spatial planning, ecosystem-based management and conservation efforts of soft-sediment intertidal areas. Mapping allows representing intertidal habitats that are basically characterised by abiotic (e.g sediments, exposure to waves…) and biotic factors such as macrobenthic communities. Macrobenthic communities are known to show zonation patterns across sandy beaches and many studies highlighted the existence of three biological zones. We tested this general model of a tripartite biological division of the shore at a geographical scale of policy, conservation and management decisions (i.e. Northern France coastline), using multivariate analyses combined with the Direct Field Observation (DFO) method. From the upper to the lower shores, the majority of the beaches exhibited three macrobenthic communities confirming the existence of the tripartite biological division of the shore. Nevertheless, in some cases, two or four zones were found: (1) two zones when the drying zone located on the upper shore was replaced by littoral rock or engineering constructions and (2) four zones on beaches and estuaries where a muddy-sand community occurred from the drift line to the mid shore. The correspondence between this zonation pattern of macrobenthic communities and the EUNIS habitat classification was investigated and the results were mapped to provide a reference state of intertidal soft-sediment beaches and estuaries. Our results showed evidence of the applicability of this EUNIS typology for the beaches and estuaries at a regional scale (Northern France coastline) with a macroecological approach. In order to fulfil the requirements of the European Directives (WFD and MFSD), this mapping appears as a practical tool for any functional study on these coastal ecosystems, for the monitoring of anthropogenic

  18. Application of RNA Stable Isotope Probing (SIP) to Link Community Activity with Microorganisms Responsible for Autotrophy in the Subseafloor at Axial Seamount

    NASA Astrophysics Data System (ADS)

    Huber, J. A.; Fortunato, C. S.

    2014-12-01

    The global ocean comprises the Earth's largest biome, with microorganisms playing a dominant biogeochemical role. However, the potential for production of new microbial biomass within the subseafloor is rarely considered in traditional oceanographic paradigms of carbon cycling or microbial food webs. In this study, we used RNA Stable Isotope Probing (RNA SIP) to determine the microbial community composition and genetic repertoire of active subseafloor autotrophs in warm venting fluids from Axial Seamount. RNA is a responsive biomarker because it is a reflection of cellular activity independent of replication, and RNA SIP thus provides access to both the function of a microbial community and the phylogeny of the organisms accountable for key functions. Diffuse fluids were incubated shipboard at 30°C, 55°C, and 80°C with 13DIC and H2. Metatranscriptomic sequencing of both the enriched and non-enriched RNA was carried out from 13C and 12C controls. In addition, filtered fluid samples were preserved in situ for comparative meta -transcriptomic and -genomic analyses. Diverse lineages of bacteria and archaea and accompanying metabolisms were detected in situ, but RNA SIP results show dominance of three different groups of autotrophs active under each experimental condition. At 30°C, members of the Sulfurimonas genus dominated, with genes for hydrogen oxidation, nitrate reduction, and carbon fixation via the rTCA cycle highly expressed. At 55°C, both Caminibacter and Nautilia transcripts were detected for rTCA cycle, hydrogen oxidation, and nitrate reduction. At 80°C, transcripts for hydrogenotrophic methanogenesis mediated by members of Methanocaldococcus were detected. These results suggest the subseafloor hosts various anaerobic chemolithoautotrophs that span a wide temperature range, with hydrogen playing a key role in microbial metabolism. Complementary experiments are currently being carried out on the seafloor with a novel in situ incubator unit to provide

  19. Microbial community dynamics linked to enhanced substrate availability and biogas production of electrokinetically pre-treated waste activated sludge.

    PubMed

    Westerholm, Maria; Crauwels, Sam; Houtmeyers, Sofie; Meerbergen, Ken; Van Geel, Maarten; Lievens, Bart; Appels, Lise

    2016-10-01

    The restricted hydrolytic degradation rate of complex organic matter presents a considerable challenge in anaerobic digestion of waste activated sludge (WAS). Within this context, application of pre-treatment of digester substrate has potential for improved waste management and enhanced biogas production. Anaerobic degradation of untreated or electrokinetically pre-treated WAS was performed in two pilot-scale digesters for 132days. WAS electrokinetically pre-treated with energy input 0.066kJ/kg sludge was used in a first phase of operation and WAS pre-treated with energy input 0.091kJ/kg sludge was used in a second phase (each phase lasted at least three hydraulic retention times). Substrate characteristics before and after pre-treatment and effects on biogas digester performance were comprehensively analysed. To gain insights into influences of altered substrate characteristics on microbial communities, the dynamics within the bacterial and archaeal communities in the two digesters were investigated using 16S rRNA gene sequencing (pyrosequencing) and quantitative PCR (qPCR). Specific primers targeting dominant operation taxonomic units (OTUs) and members of the candidate phylum Cloacimonetes were designed to further evaluate their abundance and dynamics in the digesters. Electrokinetic pre-treatment significantly improved chemical oxygen demand (COD) and carbohydrate solubility and increased biogas production by 10-11% compared with untreated sludge. Compositional similarity of the bacterial community during initial operation and diversification during later operation indicated gradual adaptation of the community to the higher solubility of organic material in the pre-treated substrate. Further analyses revealed positive correlations between gene abundance of dominant OTUs related to Clostridia and Cloacimonetes and increased substrate availability and biogas production. Among the methanogens, the genus Methanosaeta dominated in both digesters. Overall, the

  20. Microbial community dynamics linked to enhanced substrate availability and biogas production of electrokinetically pre-treated waste activated sludge.

    PubMed

    Westerholm, Maria; Crauwels, Sam; Houtmeyers, Sofie; Meerbergen, Ken; Van Geel, Maarten; Lievens, Bart; Appels, Lise

    2016-10-01

    The restricted hydrolytic degradation rate of complex organic matter presents a considerable challenge in anaerobic digestion of waste activated sludge (WAS). Within this context, application of pre-treatment of digester substrate has potential for improved waste management and enhanced biogas production. Anaerobic degradation of untreated or electrokinetically pre-treated WAS was performed in two pilot-scale digesters for 132days. WAS electrokinetically pre-treated with energy input 0.066kJ/kg sludge was used in a first phase of operation and WAS pre-treated with energy input 0.091kJ/kg sludge was used in a second phase (each phase lasted at least three hydraulic retention times). Substrate characteristics before and after pre-treatment and effects on biogas digester performance were comprehensively analysed. To gain insights into influences of altered substrate characteristics on microbial communities, the dynamics within the bacterial and archaeal communities in the two digesters were investigated using 16S rRNA gene sequencing (pyrosequencing) and quantitative PCR (qPCR). Specific primers targeting dominant operation taxonomic units (OTUs) and members of the candidate phylum Cloacimonetes were designed to further evaluate their abundance and dynamics in the digesters. Electrokinetic pre-treatment significantly improved chemical oxygen demand (COD) and carbohydrate solubility and increased biogas production by 10-11% compared with untreated sludge. Compositional similarity of the bacterial community during initial operation and diversification during later operation indicated gradual adaptation of the community to the higher solubility of organic material in the pre-treated substrate. Further analyses revealed positive correlations between gene abundance of dominant OTUs related to Clostridia and Cloacimonetes and increased substrate availability and biogas production. Among the methanogens, the genus Methanosaeta dominated in both digesters. Overall, the

  1. Linking disease and community ecology through behavioural indicators: immunochallenge of white-footed mice and its ecological impacts.

    PubMed

    Schwanz, Lisa E; Brisson, Dustin; Gomes-Solecki, Maria; Ostfeld, Richard S

    2011-01-01

    1. Pathogens and immune challenges can induce changes in host phenotype in ways that indirectly impact important community interactions, including those that affect host-pathogen interactions. 2. To explore host behavioural response to immune challenge, we exposed wild white-footed mice (Peromyscus leucopus) to an immunogen from an endemic, zoonotic pathogen, the spirochete Borrelia burgdorferi. White-footed mice are a major reservoir host of Lyme disease (LD) spirochetes in northeastern USA and an abundant member of forest communities. The activity patterns, foraging behaviour, and space use of white-footed mice have implications for population growth rates of community members upon which mice incidentally prey (i.e. gypsy moths and native thrushes), as well as potentially determining host-vector encounter rates and human risk of LD. 3. Immunochallenge led to specific humoral (antibody) and cellular (i.e. elevated neutrophils and eosinophils) immune responses, supporting use of the immunogen as a surrogate for pathogenic infection. 4. Immunochallenged mice had reduced wheel-running activity early in the night when measured in the lab. However, mouse activity, as measured by track plates in natural field experiments, did not differ between mice exposed to the immunogen and unexposed mice. 5. Foraging behaviour of wild mice in the field - assessed with giving-up densities of seed at artificial feeding stations - was affected by exposure to the immunogen. Whereas immunochallenge did not influence whether foraging mice gained information on patch quality while foraging, it led to reductions in predator avoidance during foraging, suggesting that the proportion of space used by foraging mice may be greater as a result of immunochallenge. This increased space use is predicted to increase encounter rates with patchily distributed LD vectors (ticks) and with incidental prey items. 6. Thus, immunochallenge in white-footed mice, and potentially pathogenic infection, have the

  2. The development and applications of biomarkers

    SciTech Connect

    Normandy, J.; Peeters, J.

    1994-04-15

    This report is a compilation of submitted abstracts of scientific papers presented at the second Department of Energy-supported workshop on the use and applications of biomarkers held in Santa Fe, New Mexico, from April 26--29, 1994. The abstracts present a synopsis of the latest scientific developments in biomarker research and how these developments meet with the practical needs of the occupational physician as well as the industrial hygienist and the health physicist. In addition to considering the practical applications and potential benefits of this promising technology, the potential ethical and legal ramifications of using biomarkers to monitor workers are discussed. The abstracts further present insights on the present benefits that can be derived from using biomarkers as well as a perspective on what further research is required to fully meet the needs of the medical community.

  3. Critical tissue residue approach linking accumulated metals in aquatic insects to population and community-level effects

    USGS Publications Warehouse

    Schmidt, Travis S.; Clements, William H.; Zuellig, Robert E.; Mitchell, Katharine A.; Church, Stanley E.; Wanty, Richard B.; San Juan, Carma A.; Adams, Monique; Lamothe, Paul J.

    2011-01-01

    Whole body Zn concentrations in individuals (n = 825) from three aquatic insect taxa (mayflies Rhithrogena spp. and Drunella spp. and the caddisfly Arctopsyche grandis) were used to predict effects on populations and communities (n = 149 samples). Both mayflies accumulated significantly more Zn than the caddisfly. The presence/absence of Drunella spp. most reliably distinguished sites with low and high Zn concentrations; however, population densities of mayflies were more sensitive to increases in accumulated Zn. Critical tissue residues (634 (mu or u)g/g Zn for Drunella spp. and 267 (mu or u)g/g Zn for Rhithrogena spp.) caused a 20% reduction in maximum (90th quantile) mayfly densities. These critical tissue residues were associated with exposure to 7.0 and 3.9 (mu or u)g/L dissolved Zn for Drunella spp. and Rhithrogena spp., respectively. A threshold in a measure of taxonomic completeness (observed/expected) was observed at 5.4 (mu or u)g/L dissolved Zn. Dissolved Zn concentrations associated with critical tissue residues in mayflies were also associated with adverse effects in the aquatic community as a whole. These effects on populations and communities occurred at Zn concentrations below the U.S. EPA hardness-adjusted continuous chronic criterion.

  4. Computational biomarker pipeline from discovery to clinical implementation: plasma proteomic biomarkers for cardiac transplantation.

    PubMed

    Cohen Freue, Gabriela V; Meredith, Anna; Smith, Derek; Bergman, Axel; Sasaki, Mayu; Lam, Karen K Y; Hollander, Zsuzsanna; Opushneva, Nina; Takhar, Mandeep; Lin, David; Wilson-McManus, Janet; Balshaw, Robert; Keown, Paul A; Borchers, Christoph H; McManus, Bruce; Ng, Raymond T; McMaster, W Robert

    2013-04-01

    Recent technical advances in the field of quantitative proteomics have stimulated a large number of biomarker discovery studies of various diseases, providing avenues for new treatments and diagnostics. However, inherent challenges have limited the successful translation of candidate biomarkers into clinical use, thus highlighting the need for a robust analytical methodology to transition from biomarker discovery to clinical implementation. We have developed an end-to-end computational proteomic pipeline for biomarkers studies. At the discovery stage, the pipeline emphasizes different aspects of experimental design, appropriate statistical methodologies, and quality assessment of results. At the validation stage, the pipeline focuses on the migration of the results to a platform appropriate for external validation, and the development of a classifier score based on corroborated protein biomarkers. At the last stage towards clinical implementation, the main aims are to develop and validate an assay suitable for clinical deployment, and to calibrate the biomarker classifier using the developed assay. The proposed pipeline was applied to a biomarker study in cardiac transplantation aimed at developing a minimally invasive clinical test to monitor acute rejection. Starting with an untargeted screening of the human plasma proteome, five candidate biomarker proteins were identified. Rejection-regulated proteins reflect cellular and humoral immune responses, acute phase inflammatory pathways, and lipid metabolism biological processes. A multiplex multiple reaction monitoring mass-spectrometry (MRM-MS) assay was developed for the five candidate biomarkers and validated by enzyme-linked immune-sorbent (ELISA) and immunonephelometric assays (INA). A classifier score based on corroborated proteins demonstrated that the developed MRM-MS assay provides an appropriate methodology for an external validation, which is still in progress. Plasma proteomic biomarkers of acute cardiac

  5. Are Longitudinal Patterns of Bacterial Community Composition and Dissolved Organic Matter Composition Linked Across a River Continuum? (Invited)

    NASA Astrophysics Data System (ADS)

    Mosher, J.; Kaplan, L. A.; Kan, J.; Findlay, R. H.; Podgorski, D. C.; McKenna, A. M.; Branan, T. L.; Griffith, C.

    2013-12-01

    The River Continuum Concept (RCC), an early meta-ecosystem idea, was developed without the benefit of new frontiers in molecular microbial ecology and ultra-high resolution mass spectrometry. We have applied technical advances in these areas to address a hypothesis implicit in the RCC that the upstream legacy of DOM processing contributes to the structure and function of downstream bacterial communities. DOM molecular structure and microbial community structure were measured across river networks within three distinct forested catchments. High-throughput pyrosequencing of bacterial 16S rRNA amplicons and phospholipid fatty acid analysis were used to characterize bacterial communities, and ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry characterized the molecular composition of stream water DOM. Total microbial biomass varied among river networks but showed a trend of decreasing biomass in sediment with increasing stream order. There were distinct shifts in bacterial community structure and a trend of decreasing richness was observed traveling downstream in both sediment and epilithic habitats. The bacterial richness in the first order stream sediment habitats was 7728 genera which decreased to 6597 genera in the second order sites and 4867 genera in the third order streams. The richness in the epilithic biofilm habitats was 2830 genera in the first order, 2322 genera in the second order and 1629 genera in the third order sites. Over 45% of the sediment biofilm genera and 37% of the epilithic genera were found in all three orders. In addition to shifts in bacterial richness, we observed a longitudinal shift in bacterial functional-types. In the sediment biofilms, Rhodoplanes spp. (containing rhodopsin pigment) and Bradyrhizobium spp. (nitrogen fixing bacteria) were predominately found in the heavily forested first order streams, while the cyanobacteria Limnothrix spp. was dominant in the second order streams. The third order

  6. Linking a Large-Watershed Hydrogeochemical Model to a Wetland Community-Ecosystem Model to Estimate Plant Invasion Risk in the Coastal Great Lakes Region, USA

    NASA Astrophysics Data System (ADS)

    Currie, W. S.; Bourgeau-Chavez, L. L.; Elgersma, K. J.; French, N. H. F.; Goldberg, D. E.; Hart, S.; Hyndman, D. W.; Kendall, A. D.; Martin, S. L.; Martina, J. P.

    2014-12-01

    In the Laurentian Great Lakes region of the Upper Midwest, USA, agricultural and urban land uses together with high N deposition are contributing to elevated flows of N in rivers and groundwater to coastal wetlands. The functioning of coastal wetlands, which provide a vital link between land and water, are imperative to maintaining the health of the entire Great Lakes Basin. Elevated N inflows are believed to facilitate the spread of large-stature invasive plants (cattails and Phragmites) that reduce biodiversity and have complex effects on other ecosystem services including wetland N retention and C accretion. We enhanced the ILHM (Integrated Landscape Hydrology Model) to simulate the effects of land use on N flows in streams, rivers, and groundwater throughout the Lower Peninsula of Michigan. We used the hydroperiods and N loading rates simulated by ILHM as inputs to the Mondrian model of wetland community-ecosystem processes to estimate invasion risk and other ecosystem services in coastal wetlands around the Michigan coast. Our linked models produced threshold behavior in the success of invasive plants in response to N loading, with the threshold ranging from ca. 8 to 12 g N/m2 y, depending on hydroperiod. Plant invasions increased wetland productivity 3-fold over historically oligotrophic native communities, decreased biodiversity but slightly increased wetland N retention. Regardless of invasion, elevated N loading resulted in significantly enhanced rates of C accretion, providing an important region-wide mechanism of C storage. The linked models predicted a general pattern of greater invasion risk in the southern basins of lakes Michigan and Huron relative to northern areas. The basic mechanisms of invasion have been partially validated in our field mesocosms constructed for this project. The general regional patterns of increased invasion risk have been validated through our field campaigns and remote sensing conducted for this project.

  7. Associations between vitamin K status and hemostatic and inflammatory biomarkers in community-dwelling adults: The multi-ethnic study of atherosclerosis

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vitamin K is integral to hemostatic function, and in vitro and animal experiments suggest that vitamin K can suppress production of inflammatory cytokines. To test the hypothesis that higher vitamin K status is associated with lower hemostasic activation and inflammation in community-dwelling adults...

  8. Linking Temporal Changes in Bacterial Community Structures with the Detection and Phylogenetic Analysis of Neutral Metalloprotease Genes in the Sediments of a Hypereutrophic Lake

    PubMed Central

    Tsuboi, Shun; Yamamura, Shigeki; Imai, Akio; Satou, Takayuki; Iwasaki, Kazuhiro

    2014-01-01

    We investigated spatial and temporal variations in bacterial community structures as well as the presence of three functional proteolytic enzyme genes in the sediments of a hypereutrophic freshwater lake in order to acquire an insight into dynamic links between bacterial community structures and proteolytic functions. Bacterial communities determined from 16S rRNA gene clone libraries markedly changed bimonthly, rather than vertically in the sediment cores. The phylum Firmicutes dominated in the 4–6 cm deep sediment layer sample after August in 2007, and this correlated with increases in interstitial ammonium concentrations (p < 0.01). The Firmicutes clones were mostly composed of the genus Bacillus. npr genes encoding neutral metalloprotease, an extracellular protease gene, were detected after the phylum Firmicutes became dominant. The deduced Npr protein sequences from the retrieved npr genes also showed that most of the Npr sequences used in this study were closely related to those of the genus Bacillus, with similarities ranging from 61% to 100%. Synchronous temporal occurrences of the 16S rRNA gene and Npr sequences, both from the genus Bacillus, were positively associated with increases in interstitial ammonium concentrations, which may imply that proteolysis by Npr from the genus Bacillus may contribute to the marked increases observed in ammonium concentrations in the sediments. Our results suggest that sedimentary bacteria may play an important role in the biogeochemical nitrogen cycle of freshwater lakes. PMID:25130992

  9. Applying Recovery Biomarkers to Calibrate Self-Report Measures of Energy and Protein in the Hispanic Community Health Study/Study of Latinos.

    PubMed

    Mossavar-Rahmani, Yasmin; Shaw, Pamela A; Wong, William W; Sotres-Alvarez, Daniela; Gellman, Marc D; Van Horn, Linda; Stoutenberg, Mark; Daviglus, Martha L; Wylie-Rosett, Judith; Siega-Riz, Anna Maria; Ou, Fang-Shu; Prentice, Ross L

    2015-06-15

    We investigated measurement error in the self-reported diets of US Hispanics/Latinos, who are prone to obesity and related comorbidities, by background (Central American, Cuban, Dominican, Mexican, Puerto Rican, and South American) in 2010-2012. In 477 participants aged 18-74 years, doubly labeled water and urinary nitrogen were used as objective recovery biomarkers of energy and protein intakes. Self-report was captured from two 24-hour dietary recalls. All measures were repeated in a subsample of 98 individuals. We examined the bias of dietary recalls and their associations with participant characteristics using generalized estimating equations. Energy intake was underestimated by 25.3% (men, 21.8%; women, 27.3%), and protein intake was underestimated by 18.5% (men, 14.7%; women, 20.7%). Protein density was overestimated by 10.7% (men, 11.3%; women, 10.1%). Higher body mass index and Hispanic/Latino background were associated with underestimation of energy (P<0.05). For protein intake, higher body mass index, older age, nonsmoking, Spanish speaking, and Hispanic/Latino background were associated with underestimation (P<0.05). Systematic underreporting of energy and protein intakes and overreporting of protein density were found to vary significantly by Hispanic/Latino background. We developed calibration equations that correct for subject-specific error in reporting that can be used to reduce bias in diet-disease association studies.

  10. Linking benthic community structure to terrestrial runoff and upwelling in the coral reefs of northeastern Hainan Island

    NASA Astrophysics Data System (ADS)

    Li, Xiubao; Wang, Daoru; Huang, Hui; Zhang, Jing; Lian, Jiansheng; Yuan, Xiangcheng; Yang, Jianhui; Zhang, Guoseng

    2015-04-01

    Near-shore coral reefs in northeastern Hainan Island are close to river mouths and aquaculture ponds, and also located at the center of the Qiongdong Upwelling (QDU). However, it is still unclear how terrestrial runoff and upwelling influence the community composition and spatial distribution of the benthos. During three cruises in 2010 and 2011 in Wenchang, northeastern Hainan Island, we determined a subset of environmental parameters in seawater (e.g. temperature, salinity, DO, dissolved inorganic nutrient (DIN), turbidity and transparency) and macroalgal δ15N and investigated the benthic communities (e.g. live coral cover, coral species richness, juvenile coral density, macroalgal cover and coverage of calcified algae) by video transect and visual census techniques at 10 stations (i.e. 1S-6D). The results showed that the QDU has influenced the reef waters in Wenchang. In 2011, the upwelling started in early May, peaked in July and disappeared in September and most upwelling events lasted for 1-2 weeks between May and July. The results also demonstrated that the reef water was nutrient enriched. Stations close to the river mouth and aquaculture ponds had higher levels of DIN and a higher percentage of ammonia in DIN, and there was consistently lower live coral cover, juvenile coral density and higher macroalgal cover. At some stations in this study, live coral cover was negatively correlated with macroalgal cover (i.e. 2S-6D). Live coral cover, species richness, and juvenile coral density all increased with the distance away from the river outlet and decreased with the rise of DIN. These results suggest that terrestrial runoff and upwelling stimulate nutrient enrichment, and that overgrowing macroalgae has an important influence on the coral communities in northeastern Hainan Island.

  11. Characterization of microorganisms responsible for phosphorus removal linking operation performance with microbial community structure at low temperature.

    PubMed

    Zou, Haiming; Lu, Xiwu; Saad, Abualhail

    2014-01-01

    Two enhanced biological phosphorus removal (EBPR) reactors were started up at low temperatures to obtain microorganisms responsible for aerobic and anoxic phosphorus removal, namely polyphosphate-accumulating organisms (PAO) and denitrifying PAO (DPAO), and their operational performance and microbial community were together investigated in the hope of assessment of the effectiveness of the EBPR process at low temperature by combining chemical analysis and microbial community structure evolution based on polymerase chain reaction-denaturing gradient gel electrophoresis. When two reactors reached the steady state after 40 and 80 days for the anaerobic-aerobic (AO) and anaerobic-anoxic (AA) reactor operation in AO and AA modes, respectively, a good ability of anaerobic phosphorus release and aerobic or anoxic phosphorus uptake was present both in these two reactors. During this start-up process, a total of 22 bands were detected in seed, AA and AO sludge samples, including Alpha-, Beta-, Gamma- and Deltaproteobacteria, as well as Chlorobi, Firmicutes, Bacteroidetes and Actinobacteria. Of all the bands, only four bands were present in all the lanes, suggesting that shift in microbial community occurred greatly depending on the electron acceptors in this study. From evolutionary tree, it was found that microorganisms related to DPAO mostly belong to the phylum Betaproteobacteria, while microbes corresponding to PAO were present in several phyla. Overall, the new strategy proposed here was shown to be feasible for the enrichment of PAO and DPAO at low temperature, and may be regarded as a new guidance for the application of EBPR technology to practice, especially in winter. PMID:24701905

  12. Amphidromy Links a Newly Documented Fish Community of Continental Australian Streams, to Oceanic Islands of the West Pacific

    PubMed Central

    Thuesen, Paul A.; Ebner, Brendan C.; Larson, Helen; Keith, Philippe; Silcock, Rebecca M.; Prince, Jason; Russell, David J.

    2011-01-01

    Background Indo-Pacific high island streams experience extreme hydrological variation, and are characterised by freshwater fish species with an amphidromous life history. Amphidromy is a likely adaptation for colonisation of island streams following stochastic events that lead to local extirpation. In the Wet Tropics of north-eastern Australia, steep coastal mountain streams share similar physical characteristics to island systems. These streams are poorly surveyed, but may provide suitable habitat for amphidromous species. However, due to their ephemeral nature, common non-diadromous freshwater species of continental Australia are unlikely to persist. Consequently, we hypothesise that coastal Wet Tropics streams are faunally more similar, to distant Pacific island communities, than to nearby faunas of large continental rivers. Methods/Principal Findings Surveys of coastal Wet Tropics streams recorded 26 species, 10 of which are first records for Australia, with three species undescribed. This fish community is unique in an Australian context in that it contains mostly amphidromous species, including sicydiine gobies of the genera Sicyopterus, Sicyopus, Smilosicyopus and Stiphodon. Species presence/absence data of coastal Wet Tropics streams were compared to both Wet Tropics river networks and Pacific island faunas. ANOSIM indicated the fish fauna of north-eastern Australian coastal streams were more similar to distant Pacific islands (R = 0.76), than to nearby continental rivers (R = 0.98). Main Conclusions/Significance Coastal Wet Tropics streams are faunally more similar to distant Pacific islands (79% of species shared), than to nearby continental fauna due to two factors. First, coastal Wet Tropics streams lack many non-diadromous freshwater fish which are common in nearby large rivers. Second, many amphidromous species found in coastal Wet Tropics streams and Indo-Pacific islands remain absent from large rivers of the Wet Tropics. The evolutionary and

  13. Communities of practice: the missing link for knowledge management on implementation issues in low-income countries?

    PubMed

    Meessen, Bruno; Kouanda, Seni; Musango, Laurent; Richard, Fabienne; Ridde, Valéry; Soucat, Agnès

    2011-08-01

    The implementation of policies remains a huge challenge in many low-income countries. Several factors play a role in this, but improper management of existing knowledge is no doubt a major issue. In this article, we argue that new platforms should be created that gather all stakeholders who hold pieces of relevant knowledge for successful policies. To build our case, we capitalize on our experience in our domain of practice, health care financing in sub-Saharan Africa. We recently adopted a community of practice strategy in the region. More in general, we consider these platforms as the way forward for knowledge management of implementation issues. PMID:21564426

  14. Communities of practice: the missing link for knowledge management on implementation issues in low-income countries?

    PubMed

    Meessen, Bruno; Kouanda, Seni; Musango, Laurent; Richard, Fabienne; Ridde, Valéry; Soucat, Agnès

    2011-08-01

    The implementation of policies remains a huge challenge in many low-income countries. Several factors play a role in this, but improper management of existing knowledge is no doubt a major issue. In this article, we argue that new platforms should be created that gather all stakeholders who hold pieces of relevant knowledge for successful policies. To build our case, we capitalize on our experience in our domain of practice, health care financing in sub-Saharan Africa. We recently adopted a community of practice strategy in the region. More in general, we consider these platforms as the way forward for knowledge management of implementation issues.

  15. Biomarker Utility Analysis Using an Exposure-PBPK/PD Model: A Carbaryl Case Study

    EPA Science Inventory

    There are two common biomarkers: markers of exposure and markers of health effects. The strength of the correlation between exposure or effect and a biomarker measurement determines the utility of a biomarker for assessing exposures or risks. In the current study, a linked expo...

  16. Technology use in linking criminal justice reentrants to HIV care in the community: a qualitative formative research study.

    PubMed

    Peterson, James; Cota, Michelle; Gray, Holly; Bazerman, Lauri; Kuo, Irene; Kurth, Ann; Beckwith, Curt

    2015-01-01

    Innovative interventions increasing linkage, adherence, and retention in care among HIV-infected persons in the criminal justice system are needed. The authors conducted a qualitative study to investigate technology-based tools to facilitate linkage to community-based care and viral suppression for HIV-infected jail detainees on antiretroviral medications being released to the community. The authors conducted 24 qualitative interview-12 in Rhode Island and 12 in Washington, DC-among recently incarcerated HIV-infected persons to elicit their perceptions on the use of technology tools to support linkage to HIV care among criminal justice populations. This article discusses participants' perceptions of the acceptability of technological tools such as (a) a computer-based counseling and (b) text messaging interventions. The participants reported positive experiences when previewing the technology-based tools to facilitate linkage to HIV care and adherence to HIV medications. Successful linkage to care has been shown to improve HIV-associated and non-HIV-associated health outcomes, as well as prevent criminal recidivism and facilitate reentrants' successful and meaningful transition. These findings can be used to inform the implementation of interventions aimed at promoting adherence to antiretroviral medications and linkage to care for HIV-infected persons being released from the correctional setting.

  17. NET-Works: Linking families, communities and primary care to prevent obesity in preschool-age children.

    PubMed

    Sherwood, Nancy E; French, Simone A; Veblen-Mortenson, Sara; Crain, A Lauren; Berge, Jerica; Kunin-Batson, Alicia; Mitchell, Nathan; Senso, Meghan

    2013-11-01

    Obesity prevention in children offers a unique window of opportunity to establish healthful eating and physical activity behaviors to maintain a healthful body weight and avoid the adverse proximal and distal long-term health consequences of obesity. Given that obesity is the result of a complex interaction between biological, behavioral, family-based, and community environmental factors, intervention at multiple levels and across multiple settings is critical for both short- and long-term effectiveness. The Minnesota NET-Works (Now Everybody Together for Amazing and Healthful Kids) study is one of four obesity prevention and/or treatment trials that are part of the Childhood Obesity Prevention and Treatment (COPTR) Consortium. The goal of the NET-Works study is to evaluate an intervention that integrates home, community, primary care and neighborhood strategies to promote healthful eating, activity patterns, and body weight among low income, racially/ethnically diverse preschool-age children. Critical to the success of this intervention is the creation of linkages among the settings to support parents in making home environment and parenting behavior changes to foster healthful child growth. Five hundred racially/ethnically diverse, two-four year old children and their parent or primary caregiver will be randomized to the multi-component intervention or to a usual care comparison group for a three-year period. This paper describes the study design, measurement and intervention protocols, and statistical analysis plan for the NET-Works trial.

  18. Technology Use in Linking Criminal Justice Reentrants to HIV Care in the Community: A Qualitative Formative Research Study

    PubMed Central

    PETERSON, JAMES; COTA, MICHELLE; GRAY, HOLLY; BAZERMAN, LAURI; KUO, IRENE; KURTH, ANN; BECKWITH, CURT

    2014-01-01

    Innovative interventions increasing linkage, adherence and retention in care among HIV-infected persons in the criminal justice system are needed. The authors conducted a qualitative study to investigate technology-based tools to facilitate linkage to community-based care and viral suppression for HIV-infected jail detainees on antiretroviral medications being released to the community. Twenty-four qualitative interviews were conducted in Rhode Island (12) and Washington DC (12) among HIV infected persons recently incarcerated to elicit their perceptions on the use of technology tools to support linkage to HIV care among criminal justice populations. This article discusses participants’ perceptions of the acceptability of technological tools such as (a) a computer-based counseling and (b) text messaging interventions. The participants reported positive experiences when previewing the technology-based tools to facilitate linkage to HIV care and adherence to HIV medications. Successful linkage to care has been shown to improve HIV-associated and non-HIV-associated health outcomes, as well as prevent criminal recidivism and facilitate reentrants’ successful and meaningful transition. These findings can be utilized to inform the implementation of interventions aimed at promoting adherence to antiretroviral medications and linkage to care for HIV-infected persons being released from the correctional setting. PMID:25529057

  19. A large multi-pathogen waterborne community outbreak linked to faecal contamination of a groundwater system, France, 2000.

    PubMed

    Gallay, A; De Valk, H; Cournot, M; Ladeuil, B; Hemery, C; Castor, C; Bon, F; Mégraud, F; Le Cann, P; Desenclos, J C

    2006-06-01

    A large waterborne outbreak of infection that occurred during August 2000 in a local community in France was investigated initially via a rapid survey of visits to local physicians. A retrospective cohort study was then conducted on a random cluster sample of residents. Of 709 residents interviewed, 202 (28.5%) were definite cases (at least three liquid stools/day or vomiting) and 62 (8.7%) were probable cases (less than three liquid stools/day or abdominal pain). Those who had drunk tap water had a three-fold increased risk for illness (95% CI 2.4-4.0). The risk increased with the amount of water consumed (chi-square trend: p < 0.0001). Bacteriological analyses of stools were performed for 35 patients and virological analyses for 24 patients. Campylobacter coli, group A rotavirus and norovirus were detected in 31.5%, 71.0% and 21% of samples, respectively. An extensive environmental investigation concluded that a groundwater source to this community had probably been contaminated by agricultural run-off, and a failure in the chlorination system was identified. This is the first documented waterborne outbreak of infection involving human C. coli infections. A better understanding of the factors influencing campylobacter transmission between hosts is required.

  20. Microbial Community Structure and Activity Linked to Contrasting Biogeochemical Gradients in Bog and Fen Environments of the Glacial Lake Agassiz Peatland

    PubMed Central

    Lin, X.; Green, S.; Tfaily, M. M.; Prakash, O.; Konstantinidis, K. T.; Corbett, J. E.; Chanton, J. P.; Cooper, W. T.

    2012-01-01

    The abundances, compositions, and activities of microbial communities were investigated at bog and fen sites in the Glacial Lake Agassiz Peatland of northwestern Minnesota. These sites contrast in the reactivity of dissolved organic matter (DOM) and the presence or absence of groundwater inputs. Microbial community composition was characterized using pyrosequencing and clone library construction of phylogenetic marker genes. Microbial distribution patterns were linked to pH, concentrations of dissolved organic carbon and nitrogen, C/N ratios, optical properties of DOM, and activities of laccase and peroxidase enzymes. Both bacterial and archaeal richness and rRNA gene abundance were >2 times higher on average in the fen than in the bog, in agreement with a higher pH, labile DOM content, and enhanced enzyme activities in the fen. Fungi were equivalent to an average of 1.4% of total prokaryotes in gene abundance assayed by quantitative PCR. Results revealed statistically distinct spatial patterns between bacterial and fungal communities. Fungal distribution did not covary with pH and DOM optical properties and was vertically stratified, with a prevalence of Ascomycota and Basidiomycota near the surface and much higher representation of Zygomycota in the subsurface. In contrast, bacterial community composition largely varied between environments, with the bog dominated by Acidobacteria (61% of total sequences), while the Firmicutes (52%) dominated in the fen. Acetoclastic Methanosarcinales showed a much higher relative abundance in the bog, in contrast to the dominance of diverse hydrogenotrophic methanogens in the fen. This is the first quantitative and compositional analysis of three microbial domains in peatlands and demonstrates that the microbial abundance, diversity, and activity parallel with the pronounced differences in environmental variables between bog and fen sites. PMID:22843538

  1. A Cross-Sectional Association Between Bone Mineral Density and Parathyroid Hormone and Other Biomarkers in Community-Dwelling Young Adults: The CARDIA Study

    PubMed Central

    Polgreen, Lynda E.; Hurley, Daniel L.; Gross, Myron D.; Sidney, Stephen; Jacobs, David R.

    2013-01-01

    Context: Most association studies of bone-related biomarkers (BBMs) with bone mineral density (BMD) have been conducted in postmenopausal women. Objective: We tested whether the following BBMs were cross-sectionally associated with BMD among young adults: serum 1,25-dihydroxyvitamin D (1,25(OH)2D), 25-hydroxyvitamin D (25OHD), PTH, osteocalcin, bone-specific alkaline phosphatase (BAP), and urinary pyridinoline/urinary creatinine. Setting and Participants: We studied 319 individuals (134 women, 149 black, 24–36 years) recruited during 1992 through 1993 in Oakland, California. BMD was assessed with dual-energy x-ray absorptiometry. Linear regression models estimated the association between BMD and each BBM. Results: 1,25(OH)2D was inversely associated with all BMDs. 25OHD was positively, and PTH inversely, associated with lumbar spine, total hip, and whole-body BMD. BAP was inversely associated with left arm, right arm, and whole-body BMD but not with spine or hip BMD. Neither osteocalcin nor urinary pyridinoline/urinary creatinine was associated with BMD. When we placed all BBMs (including 1,25(OH)2D) in one model, the pattern and magnitude of association was similar except for PTH, which was attenuated. The association of BMD and BBMs did not differ significantly by race or sex. Conclusions: In this cross-sectional study of healthy young men and women who had PTH levels considered normal in clinical practice, higher PTH was associated with lower BMD, particularly in weight-bearing sites (ie, spine and hip). The inverse association of 1,25(OH)2D, together with the attenuation of PTH, suggests that the observed association of PTH is mediated by 1,25(OH)2D. BAP was inversely associated with arm BMD. BBMs can be important markers of skeletal activity in young adults, but their clinical role on bone health among this population is yet to be fully determined. PMID:23966240

  2. Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration

    PubMed Central

    Liu, Jin-Feng; Sun, Xiao-Bo; Yang, Guang-Chao; Mbadinga, Serge M.; Gu, Ji-Dong; Mu, Bo-Zhong

    2015-01-01

    Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs. PMID:25873911

  3. Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration.

    PubMed

    Liu, Jin-Feng; Sun, Xiao-Bo; Yang, Guang-Chao; Mbadinga, Serge M; Gu, Ji-Dong; Mu, Bo-Zhong

    2015-01-01

    Sequestration of CO2 in oil reservoirs is considered to be one of the feasible options for mitigating atmospheric CO2 building up and also for the in situ potential bioconversion of stored CO2 to methane. However, the information on these functional microbial communities and the impact of CO2 storage on them is hardly available. In this paper a comprehensive molecular survey was performed on microbial communities in production water samples from oil reservoirs experienced CO2-flooding by analysis of functional genes involved in the process, including cbbM, cbbL, fthfs, [FeFe]-hydrogenase, and mcrA. As a comparison, these functional genes in the production water samples from oil reservoir only experienced water-flooding in areas of the same oil bearing bed were also analyzed. It showed that these functional genes were all of rich diversity in these samples, and the functional microbial communities and their diversity were strongly affected by a long-term exposure to injected CO2. More interestingly, microorganisms affiliated with members of the genera Methanothemobacter, Acetobacterium, and Halothiobacillus as well as hydrogen producers in CO2 injected area either increased or remained unchanged in relative abundance compared to that in water-flooded area, which implied that these microorganisms could adapt to CO2 injection and, if so, demonstrated the potential for microbial fixation and conversion of CO2 into methane in subsurface oil reservoirs.

  4. Validation and clinical utility of prostate cancer biomarkers

    PubMed Central

    Scher, Howard I.; Morris, Michael J.; Larson, Steven; Heller, Glenn

    2013-01-01

    To improve future drug development and patient management for patients with castration-resistant prostate cancer (CRPC), surrogate biomarkers that are linked to relevant outcomes are urgently needed. A biomarker must be measurable, reproducible, linked to relevant clinical outcomes, and demonstrate utility. This is a rapidly evolving area, with recent trials in CRPC incorporating the detection of circulating tumour cells (CTCs), imaging, and patient-reported outcome biomarkers. We discuss the framework for the development of biomarkers for CRPC, including different categories and contexts of use. We also highlight the requirements of analytical validation, the sequence of trials needed for clinical validation and regulatory approval, and the future outlook for imaging and CTC biomarkers. PMID:23459624

  5. Circulating glioma biomarkers

    PubMed Central

    Kros, Johan M.; Mustafa, Dana M.; Dekker, Lennard J.M.; Sillevis Smitt, Peter A.E.; Luider, Theo M.; Zheng, Ping-Pin

    2015-01-01

    Validated biomarkers for patients suffering from gliomas are urgently needed for standardizing measurements of the effects of treatment in daily clinical practice and trials. Circulating body fluids offer easily accessible sources for such markers. This review highlights various categories of tumor-associated circulating biomarkers identified in blood and cerebrospinal fluid of glioma patients, including circulating tumor cells, exosomes, nucleic acids, proteins, and oncometabolites. The validation and potential clinical utility of these biomarkers is briefly discussed. Although many candidate circulating protein biomarkers were reported, none of these have reached the required validation to be introduced for clinical practice. Recent developments in tracing circulating tumor cells and their derivatives as exosomes and circulating nuclear acids may become more successful in providing useful biomarkers. It is to be expected that current technical developments will contribute to the finding and validation of circulating biomarkers. PMID:25253418

  6. Metagenomic biomarker discovery and explanation

    PubMed Central

    2011-01-01

    This study describes and validates a new method for metagenomic biomarker discovery by way of class comparison, tests of biological consistency and effect size estimation. This addresses the challenge of finding organisms, genes, or pathways that consistently explain the differences between two or more microbial communities, which is a central problem to the study of metagenomics. We extensively validate our method on several microbiomes and a convenient online interface for the method is provided at http://huttenhower.sph.harvard.edu/lefse/. PMID:21702898

  7. Phenology of Australian temperate grasslands: linking near-surface phenology to C3/C4 community composition

    NASA Astrophysics Data System (ADS)

    Watson, C. J.

    2015-12-01

    Vegetation phenology is relatively well-studied in northern hemisphere temperate biomes, but limited research has been conducted on phenological drivers and responses in Australian temperate ecosystems. Australian temperate grasslands represent a broad range of plant communities from exotic pastures to native grasslands, but all are important for food security (livestock grazing) and biodiversity retention. Climate predictions for temperate Australia include higher temperatures, altered rainfall frequency/seasonality, increased drought severity and more regular wildfires. The ecosystem response to these climatic factors is unknown, and the need to improve the monitoring of these highly dynamic grassland systems at a landscape scale is acute. The aim of this research is to use high-frequency phenological data to improve the identification of grassland functional types and ultimately use this to improve the inter-annual monitoring of dynamic grassland systems. We use hourly repeat photography and the Green Chromatic Coordinate vegetation index to characterize the vegetative phenology of several native and exotic grassland communities. Monthly vegetation surveys allow us to correlate plant functional groups with indicator features on the phenology profile. C4-dominated grasslands are characterized by a consistent low greenness during winter, the commencement of greening in late spring/early summer and the retention of green vegetation throughout the summer. Exotic C4 grasslands can be distinguished from native ecosystems by their early-spring flush of annual grasses and forbs prior to the primary greening in late spring/early summer. Native C3 grasslands are more variable in response to rainfall and exhibit multiple greening/browning cycles within the year. They tend to green up earlier in the spring and brown off rapidly in response to high temperatures and low rainfall. Exotic C3 grasslands also green up in early spring but exhibit a more traditional unimodal

  8. Are cicadas (Diceroprocta apache) both a "keystone" and a "critical-link" species in lower Colorado River riparian communities?

    USGS Publications Warehouse

    Andersen, Douglas C.

    1994-01-01

    Apache cicada (Homoptera: Cicadidae: Diceroprocta apache Davis) densities were estimated to be 10 individuals/m2 within a closed-canopy stand of Fremont cottonwood (Populus fremontii) and Goodding willow (Salix gooddingii) in a revegetated site adjacent to the Colorado River near Parker, Arizona. Coupled with data drawn from the literature, I estimate that up to 1.3 cm (13 1/m2) of water may be added to the upper soil layers annually through the feeding activities of cicada nymphs. This is equivalent to 12% of the annual precipitation received in the study area. Apache cicadas may have significant effects on ecosystem functioning via effects on water transport and thus act as a critical-link species in this southwest desert riverine ecosystem. Cicadas emerged later within the cottonwood-willow stand than in relatively open saltcedar-mesquite stands; this difference in temporal dynamics would affect their availability to several insectivorous bird species and may help explain the birds' recent declines. Resource managers in this region should be sensitive to the multiple and strong effects that Apache cicadas may have on ecosystem structure and functioning.

  9. The Geisinger MyCode Community Health Initiative: an electronic health record-linked biobank for Precision Medicine research

    PubMed Central

    Carey, David J.; Fetterolf, Samantha N.; Davis, F. Daniel; Faucett, William A.; Kirchner, H. Lester; Mirshahi, Uyenlinh; Murray, Michael F.; Smelser, Diane T.; Gerhard, Glenn S.; Ledbetter, David H.

    2015-01-01

    Purpose Geisinger Health System (GHS) provides an ideal platform for Precision Medicine. Key elements are the integrated health system, stable patient population, and electronic health record (EHR) infrastructure. In 2007 Geisinger launched MyCode®, a system-wide biobanking program to link samples and EHR data for broad research use. Methods Patient-centered input into MyCode® was obtained using participant focus groups. Participation in MyCode® is based on opt-in informed consent and allows recontact, which facilitates collection of data not in the EHR, and, since 2013, the return of clinically actionable results to participants. MyCode® leverages Geisinger’s technology and clinical infrastructure for participant tracking and sample collection. Results MyCode® has a consent rate of >85% with more than 90,000 participants currently, with ongoing enrollment of ~4,000 per month. MyCode® samples have been used to generate molecular data, including high-density genotype and exome sequence data. Genotype and EHR-derived phenotype data replicate previously reported genetic associations. Conclusion The MyCode® project has created resources that enable a new model for translational research that is faster, more flexible, and more cost effective than traditional clinical research approaches. The new model is scalable, and will increase in value as these resources grow and are adopted across multiple research platforms. PMID:26866580

  10. Biomarkers for prostate cancer.

    PubMed

    Makarov, Danil V; Loeb, Stacy; Getzenberg, Robert H; Partin, Alan W

    2009-01-01

    The development of biomarkers for prostate cancer screening, detection, and prognostication has revolutionized the management of this disease. Prostate-specific antigen (PSA) is a useful, though not specific, biomarker for detecting prostate cancer. We review the literature on prostate cancer biomarkers, including serum markers (PAP, tPSA, fPSA, proPSA, PSAD, PSAV, PSADT, EPCA, and EPCA-2), tissue markers (AMACR, methylated GSTP1, and the TMPRSS2-ETS gene rearrangement), and a urine marker (DD3PCA3/UPM-3). Future research should focus on validation of already existing biomarkers and the discovery of new markers to identify men with aggressive prostate cancer.

  11. Linking the distribution of (210)Po and (210)Pb with plankton community along Line P, Northeast Subarctic Pacific.

    PubMed

    Choi, Hiu Yan; Stewart, Gillian M; Lomas, Michael W; Kelly, Roger P; Moran, S Bradley

    2014-12-01

    Depth profiles of (210)Po and (210)Pb activity and phytoplankton and zooplankton abundance were collected during two cruises along the Canadian time-series Line P in the Northeast Subarctic Pacific (ranging from 48o39 N to 50o00 N and 126o40 W to 145o00 W) in August 2010 and February 2011 to evaluate connections between the planktonic community and distributions of these radionuclides in the upper 500 m of the water column. Statistical analysis indicates that (210)Po is more effectively removed from the surface ocean when large (>0.1 mg ind(-1) dry wt) zooplankton dominate, and is less effectively scavenged when the picoplankton Synechococcus is present at high concentrations (>1 × 10(5) cells ml(-1)). While the zooplankton field data are consistent with previous lab studies and field observations, the phytoplankton results seem to conflict with recent evidence that small cells may contribute significantly to export in other oligotrophic regions. Differences in ecosystem mechanisms between the Subarctic Pacific and other oligotrophic systems that limit the contribution of small cells to sinking flux remain to be identified.

  12. Psychotic experiences are linked to cannabis use in adolescents in the community because of common underlying environmental risk factors.

    PubMed

    Shakoor, Sania; Zavos, Helena M S; McGuire, Philip; Cardno, Alastair G; Freeman, Daniel; Ronald, Angelica

    2015-06-30

    Cannabis users are more likely to have psychotic experiences (PEs). The degree to which these associations are driven by genetic or environmental influences in adolescence is unknown. This study estimated the genetic and environmental contributions to the relationship between cannabis use and PEs. Specific PEs were measured in a community-based twin sample (4830 16-year-old pairs) using self-reports and parent-reports. Adolescents reported on ever using cannabis. Multivariate liability threshold structural equation model-fitting was conducted. Cannabis use was significantly correlated with PEs. Modest heritability (37%), common environmental influences (55%) and unique environment (8%) were found for cannabis use. For PEs, modest heritability (27-54%), unique environmental influences (E=12-50%) and little common environmental influences (11-20%), with the exception of parent-rated Negative Symptoms (42%), were reported. Environmental influences explained all of the covariation between cannabis use and paranoia, cognitive disorganization and parent-rated negative symptoms (bivariate common environment=69-100%, bivariate unique environment=28-31%), whilst the relationship between cannabis use and hallucinations indicated familial influences. Cannabis use explains 2-5% of variance in positive, cognitive, and negative PEs. Cannabis use and psychotic experience co-occur due to environmental factors. Focus on specific environments may reveal why adolescent cannabis use and psychotic experiences tend to 'travel together'.

  13. Direct and indirect costs of co-infection in the wild: Linking gastrointestinal parasite communities, host hematology, and immune function☆

    PubMed Central

    Budischak, Sarah A.; Jolles, Anna E.; Ezenwa, Vanessa O.

    2012-01-01

    Most animals are concurrently infected with multiple parasites, and interactions among these parasites may influence both disease dynamics and host fitness. However, the sublethal costs of parasite infections are difficult to measure and the effects of concomitant infections with multiple parasite species on individual physiology and fitness are poorly described for wild hosts. To understand the direct and indirect physiological costs of co-infection, we investigated the relationships among gastrointestinal parasite richness, species identity, and abundance and host hematological parameters, body condition, and investment in lymphocyte defenses. Using aggregate-scale parasite data from African buffalo (Syncerus caffer), we found few direct or indirect associations between infection and hematology in male hosts, and no significant associations were observed in female hosts or with respect to body condition in either sex. These results suggest that only strong physiological effects are detectable with aggregate-scale parasite data, and that hematological variables may be more sensitive to changes in condition than standard body fat condition indices. Analyses accounting for parasite species identity in female buffalo revealed that different parasites show distinct relationships with host hematology, body condition, and immune investment. However, four of six species-specific associations were obscured when parasites were considered in combination. Overall, fitness-related physiological mediators such as hematological indices may provide assessments of direct and indirect effects of parasite infection, particularly when parasite species identity and community composition are considered. PMID:24533308

  14. Linking the distribution of (210)Po and (210)Pb with plankton community along Line P, Northeast Subarctic Pacific.

    PubMed

    Choi, Hiu Yan; Stewart, Gillian M; Lomas, Michael W; Kelly, Roger P; Moran, S Bradley

    2014-12-01

    Depth profiles of (210)Po and (210)Pb activity and phytoplankton and zooplankton abundance were collected during two cruises along the Canadian time-series Line P in the Northeast Subarctic Pacific (ranging from 48o39 N to 50o00 N and 126o40 W to 145o00 W) in August 2010 and February 2011 to evaluate connections between the planktonic community and distributions of these radionuclides in the upper 500 m of the water column. Statistical analysis indicates that (210)Po is more effectively removed from the surface ocean when large (>0.1 mg ind(-1) dry wt) zooplankton dominate, and is less effectively scavenged when the picoplankton Synechococcus is present at high concentrations (>1 × 10(5) cells ml(-1)). While the zooplankton field data are consistent with previous lab studies and field observations, the phytoplankton results seem to conflict with recent evidence that small cells may contribute significantly to export in other oligotrophic regions. Differences in ecosystem mechanisms between the Subarctic Pacific and other oligotrophic systems that limit the contribution of small cells to sinking flux remain to be identified. PMID:24629375

  15. Linking hydrologic, physical and chemical habitat environments for the potential assessment of fish community rehabilitation in a developing city

    NASA Astrophysics Data System (ADS)

    Zhao, C. S.; Yang, S. T.; Liu, C. M.; Dou, T. W.; Yang, Z. L.; Yang, Z. Y.; Liu, X. L.; Xiang, H.; Nie, S. Y.; Zhang, J. L.; Mitrovic, S. M.; Yu, Q.; Lim, R. P.

    2015-04-01

    Aquatic ecological rehabilitation is increasingly attracting considerable public and research attention. An effective method that requires less data and expertise would help in the assessment of rehabilitation potential and in the monitoring of rehabilitation activities as complicated theories and excessive data requirements on assemblage information make many current assessment models expensive and limit their wide use. This paper presents an assessment model for restoration potential which successfully 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. In this model three newly developed sub-models, integrated habitat index (IHSI), integrated ecological niche breadth (INB) and integrated ecological niche overlap (INO), are established to study spatial heterogeneity of the restoration potential of fish assemblages based on gradient methods of habitat suitability index and ecological niche models. To reduce uncertainties in the model, as many fish species as possible, including important native fish, were selected as dominant species with monitoring occurring over several seasons to comprehensively select key habitat factors. Furthermore, a detrended correspondence analysis (DCA) was employed prior to a canonical correspondence analysis (CCA) of the data to avoid the "arc effect" in the selection of key habitat factors. Application of the model to data collected at Jinan City, China proved effective reveals that three lower potential regions that should be targeted in future aquatic ecosystem rehabilitation programs. They were well validated by the distribution of two habitat parameters: river width and transparency. River width positively influenced and transparency negatively influenced fish assemblages. The model can be applied for monitoring the effects of fish assemblage restoration

  16. A link between gut community metabolism and pathogenesis: molecular hydrogen-stimulated glucarate catabolism aids Salmonella virulence

    PubMed Central

    Lamichhane-Khadka, Reena; Benoit, Stéphane L.; Maier, Susan E.; Maier, Robert J.

    2013-01-01

    Glucarate, an oxidized product of glucose, is a major serum organic acid in humans. Still, its role as a carbon source for a pathogen colonizing hosts has not been studied. We detected high-level expression of a potential glucarate permease encoding gene gudT when Salmonella enterica serovar Typhimurium are exposed to hydrogen gas (H2), a gaseous by-product of gut commensal metabolism. A gudT strain of Salmonella is deficient in glucarate-dependent growth, however, it can still use other monosaccharides, such as glucose or galactose. Complementation of the gudT mutant with a plasmid harbouring gudT restored glucarate-dependent growth to wild-type (WT) levels. The gudT mutant exhibits attenuated virulence: the mean time of death for mice inoculated with WT strain was 2 days earlier than for mice inoculated with the gudT strain. At 4 days postinoculation, liver and spleen homogenates from mice inoculated with a gudT strain contained significantly fewer viable Salmonella than homogenates from animals inoculated with the parent. The parent strain grew well H2-dependently in a minimal medium with amino acids and glucarate provided as the sole carbon sources, whereas the gudT strain achieved approximately 30% of the parent strain's yield. Glucarate-mediated growth of a mutant strain unable to produce H2 was stimulated by H2 addition, presumably owing to the positive transcriptional response to H2. Gut microbiota-produced molecular hydrogen apparently signals Salmonella to catabolize an alternative carbon source available in the host. Our results link a gut microbiome-produced diffusible metabolite to augmenting bacterial pathogenesis. PMID:24307595

  17. Linking community tolerance and structure with low metallic contamination: a field study on 13 biofilms sampled across the Seine river basin.

    PubMed

    Fechner, Lise C; Gourlay-Francé, Catherine; Tusseau-Vuillemin, Marie-Hélène

    2014-03-15

    It is difficult to assess the biological consequences of diffuse water contamination by micropollutants which are present in rivers at low, even sublethal levels. River biofilms, which respond quickly to changes of environmental parameters, are good candidates to acquire knowledge on the response of aquatic organisms to diffuse chemical contamination in the field. The study was designed as an attempt to link biofilm metal tolerance and metallic contamination in a field survey covering 13 different sampling sites in the Seine river basin (north of France) with low contamination levels. Cd and Zn tolerance of heterotrophic communities was assessed using a short-term toxicity test based on β-glucosidase activity. Metal tolerance levels varied between sites but there was no obvious correlation between tolerance and corresponding water contamination levels for Cd and Zn. Indeed, metallic contamination at the sampling sites remained subtle when compared to water quality standards (only two sampling sites had either Zn or both Cu and Zn concentrations exceeding the Environmental Quality Standards set by the EU Water Framework Directive). Yet, multivariate analysis of the data using Partial Least Squares Regression revealed that both metallic and environmental parameters were important variables explaining the variability of metal tolerance levels. Automated Ribosomal Intergenic Spacer Analysis (ARISA) was also performed on both bacterial and eukaryotic biofilm communities from the 13 sampling sites. Multivariate analysis of ARISA fingerprints revealed that biofilms with similar tolerance levels have similar ARISA profiles. Those results confirm that river biofilms are potential indicators of low, diffuse contamination levels of aquatic systems.

  18. Microbial food web mapping: linking carbon cycling and community structure in soils through pyrosequencing enabled stable isotope probing

    SciTech Connect

    Buckley, Daniel H.

    2015-03-15

    Soil represents a massive reservoir of active carbon and climate models vary dramatically in predicting how this carbon will respond to climate change over the coming century. A major cause of uncertainty is that we still have a very limited understand the microorganisms that dominate the soil carbon cycle. The vast majority of soil microbes cannot be cultivated in the laboratory and the diversity of organisms and enzymes that participate in the carbon cycle is staggeringly complex. We have developed a new toolbox for exploring the carbon cycle and the metabolic and ecological characteristics of uncultivated microorganisms. The high-resolution nucleic acid stable isotope probing approach that we have developed makes it possible to characterize microbial carbon cycling dynamics in soil. The approach allows us to track multiple 13C-labeled substrates into thousands of microbial taxa over time. Using this approach we have discovered several major lineages of uncultivated microorganisms that participate in cellulose metabolism and are found widely in soils (including Verrucomicrobia and Chloroflexi, which have not previously been implicated as major players in the soil carbon cycle). Furthermore, isotopic labelling of nucleic acids enables community genomics and permits genome fragment binning for a majority of these cellulolytic microorganisms allowing us to explore the metabolic underpinnings of cellulose degradation. This approach has allowed us to describe unexpected dynamics of carbon metabolism with different microbial taxa exhibiting characteristic patterns of carbon substrate incorporation, indicative of distinct ecological strategies. The data we describe allows us to characterize the activity of novel microorganisms as they occur in the environment and these data provide a basis for understanding how the physiological traits of discrete microorganisms sum to govern the complex responses of the soil carbon cycle.

  19. Variations in diatom communities at genus and species levels in peatlands (central China) linked to microhabitats and environmental factors.

    PubMed

    Chen, Xu; Bu, Zhaojun; Stevenson, Mark A; Cao, Yanmin; Zeng, Linghan; Qin, Bo

    2016-10-15

    Peatlands are a specialized type of organic wetlands, fulfilling essential roles as global carbon sinks, headwaters of rivers and biodiversity hotspots. Despite their importance, peatlands are being lost at an alarming rate due to human disturbance and climatic variability. Both the scientific and regulatory communities have focused considerable attention on developing tools for assessing environmental changes in peatlands. Diatoms are widely used in biomonitoring studies of lakes, rivers and streams as they have high abundance, specific ecological preferences and can respond rapidly to environmental change. However, diatom-based assessment studies in peatlands remain limited. The aims of this study were to identify indicator species and genus for three types of habitats (hummocks, hollows and ditch edges) in peatlands (central China), to examine the effects of physiochemical factors on diatom composition at genus and species levels, and to compare the efficiency of species- and genus-level identification in environmental assessment. Our results revealed that hummocks were characterized by drought-tolerant diatoms, while hollows were dominated by species and genus preferring wet conditions. Ditch edges were characterized by diatoms with different life strategies. Depth to water table, redox potential, conductivity and calcium were significant predictors of both genus- and species-level composition. According to ordination analyses, pH was not correlated with species composition while it was a significant factor associated with genus-level composition. Genus-level composition outperformed species composition in describing the response of diatoms to environmental variables. Our results indicate that diatoms can be useful environmental indicators of peatlands, and show that genus-level taxonomic analysis can be a potential tool for assessing environmental change in peatlands. PMID:27289395

  20. A community outbreak of Vero cytotoxin producing Escherichia coli O157 infection linked to a small farm dairy.

    PubMed

    Clark, A; Morton, S; Wright, P; Corkish, J; Bolton, F J; Russell, J

    1997-12-12

    A community outbreak of infection with Vero cytotoxin producing Escherichia coli O157 (VTEC 0157) occurred in a small area of north west England in 1996. An outbreak control team was established to investigate the outbreak and implement control measures. Nine people developed symptomatic infections with VTEC O157, and a further three were found to be excreting the bacteria. All were infected with the same genotype of VTEC O157. Three children under 5 years of age and one adult were admitted to hospital. One child developed haemolytic uraemic syndrome. All cases recovered. All primary cases had consumed milk from a particular farm dairy. No other common foods were identified. The farm dairy had a faulty pasteuriser and the potential for post pasteurisation contamination existed. VTEC O157 was isolated from a milk sock specimen and from two cows, but these strains differed from that infecting the cases. All local doctors and the public were alerted and advised about preventative measures. Distribution of unpasteurised milk from the farm was discontinued as was the sale of pasteurised milk when the faulty pasteuriser was discovered. A replacement pasteuriser was installed and checked before milk was released for human consumption. No conclusive evidence of the origin of this outbreak was found, but the farm was the most probable source. The investigations raised concerns about the distribution of VTEC O157 colonised dairy cattle, the natural history of such colonisation, the effectiveness of pasteurisation with respect to the elimination of VTEC O157, and the effectiveness of current legislation for the prevention and control of milkborne infection.

  1. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community

    PubMed Central

    Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

    2014-01-01

    Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

  2. Linking N2O emissions from biochar-amended soil to the structure and function of the N-cycling microbial community.

    PubMed

    Harter, Johannes; Krause, Hans-Martin; Schuettler, Stefanie; Ruser, Reiner; Fromme, Markus; Scholten, Thomas; Kappler, Andreas; Behrens, Sebastian

    2014-03-01

    Nitrous oxide (N2O) contributes 8% to global greenhouse gas emissions. Agricultural sources represent about 60% of anthropogenic N2O emissions. Most agricultural N2O emissions are due to increased fertilizer application. A considerable fraction of nitrogen fertilizers are converted to N2O by microbiological processes (that is, nitrification and denitrification). Soil amended with biochar (charcoal created by pyrolysis of biomass) has been demonstrated to increase crop yield, improve soil quality and affect greenhouse gas emissions, for example, reduce N2O emissions. Despite several studies on variations in the general microbial community structure due to soil biochar amendment, hitherto the specific role of the nitrogen cycling microbial community in mitigating soil N2O emissions has not been subject of systematic investigation. We performed a microcosm study with a water-saturated soil amended with different amounts (0%, 2% and 10% (w/w)) of high-temperature biochar. By quantifying the abundance and activity of functional marker genes of microbial nitrogen fixation (nifH), nitrification (amoA) and denitrification (nirK, nirS and nosZ) using quantitative PCR we found that biochar addition enhanced microbial nitrous oxide reduction and increased the abundance of microorganisms capable of N2-fixation. Soil biochar amendment increased the relative gene and transcript copy numbers of the nosZ-encoded bacterial N2O reductase, suggesting a mechanistic link to the observed reduction in N2O emissions. Our findings contribute to a better understanding of the impact of biochar on the nitrogen cycling microbial community and the consequences of soil biochar amendment for microbial nitrogen transformation processes and N2O emissions from soil. PMID:24067258

  3. Respiratory Toxicity Biomarkers

    EPA Science Inventory

    The advancement in high throughput genomic, proteomic and metabolomic techniques have accelerated pace of lung biomarker discovery. A recent growth in the discovery of new lung toxicity/disease biomarkers have led to significant advances in our understanding of pathological proce...

  4. Organic biomarker records spanning the last 34,800 years from the southeastern Brazilian upper slope: links between sea surface temperature, displacement of the Brazil Current, and marine productivity

    NASA Astrophysics Data System (ADS)

    Lourenço, Rafael André; de Mahiques, Michel Michaelovitch; Wainer, Ilana Elazari Klein Coaracy; Rosell-Melé, Antoni; Bícego, Márcia Caruso

    2016-06-01

    Collective assessment of marine and terrigenous organic biomarkers was performed on a sediment core spanning the last 34,800 years on the upper slope southeast of Brazil to verify the signatures of climatic variations in sea surface temperature (SST), marine productivity, and the flux of terrigenous material in this region. This evaluation is based on marine and terrigenous proxies including alkenones, chlorins, aliphatic hydrocarbons, n-alcohols, and fatty acids. This first report of organic biomarker data for this region confirms a correlation between SST, changes in terrigenous organic matter flow into the ocean, and marine productivity over the last 34.8 ka as a response to the displacement of the Brazil Current. Conditions prevailing during marine isotopic stage (MIS) 3 may be considered intermediate between the last glacial maximum (LGM) and the Late Holocene. For MIS 2, a period of low relative sea level, it was verified that the lowest SSTs were associated with the LGM and higher marine productivity. SST increased by up to 4.4 °C between the LGM and the Holocene. This reveals synchronicity between SST on the southeastern Brazilian upper slope and the North Atlantic Ocean SST records reported in earlier studies.

  5. Organic biomarker records spanning the last 34,800 years from the southeastern Brazilian upper slope: links between sea surface temperature, displacement of the Brazil Current, and marine productivity

    NASA Astrophysics Data System (ADS)

    Lourenço, Rafael André; de Mahiques, Michel Michaelovitch; Wainer, Ilana Elazari Klein Coaracy; Rosell-Melé, Antoni; Bícego, Márcia Caruso

    2016-10-01

    Collective assessment of marine and terrigenous organic biomarkers was performed on a sediment core spanning the last 34,800 years on the upper slope southeast of Brazil to verify the signatures of climatic variations in sea surface temperature (SST), marine productivity, and the flux of terrigenous material in this region. This evaluation is based on marine and terrigenous proxies including alkenones, chlorins, aliphatic hydrocarbons, n-alcohols, and fatty acids. This first report of organic biomarker data for this region confirms a correlation between SST, changes in terrigenous organic matter flow into the ocean, and marine productivity over the last 34.8 ka as a response to the displacement of the Brazil Current. Conditions prevailing during marine isotopic stage (MIS) 3 may be considered intermediate between the last glacial maximum (LGM) and the Late Holocene. For MIS 2, a period of low relative sea level, it was verified that the lowest SSTs were associated with the LGM and higher marine productivity. SST increased by up to 4.4 °C between the LGM and the Holocene. This reveals synchronicity between SST on the southeastern Brazilian upper slope and the North Atlantic Ocean SST records reported in earlier studies.

  6. Biomarkers in overactive bladder.

    PubMed

    Bhide, Alka A; Cartwright, Rufus; Khullar, Vik; Digesu, G Alessandro

    2013-07-01

    A biomarker is an indicator of a particular disease. It is generally used to define the presence (diagnostic biomarker), severity, progression (prognostic biomarker) of a condition and/or its response to a specific treatment (predictive biomarker). Biomarkers can be specific cells, enzymes, hormones, genes or gene products, which can be detected and measured in parts of the body such as blood, urine or tissue. Therefore, biomarkers have been suggested to play an important role in both the clinical assessment and the management of patients, as well as in the research setting. Recently, interest has gathered in urinary biomarkers as a tool to assess overactive bladder (OAB), potentially playing a role in the diagnosis, disease progression and monitoring response to treatment. Urinary biomarkers identified so far include nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), prostaglandins, cytokines and C-reactive protein. The aim of this review was to review the published literature on biomarkers in OAB. A literature review using Pub Med, clinicaltrials.gov and the controlled trials online registries was performed from 1970 up to June 2012. The search keywords were: the International Continence Society (ICS) definition of "OAB", "nerve growth fac- tor" (NGF), "brain derived growth factor" (BDNF), "prostaglandins," "cytokines," "genetic biomarkers" and "C reactive protein".The results were limited for fully published English-language articles. The search was then subsequently expanded to include urinary biomarkers in interstitial cystitis and bladder pain where relevant. Each of the studies/articles was reviewed, interpreted and discussed to consider the role of urinary biomarkers in OAB. Using the search criteria, a total of 20 studies (animal and human) that investigated the role of urinary biomarkers in OAB were identified. Full text versions of these articles were obtained and reviewed. Studies on NGF suggested that urinary levels were higher in OAB

  7. A Case Study of Community College Students' Perceptions of Linked Courses Instructors' Use of Chickering and Gamson's (1987) "Principles for Good Practice in Undergraduate Education" within Student Learning-Communities and the Importance of the Principles in Helping Students with Their Academic Writing Skills

    ERIC Educational Resources Information Center

    Cousins, Claudia L.

    2012-01-01

    The purpose of this single-site case study was to explore and describe community college students' perceptions of linked courses instructors' use of Chickering and Gamson's (1987) Principles for Good Practice in Undergraduate Education within student learning communities and students' perceptions of how important the principles were in helping…

  8. Effectiveness of a school-community linked program on physical activity levels and health-related quality of life for adolescent girls

    PubMed Central

    2014-01-01

    Background This study evaluated the effectiveness of a school-community program on Health-Related Quality of Life (HRQoL; the primary outcome), physical activity (PA), and potential mediators of PA among adolescent girls living in low-socioeconomic rural/regional settings. Method The study was a cluster-randomized controlled trial. Twelve communities with the requisite sports clubs and facilities were paired according to relevant criteria; one of each pair was randomly assigned to the intervention or control condition. Eight schools per condition were randomly selected from these communities and the intervention was conducted over one school year (2011). Female students in grades 7–9 in intervention schools participated in two 6-session PA units – a sport unit (football or tennis) and a recreational unit (leisure centre-based). These were incorporated into physical education (PE) curriculum and linked to PA opportunities for participation outside school. Students were surveyed at baseline and endpoint, self-reporting impact on primary and secondary outcome measures (HRQoL, PA) and PA mediators (e.g. self-efficacy). Linear mixed models for two-group (intervention, control) and three-group (completers, non-completers, control) analyses were conducted with baseline value, age and BMI as covariates, group as a fixed effect and school as random cluster effect. Results Participants completing baseline and endpoint measures included: 358 intervention (baseline response rate 33.7%, retention rate 61.3%) and 256 control (14.1% and 84.0%). Adjustment for age and BMI made no substantive difference to outcomes, and there were no cluster effects. For HRQoL, after adjustment for baseline scores, the intervention group showed significantly higher scores on all three PedsQL scores (physical functioning: M ± SE = 83.9 ± 0.7, p = .005; psychosocial: 79.9 ± 0.8, p = .001; total score: 81.3 ± 0.7, p = .001) than the control group (80.9 ± 0

  9. Biomarkers in Autism

    PubMed Central

    Goldani, Andre A. S.; Downs, Susan R.; Widjaja, Felicia; Lawton, Brittany; Hendren, Robert L.

    2014-01-01

    Autism spectrum disorders (ASDs) are complex, heterogeneous disorders caused by an interaction between genetic vulnerability and environmental factors. In an effort to better target the underlying roots of ASD for diagnosis and treatment, efforts to identify reliable biomarkers in genetics, neuroimaging, gene expression, and measures of the body’s metabolism are growing. For this article, we review the published studies of potential biomarkers in autism and conclude that while there is increasing promise of finding biomarkers that can help us target treatment, there are none with enough evidence to support routine clinical use unless medical illness is suspected. Promising biomarkers include those for mitochondrial function, oxidative stress, and immune function. Genetic clusters are also suggesting the potential for useful biomarkers. PMID:25161627

  10. Fault2SHA- A European Working group to link faults and Probabilistic Seismic Hazard Assessment communities in Europe

    NASA Astrophysics Data System (ADS)

    Scotti, Oona; Peruzza, Laura

    2016-04-01

    The key questions we ask are: What is the best strategy to fill in the gap in knowledge and know-how in Europe when considering faults in seismic hazard assessments? Are field geologists providing the relevant information for seismic hazard assessment? Are seismic hazard analysts interpreting field data appropriately? Is the full range of uncertainties associated with the characterization of faults correctly understood and propagated in the computations? How can fault-modellers contribute to a better representation of the long-term behaviour of fault-networks in seismic hazard studies? Providing answers to these questions is fundamental, in order to reduce the consequences of future earthquakes and improve the reliability of seismic hazard assessments. An informal working group was thus created at a meeting in Paris in November 2014, partly financed by the Institute of Radioprotection and Nuclear Safety, with the aim to motivate exchanges between field geologists, fault modellers and seismic hazard practitioners. A variety of approaches were presented at the meeting and a clear gap emerged between some field geologists, that are not necessarily familiar with probabilistic seismic hazard assessment methods and needs and practitioners that do not necessarily propagate the "full" uncertainty associated with the characterization of faults. The group thus decided to meet again a year later in Chieti (Italy), to share concepts and ideas through a specific exercise on a test case study. Some solutions emerged but many problems of seismic source characterizations with people working in the field as well as with people tackling models of interacting faults remained. Now, in Wien, we want to open the group and launch a call for the European community at large to contribute to the discussion. The 2016 EGU session Fault2SHA is motivated by such an urgency to increase the number of round tables on this topic and debate on the peculiarities of using faults in seismic hazard

  11. The Link: Business, Education.

    ERIC Educational Resources Information Center

    AGB Reports, 1984

    1984-01-01

    An excerpt from "Corporate and Campus Cooperation: An Action Agenda" (a report from the Business-Higher Education Forum) explains some methods for strengthening the link between the business and education communities. (Author/MLW)

  12. Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data

    PubMed Central

    Tosas Auguet, Olga; Betley, Jason R.; Stabler, Richard A.; Patel, Amita; Ioannou, Avgousta; Marbach, Helene; Hearn, Pasco; Aryee, Anna; Goldenberg, Simon D.; Otter, Jonathan A.; Desai, Nergish; Karadag, Tacim; Grundy, Chris; Gaunt, Michael W.; Cooper, Ben S.; Edgeworth, Jonathan D.; Kypraios, Theodore

    2016-01-01

    Background Identifying and tackling the social determinants of infectious diseases has become a public health priority following the recognition that individuals with lower socioeconomic status are disproportionately affected by infectious diseases. In many parts of the world, epidemiologically and genotypically defined community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) strains have emerged to become frequent causes of hospital infection. The aim of this study was to use spatial models with adjustment for area-level hospital attendance to determine the transmission niche of genotypically defined CA- and health-care-associated (HA)-MRSA strains across a diverse region of South East London and to explore a potential link between MRSA carriage and markers of social and material deprivation. Methods and Findings This study involved spatial analysis of cross-sectional data linked with all MRSA isolates identified by three National Health Service (NHS) microbiology laboratories between 1 November 2011 and 29 February 2012. The cohort of hospital-based NHS microbiology diagnostic services serves 867,254 usual residents in the Lambeth, Southwark, and Lewisham boroughs in South East London, United Kingdom (UK). Isolates were classified as HA- or CA-MRSA based on whole genome sequencing. All MRSA cases identified over 4 mo within the three-borough catchment area (n = 471) were mapped to small geographies and linked to area-level aggregated socioeconomic and demographic data. Disease mapping and ecological regression models were used to infer the most likely transmission niches for each MRSA genetic classification and to describe the spatial epidemiology of MRSA in relation to social determinants. Specifically, we aimed to identify demographic and socioeconomic population traits that explain cross-area extra variation in HA- and CA-MRSA relative risks following adjustment for hospital attendance data. We explored the potential for associations with

  13. Impact of biomarker development on drug safety assessment

    SciTech Connect

    Marrer, Estelle; Dieterle, Frank

    2010-03-01

    Drug safety has always been a key aspect of drug development. Recently, the Vioxx case and several cases of serious adverse events being linked to high-profile products have increased the importance of drug safety, especially in the eyes of drug development companies and global regulatory agencies. Safety biomarkers are increasingly being seen as helping to provide the clarity, predictability, and certainty needed to gain confidence in decision making: early-stage projects can be stopped quicker, late-stage projects become less risky. Public and private organizations are investing heavily in terms of time, money and manpower on safety biomarker development. An illustrative and 'door opening' safety biomarker success story is the recent recognition of kidney safety biomarkers for pre-clinical and limited translational contexts by FDA and EMEA. This milestone achieved for kidney biomarkers and the 'know how' acquired is being transferred to other organ toxicities, namely liver, heart, vascular system. New technologies and molecular-based approaches, i.e., molecular pathology as a complement to the classical toolbox, allow promising discoveries in the safety biomarker field. This review will focus on the utility and use of safety biomarkers all along drug development, highlighting the present gaps and opportunities identified in organ toxicity monitoring. A last part will be dedicated to safety biomarker development in general, from identification to diagnostic tests, using the kidney safety biomarkers success as an illustrative example.

  14. Biomarker studies in northern Bohemia.

    PubMed Central

    Binková, B; Lewtas, J; Mísková, I; Rössner, P; Cerná, M; Mrácková, G; Peterková, K; Mumford, J; Meyer, S; Srám, R

    1996-01-01

    Studies were conducted in northern Bohemia to simultaneously evaluate personal exposures to air pollution in the form of respirable particles containing polycyclic aromatic hydrocarbons (PAHs) and biomarkers of exposure, biological effective dose, genetic effects, and metabolic susceptibility. The series of biomarkers included PAH metabolites in urine, urine mutagenicity, PAH-DNA adducts in white blood cells determined by 32P-postlabeling, PAH-albumin adducts determined by enzyme-linked immunosorbent assay (ELISA), DNA damage in lymphocytes detected by comet assay, chromosomal aberrations, sister chromatid exchanges, and glutathione S-transferase M1 (GSTM1) genotypes. For these studies, a group of women who work outdoors about 30% of their daily time was selected. In a pilot study, a group of women from a polluted area of the Teplice district (northern Bohemia) was compared with a group of women from a control district of southern Bohemia (Prachatice). In a follow-up repeated-measures study, a group of nonsmoking women from Teplice was sampled repeatedly during the winter season of 1993 to 1994. Personal exposure monitoring for respirable particles (< 2.5 microns) was conducted for the 24-hr period before collection of blood and urine. Particle extracts were analyzed for carcinogenic PAHs. In the pilot study and in the follow-up study, a highly significant correlation between individual personal exposures to PAHs and DNA adducts was found (r = 0.54, p = 0.016; r = 0.710, p < 0.001, respectively). The comet parameter (percentage DNA in tail; %T) correlated with exposures to respirable particles (r = 0.304, p = 0.015). The GSTM1 genotype had a significant effect on urinary PAH metabolites, urine mutagenicity, and comet parameters (% T and tail moment) when the GSTM1 genotype was considered as a single factor affecting these biomarkers. Multifactor analysis o variance considering exposure and adjusting the data for GSTM1, age, and diet showed that the effect of

  15. Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs

    SciTech Connect

    Parenteau, Mary N.; Jahnke, Linda L.; Farmer, Jack D.; Cady, Sherry L.

    2014-06-01

    The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5–6.0, and are very high in dissolved Fe(II) at 5.8–5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. Finally, this study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs—environmental conditions that have been previously identified as highly relevant for Mars exploration.

  16. Production and Early Preservation of Lipid Biomarkers in Iron Hot Springs

    PubMed Central

    Jahnke, Linda L.; Farmer, Jack D.; Cady, Sherry L.

    2014-01-01

    Abstract The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51–54°C, pH 5.5–6.0, and are very high in dissolved Fe(II) at 5.8–5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs—environmental conditions that have been previously identified as highly relevant for Mars exploration. Key Words: Lipid biomarkers—Photosynthesis—Iron—Hot springs—Mars. Astrobiology 14, 502–521. PMID:24886100

  17. Production and early preservation of lipid biomarkers in iron hot springs.

    PubMed

    Parenteau, Mary N; Jahnke, Linda L; Farmer, Jack D; Cady, Sherry L

    2014-06-01

    The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51-54°C, pH 5.5-6.0, and are very high in dissolved Fe(II) at 5.8-5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs--environmental conditions that have been previously identified as highly relevant for Mars exploration.

  18. Production and early preservation of lipid biomarkers in iron hot springs.

    PubMed

    Parenteau, Mary N; Jahnke, Linda L; Farmer, Jack D; Cady, Sherry L

    2014-06-01

    The bicarbonate-buffered anoxic vent waters at Chocolate Pots hot springs in Yellowstone National Park are 51-54°C, pH 5.5-6.0, and are very high in dissolved Fe(II) at 5.8-5.9 mg/L. The aqueous Fe(II) is oxidized by a combination of biotic and abiotic mechanisms and precipitated as primary siliceous nanophase iron oxyhydroxides (ferrihydrite). Four distinct prokaryotic photosynthetic microbial mat types grow on top of these iron deposits. Lipids were used to characterize the community composition of the microbial mats, link source organisms to geologically significant biomarkers, and investigate how iron mineralization degrades the lipid signature of the community. The phospholipid and glycolipid fatty acid profiles of the highest-temperature mats indicate that they are dominated by cyanobacteria and green nonsulfur filamentous anoxygenic phototrophs (FAPs). Diagnostic lipid biomarkers of the cyanobacteria include midchain branched mono- and dimethylalkanes and, most notably, 2-methylbacteriohopanepolyol. Diagnostic lipid biomarkers of the FAPs (Chloroflexus and Roseiflexus spp.) include wax esters and a long-chain tri-unsaturated alkene. Surprisingly, the lipid biomarkers resisted the earliest stages of microbial degradation and diagenesis to survive in the iron oxides beneath the mats. Understanding the potential of particular sedimentary environments to capture and preserve fossil biosignatures is of vital importance in the selection of the best landing sites for future astrobiological missions to Mars. This study explores the nature of organic degradation processes in moderately thermal Fe(II)-rich groundwater springs--environmental conditions that have been previously identified as highly relevant for Mars exploration. PMID:24886100

  19. [Biomarkers in Alzheimer's disease].

    PubMed

    García-Ribas, G; López-Sendón Moreno, J L; García-Caldentey, J

    2014-04-01

    The new diagnostic criteria for Alzheimer's disease (AD) include brain imaging and cerebrospinal fluid (CSF) biomarkers, with the aim of increasing the certainty of whether a patient has an ongoing AD neuropathologic process or not. Three CSF biomarkers, Aß42, total tau, and phosphorylated tau, reflect the core pathological features of AD. It is already known that these pathological processes of AD starts decades before the first symptoms, so these biomarkers may provide means of early disease detection. At least three stages of AD could be identified: preclinical AD, mild cognitive impairment due to AD, and dementia due to AD. In this review, we aim to summarize the CSF biomarker data available for each of these stages. We also review the actual research on blood-based biomarkers. Recent studies on healthy elderly subjects and on carriers of dominantly inherited AD mutations have also found biomarker changes that allow separate groups in these preclinical stages. These studies may aid for segregate populations in clinical trials and objectively evaluate if there are changes over the pathological processes of AD. Limits to widespread use of CSF biomarkers, apart from the invasive nature of the process itself, is the higher coefficient of variation for the analyses between centres. It requires strict pre-analytical and analytical procedures that may make feasible multi-centre studies and global cut-off points for the different stages of AD.

  20. New serological biomarkers of inflammatory bowel disease.

    PubMed

    Li, Xuhang; Conklin, Laurie; Alex, Philip

    2008-09-01

    Serological biomarkers in inflammatory bowel disease (IBD) are a rapidly expanding list of non-invasive tests for objective assessments of disease activity, early diagnosis, prognosis evaluation and surveillance. This review summarizes both old and new biomarkers in IBD, but focuses on the development and characterization of new serological biomarkers (identified since 2007). These include five new anti-glycan antibodies, anti-chitobioside IgA (ACCA), anti-laminaribioside IgG (ALCA), anti-manobioside IgG (AMCA), and antibodies against chemically synthesized (Sigma) two major oligomannose epitopes, Man alpha-1,3 Man alpha-1,2 Man (SigmaMan3) and Man alpha-1,3 Man alpha-1,2 Man alpha-1,2 Man (SigmaMan4). These new biomarkers serve as valuable complementary tools to existing biomarkers not only in differentiating Crohn's disease (CD), ulcerative colitis (UC), normal and other non-IBD gut diseases, but also in predicting disease involvement (ileum vs colon), IBD risk (as subclinical biomarkers), and disease course (risk of complication and surgery). Interestingly, the prevalence of the antiglycan antibodies, including anti-Saccharomyces cerevisiae antibodies (ASCA), ALCA and AMCA, was found to be associated with single nucleotide polymorphisms (SNPs) of IBD susceptible genes such as NOD2/CARD15, NOD1/CARD4, toll-like receptors (TLR) 2 and 4, and beta-defensin-1. Furthermore, a gene dosage effect was observed: anti-glycan positivity became more frequent as the number of NOD2/CARD15 SNPS increased. Other new serum/plasma IBD biomarkers reviewed include ubiquitination factor E4A (UBE4A), CXCL16 (a chemokine), resistin, and apolipoprotein A-IV. This review also discusses the most recent studies in IBD biomarker discovery by the application of new technologies such as proteomics, fourier transform near-infrared spectroscopy, and multiplex enzyme-linked immunosorbent assay (ELISA)'s (with an emphasis on cytokine/chemokine profiling). Finally, the prospects of developing more

  1. New serological biomarkers of inflammatory bowel disease.

    PubMed

    Li, Xuhang; Conklin, Laurie; Alex, Philip

    2008-09-01

    Serological biomarkers in inflammatory bowel disease (IBD) are a rapidly expanding list of non-invasive tests for objective assessments of disease activity, early diagnosis, prognosis evaluation and surveillance. This review summarizes both old and new biomarkers in IBD, but focuses on the development and characterization of new serological biomarkers (identified since 2007). These include five new anti-glycan antibodies, anti-chitobioside IgA (ACCA), anti-laminaribioside IgG (ALCA), anti-manobioside IgG (AMCA), and antibodies against chemically synthesized (Sigma) two major oligomannose epitopes, Man alpha-1,3 Man alpha-1,2 Man (SigmaMan3) and Man alpha-1,3 Man alpha-1,2 Man alpha-1,2 Man (SigmaMan4). These new biomarkers serve as valuable complementary tools to existing biomarkers not only in differentiating Crohn's disease (CD), ulcerative colitis (UC), normal and other non-IBD gut diseases, but also in predicting disease involvement (ileum vs colon), IBD risk (as subclinical biomarkers), and disease course (risk of complication and surgery). Interestingly, the prevalence of the antiglycan antibodies, including anti-Saccharomyces cerevisiae antibodies (ASCA), ALCA and AMCA, was found to be associated with single nucleotide polymorphisms (SNPs) of IBD susceptible genes such as NOD2/CARD15, NOD1/CARD4, toll-like receptors (TLR) 2 and 4, and beta-defensin-1. Furthermore, a gene dosage effect was observed: anti-glycan positivity became more frequent as the number of NOD2/CARD15 SNPS increased. Other new serum/plasma IBD biomarkers reviewed include ubiquitination factor E4A (UBE4A), CXCL16 (a chemokine), resistin, and apolipoprotein A-IV. This review also discusses the most recent studies in IBD biomarker discovery by the application of new technologies such as proteomics, fourier transform near-infrared spectroscopy, and multiplex enzyme-linked immunosorbent assay (ELISA)'s (with an emphasis on cytokine/chemokine profiling). Finally, the prospects of developing more

  2. Linking community tolerance and structure with low metallic contamination: a field study on 13 biofilms sampled across the Seine river basin.

    PubMed

    Fechner, Lise C; Gourlay-Francé, Catherine; Tusseau-Vuillemin, Marie-Hélène

    2014-03-15

    It is difficult to assess the biological consequences of diffuse water contamination by micropollutants which are present in rivers at low, even sublethal levels. River biofilms, which respond quickly to changes of environmental parameters, are good candidates to acquire knowledge on the response of aquatic organisms to diffuse chemical contamination in the field. The study was designed as an attempt to link biofilm metal tolerance and metallic contamination in a field survey covering 13 different sampling sites in the Seine river basin (north of France) with low contamination levels. Cd and Zn tolerance of heterotrophic communities was assessed using a short-term toxicity test based on β-glucosidase activity. Metal tolerance levels varied between sites but there was no obvious correlation between tolerance and corresponding water contamination levels for Cd and Zn. Indeed, metallic contamination at the sampling sites remained subtle when compared to water quality standards (only two sampling sites had either Zn or both Cu and Zn concentrations exceeding the Environmental Quality Standards set by the EU Water Framework Directive). Yet, multivariate analysis of the data using Partial Least Squares Regression revealed that both metallic and environmental parameters were important variables explaining the variability of metal tolerance levels. Automated Ribosomal Intergenic Spacer Analysis (ARISA) was also performed on both bacterial and eukaryotic biofilm communities from the 13 sampling sites. Multivariate analysis of ARISA fingerprints revealed that biofilms with similar tolerance levels have similar ARISA profiles. Those results confirm that river biofilms are potential indicators of low, diffuse contamination levels of aquatic systems. PMID:24429101

  3. Why commercial broadband satellites absolutely must have laser intersatellite links (ISLs) and how the free-space laser communications community could let them down

    NASA Astrophysics Data System (ADS)

    Freidell, James E.

    1998-05-01

    Large commercial satellite programs needing high bandwidth inter-satellite links (ISLs) are growing rapidly in number. Precious few are visibly maturing. These commercial needs present greater customer diversity and opportunity for free- space laser communications application than the current plans of all the world's governments combined, multiplied manyfold. However, commercial customers generally do not have access to the independent, knowledgeable, but often heterogeneous laser communications expertise upon which government programs have historically relied. Moreover, commercial needs differ substantially from those of governments, particularly in the areas of price sensitivity and assured delivery on schedule and meeting all requirements. And the number of would-be laser ISL terminal suppliers also grows despite little verifiable expertise in actually delivering complete, working space-based laser ISL terminals, regardless of price or performance. Consequently, the opportunity for mistakes, disappointments, and outright failure is intensified. More 'red meatballs' are unfortunately on the horizon and neither customers nor suppliers recognize the warning signs. Is ignorance bliss? Virtually the entire space communications community appears oblivious to emerging terrestrial broadband communications projects which appear better backed with superior management far more attentive to time-to-market and other schedule and business considerations than any space venture. Space systems offer advantages through realizing global network operations not possible terrestrially, yet few promoters recogni the potential. Might these be omens worth capitalizing upon, or perhaps from which escape may be warranted? This paper provides a commercial market status update to that presented in preceding years' papers. Laser ISL applications are reviewed which enable commercial broadband satellite customer opportunities not yet recognized among most in the customer community, despite

  4. Biomarkers in Severe Asthma.

    PubMed

    Wan, Xiao Chloe; Woodruff, Prescott G

    2016-08-01

    Biomarkers have been critical for studies of disease pathogenesis and the development of new therapies in severe asthma. In particular, biomarkers of type 2 inflammation have proven valuable for endotyping and targeting new biological agents. Because of these successes in understanding and marking type 2 inflammation, lack of knowledge regarding non-type 2 inflammatory mechanisms in asthma will soon be the major obstacle to the development of new treatments and management strategies in severe asthma. Biomarkers can play a role in these investigations as well by providing insight into the underlying biology in human studies of patients with severe asthma. PMID:27401625

  5. Metabolic products as biomarkers

    USGS Publications Warehouse

    Melancon, M.J.; Alscher, R.; Benson, W.; Kruzynski, G.; Lee, R.F.; Sikka, H.C.; Spies, R.B.; Huggett, Robert J.; Kimerle, Richard A.; Mehrle, Paul M.=; Bergman, Harold L.

    1992-01-01

    Ideally, endogenous biomarkers would indicate both exposure and environmental effects of toxic chemicals; however, such comprehensive biochemical and physiological indices are currently being developed and, at the present time, are unavailable for use in environmental monitoring programs. Continued work is required to validate the use of biochemical and physiological stress indices as useful components of monitoring programs. Of the compounds discussed only phytochelatins and porphyrins are currently in biomarkers in a useful state; however, glutathione,metallothioneins, stress ethylene, and polyamines are promising as biomarkers in environmental monitoring.

  6. Linking Nitrogen-Cycling Microbial Communities to Environmental Fluctuations and Biogeochemical Activity in a Large, Urban Estuary: the San Francisco Bay-Delta

    NASA Astrophysics Data System (ADS)

    Francis, C.

    2015-12-01

    Nitrogen (N) availability is an important factor controlling productivity and thus carbon cycling in estuaries. The fate of N in estuaries depends on the activities of the microbes that carry out the N-cycle, which in turn depend on factors such as organic matter availability, dissolved inorganic N, salinity, oxygen, and temperature. Key microbial N transformations include nitrification (the aerobic oxidation of ammonia to nitrite and nitrate) and denitrification (the anaerobic reduction of nitrate to dinitrogen gas). While denitrification leads to N loss, nitrification is the only link between reduced N (produced by decomposition) and oxidized N (substrates for N loss processes), and both processes are known to produce nitrous oxide (N2O), a potent greenhouse gas. Understanding controls of N-cycling in the San Francisco Bay-Delta (SFBD)—the largest estuary on the west coast of North America—is particularly important, as this urban estuary is massively polluted with N, even compared to classic "eutrophic" systems. Interestingly, the SFBD has been spared the detrimental consequences of nutrient enrichment, largely due to high suspended sediment concentrations (and thus low light penetration) throughout the water column, combined with high grazing pressure. However, the recent "clearing" of SFBD waters due to a sharp decrease in suspended sediments may significantly alter the ecology of the estuary, by increasing phytoplankton growth. Thus, the SFBD may be losing its historical resilience to eutrophication, and may soon be "high-nutrient, low-chlorophyll" no more. Elucidating the environmental factors affecting the community structure, activity, and functioning of N-cycling microbes in SFBD is crucial for determining how changes in turbidity and productivity will be propagated throughout the ecosystem. While substantial ecological research in the SFBD has focused on phytoplankton and food webs, bacterial and archaeal communities have received far less attention

  7. 2-Furoylglycine as a Candidate Biomarker of Coffee Consumption.

    PubMed

    Heinzmann, Silke S; Holmes, Elaine; Kochhar, Sunil; Nicholson, Jeremy K; Schmitt-Kopplin, Philippe

    2015-09-30

    Specific and sensitive food biomarkers are necessary to support dietary intake assessment and link nutritional habits to potential impact on human health. A multistep nutritional intervention study was conducted to suggest novel biomarkers for coffee consumption. (1)H NMR metabolic profiling combined with multivariate data analysis resolved 2-furoylglycine (2-FG) as a novel putative biomarker for coffee consumption. We relatively quantified 2-FG in the urine of coffee drinkers and investigated its origin, metabolism, and excretion kinetics. When searching for its potential precursors, we found different furan derivatives in coffee products, which are known to get metabolized to 2-FG. Maximal urinary excretion of 2-FG occurred 2 h after consumption (p = 0.0002) and returned to baseline after 24 h (p = 0.74). The biomarker was not excreted after consumption of coffee substitutes such as tea and chicory coffee and might therefore be a promising acute biomarker for the detection of coffee consumption in human urine.

  8. 2-Furoylglycine as a Candidate Biomarker of Coffee Consumption.

    PubMed

    Heinzmann, Silke S; Holmes, Elaine; Kochhar, Sunil; Nicholson, Jeremy K; Schmitt-Kopplin, Philippe

    2015-09-30

    Specific and sensitive food biomarkers are necessary to support dietary intake assessment and link nutritional habits to potential impact on human health. A multistep nutritional intervention study was conducted to suggest novel biomarkers for coffee consumption. (1)H NMR metabolic profiling combined with multivariate data analysis resolved 2-furoylglycine (2-FG) as a novel putative biomarker for coffee consumption. We relatively quantified 2-FG in the urine of coffee drinkers and investigated its origin, metabolism, and excretion kinetics. When searching for its potential precursors, we found different furan derivatives in coffee products, which are known to get metabolized to 2-FG. Maximal urinary excretion of 2-FG occurred 2 h after consumption (p = 0.0002) and returned to baseline after 24 h (p = 0.74). The biomarker was not excreted after consumption of coffee substitutes such as tea and chicory coffee and might therefore be a promising acute biomarker for the detection of coffee consumption in human urine. PMID:26357997

  9. Going retro: Oxidative stress biomarkers in modern redox biology.

    PubMed

    Margaritelis, N V; Cobley, J N; Paschalis, V; Veskoukis, A S; Theodorou, A A; Kyparos, A; Nikolaidis, M G

    2016-09-01

    The field of redox biology is inherently intertwined with oxidative stress biomarkers. Oxidative stress biomarkers have been utilized for many different objectives. Our analysis indicates that oxidative stress biomarkers have several salient applications: (1) diagnosing oxidative stress, (2) pinpointing likely redox components in a physiological or pathological process and (3) estimating the severity, progression and/or regression of a disease. On the contrary, oxidative stress biomarkers do not report on redox signaling. Alternative approaches to gain more mechanistic insights are: (1) measuring molecules that are integrated in pathways linking redox biochemistry with physiology, (2) using the exomarker approach and (3) exploiting -omics techniques. More sophisticated approaches and large trials are needed to establish oxidative stress biomarkers in the clinical setting.

  10. Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data

    PubMed Central

    Tosas Auguet, Olga; Betley, Jason R.; Stabler, Richard A.; Patel, Amita; Ioannou, Avgousta; Marbach, Helene; Hearn, Pasco; Aryee, Anna; Goldenberg, Simon D.; Otter, Jonathan A.; Desai, Nergish; Karadag, Tacim; Grundy, Chris; Gaunt, Michael W.; Cooper, Ben S.; Edgeworth, Jonathan D.; Kypraios, Theodore

    2016-01-01

    Background Identifying and tackling the social determinants of infectious diseases has become a public health priority following the recognition that individuals with lower socioeconomic status are disproportionately affected by infectious diseases. In many parts of the world, epidemiologically and genotypically defined community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) strains have emerged to become frequent causes of hospital infection. The aim of this study was to use spatial models with adjustment for area-level hospital attendance to determine the transmission niche of genotypically defined CA- and health-care-associated (HA)-MRSA strains across a diverse region of South East London and to explore a potential link between MRSA carriage and markers of social and material deprivation. Methods and Findings This study involved spatial analysis of cross-sectional data linked with all MRSA isolates identified by three National Health Service (NHS) microbiology laboratories between 1 November 2011 and 29 February 2012. The cohort of hospital-based NHS microbiology diagnostic services serves 867,254 usual residents in the Lambeth, Southwark, and Lewisham boroughs in South East London, United Kingdom (UK). Isolates were classified as HA- or CA-MRSA based on whole genome sequencing. All MRSA cases identified over 4 mo within the three-borough catchment area (n = 471) were mapped to small geographies and linked to area-level aggregated socioeconomic and demographic data. Disease mapping and ecological regression models were used to infer the most likely transmission niches for each MRSA genetic classification and to describe the spatial epidemiology of MRSA in relation to social determinants. Specifically, we aimed to identify demographic and socioeconomic population traits that explain cross-area extra variation in HA- and CA-MRSA relative risks following adjustment for hospital attendance data. We explored the potential for associations with

  11. Biomarker analysis for oncology.

    PubMed

    Ma, Yinfa; Gamagedara, Sanjeewa

    2015-01-01

    Cancer biomarkers are biological, chemical or biophysical entities that are present in tumor tissues or body fluids which give valuable information about current and future behavior of cancer. This review discusses the applicability of biomarkers in different stages of cancer from cancer risk assessment to recurrence. In medical practice, biomarkers can be helpful in finding out one's potential cancer risk, confirming whether or not one is already affected with a particular type of cancer, to which drug will the cancer respond best and in what doses should it be administered, the effectiveness of the treatment and whether the cancer will recur. Although biomarker discovery and validation is a very challenging process, when considering its applications and advantages, it is well worth the effort.

  12. Biomarker time out.

    PubMed

    Petzold, Axel; Bowser, Robert; Calabresi, Paolo; Zetterberg, Henrik; Uitdehaag, Bernard M J

    2014-10-01

    The advancement of knowledge relies on scientific investigations. The timing between asking a question and data collection defines if a study is prospective or retrospective. Prospective studies look forward from a point in time, are less prone to bias and are considered superior to retrospective studies. This conceptual framework conflicts with the nature of biomarker research. New candidate biomarkers are discovered in a retrospective manner. There are neither resources nor time for prospective testing in all cases. Relevant sources for bias are not covered. Ethical questions arise through the time penalty of an overly dogmatic concept. The timing of sample collection can be separated from testing biomarkers. Therefore the moment of formulating a hypothesis may be after sample collection was completed. A conceptual framework permissive to asking research questions without the obligation to bow to the human concept of calendar time would simplify biomarker research, but will require new safeguards against bias.

  13. Hopanoid Biomarker Preservation In Coniform (Phormidium) Stromatolites in Siliceous Thermal Springs, Yellowstone National Park

    NASA Technical Reports Server (NTRS)

    Jahnke, Linda L.; Summons, Roger E.; Farmer, Jack D.; Klein, Harold P.; DeVincenzi, Donald L. (Technical Monitor)

    2000-01-01

    The microbial communities that characterize modem hydrothermal ecosystems serve as modern analogs to those thought to have dominated early environments on Earth and possibly Mars. The importance of such hydrothermal systems as targets in exploring for an early biosphere on Mars is well established. Such work provides an important basis for the analysis of Martian samples associated with such environments. The surviving molecular structure and isotopic signature of diagnostic lipid biomarkers found as chemical fossils can provide a link between modern bacterially dominated ecosystems and their ancient counterparts. We are interested in the processes involved in the deposition and/or degradation of organic material in moderately thermal, silicifying microbial mats, particularly as this relates to the potential for preservation of some biomarker components known to be more highly resistant to microbial degradation. Several excellent biomarker molecules are associated with the cyanobacteria that dominate these mats, particularly the 2-methylbacteriohopanepolyols (2-MeBHP). These compounds are ubiquitous on Earth and are not easily degraded in nature, a fact documented by their detection in ancient Earth rocks dating back as far as 2,700 Ma.

  14. Biomarkers for neuromyelitis optica.

    PubMed

    Chang, Kuo-Hsuan; Ro, Long-Sun; Lyu, Rong-Kuo; Chen, Chiung-Mei

    2015-02-01

    Neuromyelitis optica (NMO) is an acquired, heterogeneous inflammatory disorder, which is characterized by recurrent optic neuritis and longitudinally extensive spinal cord lesions. The discovery of the serum autoantibody marker, anti-aquaporin 4 (anti-AQP4) antibody, revolutionizes our understanding of pathogenesis of NMO. In addition to anti-AQP4 antibody, other biomarkers for NMO are also reported. These candidate biomarkers are particularly involved in T helper (Th)17 and astrocytic damages, which play a critical role in the development of NMO lesions. Among them, IL-6 in the peripheral blood is associated with anti-AQP4 antibody production. Glial fibrillary acidic protein (GFAP) in CSF demonstrates good correlations with clinical severity of NMO relapses. Detecting these useful biomarkers may be useful in the diagnosis and evaluation of disease activity of NMO. Development of compounds targeting these biomarkers may provide novel therapeutic strategies for NMO. This article will review the related biomarker studies in NMO and discuss the potential therapeutics targeting these biomarkers.

  15. Methodological and analytic considerations for blood biomarkers.

    PubMed

    Christenson, Robert H; Duh, Show-Hong

    2012-01-01

    Biomarkers typically evolve from a research setting to use in clinical care as evidence for their independent contribution to patient management accumulates. This evidence relies heavily on knowledge of the preanalytical, analytical, and postanalytical characteristics of the biomarker's measurement. For the preanalytical phase, considerations such specimen type, acceptable anticoagulants for blood samples, biologic variation and stability of the biomarker under various conditions are key. The analytical phase entails critical details for development and maintenance of assays having performance characteristics that are "fit for service" for the clinical application at hand. Often, these characteristics describe the ability to measure minute quantities in the biologic matrix used for measurement. Although techniques such as mass spectrometry are used effectively for biomarker discovery, routine quantification often relies on use of immunoassays; early in development, the most common immunoassay used is the enzyme-linked immunosorbent assay format. As biomarkers evolve successfully, they will be adapted to large main laboratory platforms or, depending on the need for speed, point-of-care devices. Users must pay particular attention to performance parameters of assays they are considering for clinical implementation. These parameters include the limit of blank, a term used to describe the limit of analytical noise for an assay; limit of detection, which describes the lowest concentration that can reliably be discriminated from analytical noise; and perhaps most importantly, the limit of quantitation, which is the lowest concentration at which a biomarker can be reliably measured within some predefined specifications for total analytical error that is based on clinical requirements of the test. The postanalytical phase involves reporting biomarker values, which includes reporting units, any normalization factors, and interpretation. Standardization, a process that

  16. Biomarkers and pediatric environmental health.

    PubMed

    Lubin, B; Lewis, R

    1995-09-01

    It is now possible to identify biochemical and/or cellular changes in humans due to exposure to an environmental toxin. These changes are called biomarkers and are currently used in research studies to identify individuals exposed to specific toxic substances. Advances in the field of biomarker technology may have important implications for the detection, prevention, and treatment of certain diseases in children. This technology may enable physicians to screen children who have no clinically detectable illness for evidence of exposure to specific toxins. Such information could lead to implementation of preventive measures and development of new therapeutic strategies. However, several important issues, including potential adverse consequences resulting from the widespread use of this technology, must be considered prior to its utilization within a clinical setting. Leaders of the pediatric and public health communities should recognize the paucity of scientific data in the pediatric environmental health area, and new approaches to this important aspect of child health should be developed. This article will address several of the issues involved in pediatric environmental health and consider questions that should be answered as the potential for technology transfer becomes a reality. PMID:8549501

  17. Kidney biomarkers in cirrhosis.

    PubMed

    Francoz, Claire; Nadim, Mitra K; Durand, François

    2016-10-01

    Impaired renal function due to acute kidney injury (AKI) and/or chronic kidney diseases (CKD) is frequent in cirrhosis. Recurrent episodes of AKI may occur in end-stage cirrhosis. Differential diagnosis between functional (prerenal and hepatorenal syndrome) and acute tubular necrosis (ATN) is crucial. The concept that AKI and CKD represent a continuum rather than distinct entities, is now emerging. Not all patients with AKI have a potential for full recovery. Precise evaluation of kidney function and identification of kidney changes in patients with cirrhosis is central in predicting reversibility. This review examines current biomarkers for assessing renal function and identifying the cause and mechanisms of impaired renal function. When CKD is suspected, clearance of exogenous markers is the reference to assess glomerular filtration rate, as creatinine is inaccurate and cystatin C needs further evaluation. Recent biomarkers may help differentiate ATN from hepatorenal syndrome. Neutrophil gelatinase-associated lipocalin has been the most extensively studied biomarker yet, however, there are no clear-cut values that differentiate each of these conditions. Studies comparing ATN and hepatorenal syndrome in cirrhosis, do not include a gold standard. Combinations of innovative biomarkers are attractive to identify patients justifying simultaneous liver and kidney transplantation. Accurate biomarkers of underlying CKD are lacking and kidney biopsy is often contraindicated in this population. Urinary microRNAs are attractive although not definitely validated. Efforts should be made to develop biomarkers of kidney fibrosis, a common and irreversible feature of CKD, whatever the cause. Biomarkers of maladaptative repair leading to irreversible changes and CKD after AKI are also promising.

  18. A scoping review to understand the effectiveness of linking schemes from healthcare providers to community resources to improve the health and well-being of people with long-term conditions.

    PubMed

    Mossabir, Rahena; Morris, Rebecca; Kennedy, Anne; Blickem, Christian; Rogers, Anne

    2015-09-01

    The prevalence of people living with long-term conditions is increasing, accompanied by an increased expectation that patients will become more involved in self-management. Long-term conditions are associated with increased social isolation and poor physical and mental health. But there remains a gap in health provision between providing medical treatment and effectively addressing psychosocial well-being. One potential way of addressing this gap is by utilising social interventions which link patients from health services to community-based sources of support. However, the mechanisms involved in the delivery of interventions providing that link and their effectiveness remain unclear. This review adopted the methodological framework for conducting scoping studies, searching for both academic and grey literature on social interventions which link people from healthcare settings to a range of community and voluntary sector organisations. A literature search between May and June 2013, involving five electronic databases, hand searching of two journals and the use of Google search engine, identified seven studies relevant to the review question. In terms of key characteristics and mechanisms of the interventions, mental health conditions and social isolation were the most common reasons for referral to the interventions, and referrals were usually made through general practices. Almost all the interventions were facilitator-led, whereby the facilitator worked to identify and link participants to appropriate community-based resources. In regard to health and social outcomes and their cost-effectiveness, studies reported improvement to participants' psychological and social well-being as well as their decreased use of health services, although there were limited measures of participants' physical health outcomes. Interventions for linking patients from healthcare setting to community-based resources target and address psychosocial needs of participants. The review

  19. Etiology of community-acquired pneumonia in a population-based study: Link between etiology and patients characteristics, process-of-care, clinical evolution and outcomes

    PubMed Central

    2012-01-01

    Background The etiologic profile of community-acquired pneumonia (CAP) for each age group could be similar among inpatients and outpatients. This fact brings up the link between etiology of CAP and its clinical evolution and outcome. Furthermore, the majority of pneumonia etiologic studies are based on hospitalized patients, whereas there have been no recent population-based studies encompassing both inpatients and outpatients. Methods To evaluate the etiology of CAP, and the relationship among the different pathogens of CAP to patients characteristics, process-of-care, clinical evolution and outcomes, a prospective population-based study was conducted in Spain from April 1, 2006, to June 30, 2007. Patients (age >18) with CAP were identified through the family physicians and the hospital area. Results A total of 700 patients with etiologic evaluation were included: 276 hospitalized and 424 ambulatory patients. We were able to define the aetiology of pneumonia in 55.7% (390/700). The most frequently isolated organism was S. pneumoniae (170/390, 43.6%), followed by C. burnetti (72/390, 18.5%), M. pneumoniae (62/390, 15.9%), virus as a group (56/390, 14.4%), Chlamydia species (39/390, 106%), and L. pneumophila (17/390, 4.4%). The atypical pathogens and the S. pneumoniae are present in pneumonias of a wide spectrum of severity and age. Patients infected by conventional bacteria were elderly, had a greater hospitalization rate, and higher mortality within 30 days. Conclusions Our study provides information about the etiology of CAP in the general population. The microbiology of CAP remains stable: infections by conventional bacteria result in higher severity, and the S. pneumoniae remains the most important pathogen. However, atypical pathogens could also infect patients in a wide spectrum of severity and age. PMID:22691449

  20. Molecular indicators (biomarkers) of past life.

    PubMed

    Simoneit, Bernd R T

    2002-11-01

    Biomarkers in geological samples on Earth are products derived from biochemical precursors (i.e., natural products) by reductive and oxidative alteration processes (e.g., cholestanes from cholesterol). Generally, lipids, pigments, and some biomembranes are preserved best over longer geological times, and labile compounds such as amino acids, sugars, etc. are useful biomarkers for recent times. Thus, the detailed characterization of biomarker composition permits the assessment of the major contributing species of extinct and/or extant life. Nonbiomarkers and abiogenic organic compounds are also discussed. In the case of the early Earth, work has progressed to elucidate biomarker structures and carbon isotopic signals preserved in ancient sedimentary rocks. In addition, the combination of bacterial biochemistry with the organic geochemistry of contemporary and ancient hydrothermal ecosystems permits the modeling of the nature, behavior, and preservation potential of primitive microbial communities. This approach entails combined molecular and isotopic analyses to characterize lipids and biopolymers produced by cultured bacteria (representative of ancient strains) and to test a variety of culture conditions that affect their biosynthesis processes. In regards to Mars, the biomarkers from lipids and biopolymers would be expected to be preserved best if life flourished there during its early history (3.5-4 x 10(9) years ago). Both oxidized and reduced products would be expected. This is based on the inference that hydrothermal activity occurred during that time, with the concomitant preservation of biochemically-derived carbonaceous matter. Known biomarkers (i.e., as elucidated for early terrestrial samples and for primitive terrestrial microbiota) as well as novel, potentially unknown compounds, should be characterized.

  1. The link in Linking

    PubMed Central

    Caldwell, Jane C; Chiale, Pablo A; Gonzalez, Mario D; Baranchuk, Adrian

    2013-01-01

    We present 2 cases of the slow-fast form of AVNRT with initially narrow QRS complexes followed by sudden unexpected transition to persistently wide QRS complexes due to aberrant intraventricular conduction. Introduction of a properly timed extrastimulus in one case and critical oscillations in cycle length due to short-long coupling in the second case set the stage for the initial bundle branch block. However, persistence of the aberrancy pattern once the initial event abated was maintained by the "linking" phenomenon. Delayed, retrograde concealed activation from the contralateral bundle branch perpetuated the initial bundle branch block. PMID:23840106

  2. Mass spectrometry for biomarker development

    SciTech Connect

    Wu, Chaochao; Liu, Tao; Baker, Erin Shammel; Rodland, Karin D.; Smith, Richard D.

    2015-06-19

    Biomarkers potentially play a crucial role in early disease diagnosis, prognosis and targeted therapy. In the past decade, mass spectrometry based proteomics has become increasingly important in biomarker development due to large advances in technology and associated methods. This chapter mainly focuses on the application of broad (e.g. shotgun) proteomics in biomarker discovery and the utility of targeted proteomics in biomarker verification and validation. A range of mass spectrometry methodologies are discussed emphasizing their efficacy in the different stages in biomarker development, with a particular emphasis on blood biomarker development.

  3. Candidate List of yoUr Biomarker (CLUB): A Web-based Platform to Aid Cancer Biomarker Research

    PubMed Central

    Lee, Bernett T.K.; Liew, Lailing; Lim, Jiahao; Tan, Jonathan K.L.; Lee, Tze Chuen; Veladandi, Pardha S.; Lim, Yun Ping; Han, Hao; Rajagopal, Gunaretnam; Anderson, N. Leigh

    2008-01-01

    CLUB (“Candidate List of yoUr Biomarkers”) is a freely available, web-based resource designed to support Cancer biomarker research. It is targeted to provide a comprehensive list of candidate biomarkers for various cancers that have been reported by the research community. CLUB provides tools for comparison of marker candidates from different experimental platforms, with the ability to filter, search, query and explore, molecular interaction networks associated with cancer biomarkers from the published literature and from data uploaded by the community. This complex and ambitious project is implemented in phases. As a first step, we have compiled from the literature an initial set of differentially expressed human candidate cancer biomarkers. Each candidate is annotated with information from publicly available databases such as Gene Ontology, Swiss-Prot database, National Center for Biotechnology Information’s reference sequences, Biomolecular Interaction Network Database and IntAct interaction. The user has the option to maintain private lists of biomarker candidates or share and export these for use by the community. Furthermore, users may customize and combine commonly used sets of selection procedures and apply them as a stored workflow using selected candidate lists. To enable an assessment by the user before taking a candidate biomarker to the experimental validation stage, the platform contains the functionality to identify pathways associated with cancer risk, staging, prognosis, outcome in cancer and other clinically associated phenotypes. The system is available at http://club.bii.a-star.edu.sg. PMID:19578495

  4. Making the Collaborative Process Work. (Benefits)[Squared]: The Exponential Results of Linking School Improvement and Community Development, Issue Number Six.

    ERIC Educational Resources Information Center

    Boethel, Martha

    Joint rural school-community projects are best sustained when developed by a collaborative group. The two basic dimensions of working collaboratively are team building and team planning. Critical elements of the collaborative process are: 1) community readiness--an assessment of community readiness should be performed, taking into consideration…

  5. Biomarkers for systemic lupus erythematosus.

    PubMed

    Ahearn, Joseph M; Liu, Chau-Ching; Kao, Amy H; Manzi, Susan

    2012-04-01

    The urgent need for lupus biomarkers was demonstrated in September 2011 during a Workshop sponsored by the Food and Drug Administration: Potential Biomarkers Predictive of Disease Flare. After 2 days of discussion and more than 2 dozen presentations from thought leaders in both industry and academia, it became apparent that highly sought biomarkers to predict lupus flare have not yet been identified. Even short of the elusive biomarker of flare, few biomarkers for systemic lupus erythematosus (SLE) diagnosis, monitoring, and stratification have been validated and employed for making clinical decisions. This lack of reliable, specific biomarkers for SLE hampers proper clinical management of patients with SLE and impedes development of new lupus therapeutics. As such, the intensity of investigation to identify lupus biomarkers is climbing a steep trajectory, lending cautious optimism that a validated panel of biomarkers for lupus diagnosis, monitoring, stratification, and prediction of flare may soon be in hand.

  6. Biomarkers in Barrett's esophagus.

    PubMed

    Reid, Brian J; Blount, Patricia L; Rabinovitch, Peter S

    2003-04-01

    This article provides a framework for clinicians who are attempting the difficult task of interpreting the Barrett's biomarker literature with the goal of improving care for their patients. Although many articles. including more that 60 proposed biomarkers, have been published on this subject, only a few describe phase 3 and 4 studies that are of interest to the clinical gastroenterologist (Table 1). For year, dysplasia grade has been the sole means of risk stratification for patients with BE, and it likely will continue to be used in the foreseeable future. The current authors believe that dysplasia classification can be valuable using the team management approach and quality controls described previously. Significant problems, however, have emerged in phase 2 through 4 studies of dysplasia that make it imperative for the Barrett's field to incorporate additional biomarkers as they are validated. These problems include poor reproducibility of dysplasia interpretations, poor predictive value for negative, indefinite, and low-grade dysplasia, and inconsistent results for HGD in different centers, all of which makes it virtually impossible to develop national guidelines for surveillance. Some studies have even suggested that endoscopic biopsy surveillance using dysplasia may not be worthwhile. Currently, flow cytometric tetraploidy and aneuploidy have progressed furthest in biomarker validation (see Table 1). With proper handling, endoscopic biopsy specimens can be shipped to reference laboratories that have the instruments, computer analytic methods, and expertise to reproducibly detect tetraploidy and aneuploidy. The results of phase 4 studies indicate that flow cytometry appears to be useful in detecting a subset of patients who do not have HGD and yet have an increased risk of progression to cancer that cannot be identified by dysplasia grade. For many reasons, the authors anticipate that the number of validated biomarkers will increase substantially in the

  7. Industry perspectives on biomarker qualification

    PubMed Central

    Womack, AW

    2015-01-01

    Biomarkers have the potential to expedite drug development, increase patient safety, and optimize clinical response. Yet few have achieved regulatory qualification. A survey was conducted to clarify industry's perspective on biomarker qualification and identify the most promising biomarkers for drug development. The results across toxicities/clinical areas highlight challenges in regulatory qualification, although early prioritization and alignment on an evidentiary standard framework are key factors in facilitating biomarker development and qualification. PMID:26378777

  8. Biomarkers of cell senescence

    DOEpatents

    Dirmi, G.P.; Campisi, J.; Peacocke, M.

    1996-02-13

    The present invention provides a biomarker system for the in vivo and in vitro assessment of cell senescence. In the method of the present invention, {beta}-galactosidase activity is utilized as a means by which cell senescence may be assessed either in in vitro cell cultures or in vivo. 1 fig.

  9. Biomarkers of cell senescence

    DOEpatents

    Dimri, G.P.; Campisi, J.; Peacocke, M.

    1998-08-18

    The present invention provides a biomarker system for the in vivo and in vitro assessment of cell senescence. In the method of the present invention, {beta}-galactosidase activity is utilized as a means by which cell senescence may be assessed either in vitro cell cultures or in vivo. 1 fig.

  10. [Biomarkers of tobacco smoke].

    PubMed

    Sobczak, Andrzej; Wardas, Władysław; Zielińska-Danch, Wioleta; Szołtysek-Bołdys, Izabela

    2005-01-01

    In order to estimate the exposure of passive and active smokers to tobacco smoke one can use the questionnaire method or laboratory examination of chemical compounds being widely accepted exposure biomarkers. Substances that make such biomarkers include some of the tobacco smoke components and its metabolites formed in the body. The study discusses two groups of biomarkers. First, includes substances that serve as exposure markers of carcinogenous properties (metabolites of polycyclic aromatic hydrocarbons, N-nitrosamines, trans,transmuconic acid, S-phenylmercapturic acid). Second group includes substances which role is limited to the evaluation of exposure to tobacco smoke (nicotine, cotinine, anatabine, anabasine, trans-3'-hydroxycotinine, thiocyanate, carboxyhemoglobin, carbon monoxide). Sensitivity and specificity of biomakers used were evaluated, their concentration ranges in physiological fluids in non-smokers, passive-, and active smokers. The simplicity of the examination method was evaluated. Articles published during last two decades indicate that the substance that have all features that make it the most appropriate biomarker is cotinine. It can be assessed in plasma and in urine of smokers and persons exposed to environmental tobacco smoke.

  11. Biomarkers of cell senescence

    DOEpatents

    Dimri, Goberdhan P.; Campisi, Judith; Peacocke, Monica

    1998-01-01

    The present invention provides a biomarker system for the in vivo and in vitro assessment of cell senescence. In the method of the present invention, .beta.-galactosidase activity is utilized as a means by which cell senescence may be assessed either in vitro cell cultures or in vivo.

  12. Biomarkers of cell senescence

    DOEpatents

    Dirmi, Goberdhan P.; Campisi, Judith; Peacocke, Monica

    1996-01-01

    The present invention provides a biomarker system for the in vivo and in vitro assessment of cell senescence. In the method of the present invention, .beta.-galactosidase activity is utilized as a means by which cell senescence may be assessed either in in vitro cell cultures or in vivo.

  13. System-wide peripheral biomarker discovery using information theory.

    PubMed

    Alterovitz, Gil; Xiang, Michael; Liu, Jonathan; Chang, Amelia; Ramoni, Marco F

    2008-01-01

    The identification of reliable peripheral biomarkers for clinical diagnosis, patient prognosis, and biological functional studies would allow for access to biological information currently available only through invasive methods. Traditional approaches have so far considered aspects of tissues and biofluid markers independently. Here we introduce an information theoretic framework for biomarker discovery, integrating biofluid and tissue information. This allows us to identify tissue information in peripheral biofluids. We treat tissue-biofluid interactions as an information channel through functional space using 26 proteomes from 45 different sources to determine quantitatively the correspondence of each biofluid for specific tissues via relative entropy calculation of proteomes mapped onto phenotype, function, and drug space. Next, we identify candidate biofluids and biomarkers responsible for functional information transfer (p < 0.01). A total of 851 unique candidate biomarkers proxies were identified. The biomarkers were found to be significant functional tissue proxies compared to random proteins (p < 0.001). This proxy link is found to be further enhanced by filtering the biofluid proteins to include only significant tissue-biofluid information channels and is further validated by gene expression. Furthermore, many of the candidate biomarkers are novel and have yet to be explored. In addition to characterizing proteins and their interactions with a systemic perspective, our work can be used as a roadmap to guide biomedical investigation, from suggesting biofluids for study to constraining the search for biomarkers. This work has applications in disease screening, diagnosis, and protein function studies. PMID:18229689

  14. The role of metabolic biomarkers in drug toxicity studies.

    PubMed

    Schnackenberg, Laura K; Beger, Richard D

    2008-01-01

    ABSTRACT Metabolic profiling is a technique that can potentially provide more sensitive and specific biomarkers of toxicity than the current clinical measures benefiting preclinical and clinical drug studies. Both nuclear magnetic resonance (NMR) and mass spectrometry (MS) platforms have been used for metabolic profiling studies of drug toxicity. Not only can both techniques provide novel biomarker(s) of toxicity but the combination of both techniques gives a broader range of metabolites evaluated. Changes in metabolic patterns can provide insight into mechanism(s) of toxicity and help to eliminate a potentially toxic new chemical entity earlier in the developmental process. Metabolic profiling offers numerous advantages in toxicological research and screening as sample collection and preparation are relatively simple. Further, sample throughput, reproducibility, and accuracy are high. The area of drug toxicity of therapeutic compounds has already been impacted by metabolic profiling studies and will continue to be impacted as new, more specific biomarker(s) are found. In order for a biomarker or pattern of biomarkers to be accepted, it must be shown that they originate from the target tissue of interest. Metabolic profiling studies are amenable to any biofluid or tissue sample making it possible to link the changes noted in urine for instance as originating from renal injury. Additionally, the ease of sample collection makes it possible to follow a single animal or subject over time in order to determine whether and when the toxicity resolves itself. This review focuses on the advantages of metabolic profiling for drug toxicity studies.

  15. Salivary Biomarkers in Pediatric Metabolic Disease Research.

    PubMed

    Hartman, Mor-Li; Goodson, J Max; Barake, Roula; Alsmadi, Osama; Al-Mutawa, Sabiha; Ariga, Jitendra; Soparkar, Pramod; Behbehani, Jawad; Behbehani, Kazem

    2016-03-01

    The increasing prevalence of childhood obesity and obesity-related metabolic disorders is now considered a global pandemic. The main goal of the pediatric obesity research community is to identify children who are at risk of becoming obese before their body mass index rises above age norms. To do so, we must identify biomarkers of metabolic health and immunometabolism that can be used for large-scale screening and diagnosis initiatives among at-risk children. Because blood sampling is often unacceptable to both parents and children when there is no direct benefit to the child, as in a community-based research study, there is a clear need for a low-risk, non-invasive sampling strategy. Salivary analysis is now well recognized as a likely candidate for this purpose. In this review, we discuss the physiologic role of saliva and its strengths and limitations as a fluid for biomarker discovery, obesity screening, metabolic disease diagnosis, and response monitoring after interventions. We also describe the current state of the salivary biomarker field as it pertains to metabolic research, with a special emphasis on studies conducted in children and adolescents. Finally, we look forward to technological developments, such as salivary "omics" and point of service diagnostic devices, which have the potential to accelerate the pace of research and discovery in this vitally important field. PMID:27116847

  16. Neuroimaging Biomarkers for Psychosis

    PubMed Central

    Hager, Brandon M.

    2015-01-01

    Background Biomarkers provide clinicians with a predictable model for the diagnosis, treatment and follow-up of medical ailments. Psychiatry has lagged behind other areas of medicine in the identification of biomarkers for clinical diagnosis and treatment. In this review, we investigated the current state of neuroimaging as it pertains to biomarkers for psychosis. Methods We reviewed systematic reviews and meta-analyses of the structural (sMRI), functional (fMRI), diffusion-tensor (DTI), Positron emission tomography (PET) and spectroscopy (MRS) studies of subjects at-risk or those with an established schizophrenic illness. Only articles reporting effect-sizes and confidence intervals were included in an assessment of robustness. Results Out of the identified meta-analyses and systematic reviews, 21 studies met the inclusion criteria for assessment. There were 13 sMRI, 4 PET, 3 MRS, and 1 DTI studies. The search terms included in the current review encompassed familial high risk (FHR), clinical high risk (CHR), First episode (FES), Chronic (CSZ), schizophrenia spectrum disorders (SSD), and healthy controls (HC). Conclusions Currently, few neuroimaging biomarkers can be considered ready for diagnostic use in patients with psychosis. At least in part, this may be related to the challenges inherent in the current symptom-based approach to classifying these disorders. While available studies suggest a possible value of imaging biomarkers for monitoring disease progression, more systematic research is needed. To date, the best value of imaging data in psychoses has been to shed light on questions of disease pathophysiology, especially through the characterization of endophenotypes. PMID:25883891

  17. Building Community.

    ERIC Educational Resources Information Center

    Gardner, John

    1996-01-01

    Offers 10 attributes of community: (1) wholeness incorporating diversity; (2) shared values; (3) mutual obligations; (4) effective internal communication; (5) participation; (6) continuous reaffirmation; (7) links beyond itself; (8) concern for youth; (9) forward-looking viewpoint; and (10) well-developed community maintenance. (JOW)

  18. A Study of the Impacts of Navigational Links, Task Complexity, and Experience with the Older User on Website Usability in a Community College Domain

    ERIC Educational Resources Information Center

    Garrett, Robin Eileen

    2014-01-01

    Community colleges serve a diverse population of learners including many older students counting on the community college for enhanced skills or personal enrichment. Many of these colleges target this population with programs designed specifically to meet the needs and goals of the older adult but may not consider this population when designing a…

  19. Biomarker Modeling of Alzheimer's Disease

    PubMed Central

    Jack, Clifford R; Holtzman, David M

    2014-01-01

    Alzheimer's disease (AD) is a slowly progressing disorder in which pathophysiological abnormalities, detectable in vivo by biomarkers, precede overt clinical symptoms by many years to decades. Five AD biomarkers are sufficiently validated to have been incorporated into clinical diagnostic criteria and commonly used in therapeutic trials. Current AD biomarkers fall into 2 categories: biomarkers of amyloid-β plaques and of tau-related neurodegeneration. Three of the 5 are imaging measures and two are cerebrospinal fluid analytes. AD biomarkers do not evolve in an identical manner but rather in a sequential but temporally overlapping manner. Models of the temporal evolution of AD biomarkers can take the form of plots of biomarker severity (degree of abnormality) vs. time. In this review we discuss several time-dependent models of AD which take into consideration varying age of onset (early vs. late) and the influence of aging and co-occurring brain pathologies that commonly arise in the elderly. PMID:24360540

  20. Fossil fuel biomarkers in sewage sludges: environmental significance

    PubMed

    Payet; Bryselbout; Morel; Lichtfouse

    1999-10-01

    Fossil fuel biomarkers, or "molecular fossils," are specific organic substances found in coals, petroleums, and sedimentary rocks. They are formed during millions of years of sedimentary burial by geochemical alteration of biological molecules, such as cholesterol, under the effect of biodegradation, temperature, pressure, and mineral catalysis, to produce geochemically mature molecules, for example, aromatic steroids (Fig. 1). Since fossil fuel biomarkers have a very specific molecular structure betraying fossil fuel sources, such markers should be useful in assessing the fossil fuel contamination of various modern media such as soils, plants, waters, and modern sediments. Here the identification of fossil fuel biomarkers of high geothermal maturity in sewage sludges provides evidence of the contamination of sludges by petroleum products. The most likely sources of contamination are contaminated vegetal food, road dust, and soil particles carried by rain water.http://link. springer.de/link/service/journals/00114/bibs/9086010/90860484. htm

  1. Tear biomarkers for keratoconus.

    PubMed

    Nishtala, Krishnatej; Pahuja, Natasha; Shetty, Rohit; Nuijts, Rudy M M A; Ghosh, Arkasubhra

    2016-01-01

    Keratoconus is a progressive corneal thinning, ectatic condition, which affects vision. Recent advances in corneal topography measurements has helped advance proper diagnosis of this condition and increased research and clinical interests in the disease etiopathogenesis. Considerable progress has been achieved in understanding the progression of the disease and tear fluid has played a major role in the progress. This review discusses the importance of tear fluid as a source of biomarker for keratoconus and how advances in technology have helped map the complexity of tears and thereby molecular readouts of the disease. Expanding knowledge of the tear proteome, lipidome and metabolome opened up new avenues to study keratoconus and to identify probable prognostic or diagnostic biomarkers for the disease. A multidimensional approach of analyzing tear fluid of patients layering on proteomics, lipidomics and metabolomics is necessary in effectively decoding keratoconus and thereby identifying targets for its treatment. PMID:27493978

  2. Biomarkers of environmental contamination

    SciTech Connect

    McCarthy, J.F.; Shugart, L.R.

    1990-01-01

    Biological markers are measurements at the molecular, biochemical, or cellular level in either wild populations from contaminated habitats or in organisms experimentally exposed to pollutants that indicate that the organism has been exposed to toxic chemicals, and the magnitude of the organisms response to the contaminant. Biological markers measured in wild animals can directly contribute to detecting, quantifying, and understanding the significance of exposure to chemicals in the environment. These measurements in environmental species may also help assess the potential for human exposure to environmental pollutants, and for predicting the human health risks. It is the objective of this volume to review the current state of science as it pertains to the scientific basis, current state of development, validation, and use of biological markers in environmental research. The emphasis is on identifying and evaluating exposure of environmental species and effects on the health of environmental species and the integrity of their ecosystem. The various chapters describe different types of biomarkers that offer promise for environmental monitoring. The biomarkers are arranged in categories defined by the nature of the toxic endpoint being probed: anatomical and cytological endpoints; detoxification, adaptive and immunological responses; genotoxic responses; metal metabolism; and application of biomarkers in field evaluation.

  3. BIOMARKER LIPIDS IN RED TIDE (GYMNODINIUM BREVE) BLOOMS ALONG THE NORTHWEST FLORIDA COAST

    EPA Science Inventory

    The ability to characterize phytoplankton communities and algal blooms using lipids as biomarkers requires knowledge of their distribution and taxonomic significance. Such an approach would have application, for example, in distinguishing and tracking certain dinoflagellates suc...

  4. Organic Biomarker Preservation in Silica-Rich Hydrothermal Systems with Implications to Mars

    NASA Astrophysics Data System (ADS)

    Jahnke, L. L.; Parenteau, M. N.; Farmer, J. D.

    2016-05-01

    Microbial community structure and preservation of organic matter in siliceous hydrothermal environments is a critical issue given the discovery of hydrothermal vents and silica on Mars. Here we discuss preservation of cyanobacterial biomarker lipid.

  5. Cancer biomarker discovery and validation

    PubMed Central

    Goossens, Nicolas; Nakagawa, Shigeki; Sun, Xiaochen; Hoshida, Yujin

    2015-01-01

    With the emergence of genomic profiling technologies and selective molecular targeted therapies, biomarkers play an increasingly important role in the clinical management of cancer patients. Single gene/protein or multi-gene “signature”-based assays have been introduced to measure specific molecular pathway deregulations that guide therapeutic decision-making as predictive biomarkers. Genome-based prognostic biomarkers are also available for several cancer types for potential incorporation into clinical prognostic staging systems or practice guidelines. However, there is still a large gap between initial biomarker discovery studies and their clinical translation due to the challenges in the process of cancer biomarker development. In this review we summarize the steps of biomarker development, highlight key issues in successful validation and implementation, and overview representative examples in the oncology field. We also discuss regulatory issues and future perspectives in the era of big data analysis and precision medicine. PMID:26213686

  6. A Bayesian network model for biomarker-based dose response.

    PubMed

    Hack, C Eric; Haber, Lynne T; Maier, Andrew; Shulte, Paul; Fowler, Bruce; Lotz, W Gregory; Savage, Russell E

    2010-07-01

    A Bayesian network model was developed to integrate diverse types of data to conduct an exposure-dose-response assessment for benzene-induced acute myeloid leukemia (AML). The network approach was used to evaluate and compare individual biomarkers and quantitatively link the biomarkers along the exposure-disease continuum. The network was used to perform the biomarker-based dose-response analysis, and various other approaches to the dose-response analysis were conducted for comparison. The network-derived benchmark concentration was approximately an order of magnitude lower than that from the usual exposure concentration versus response approach, which suggests that the presence of more information in the low-dose region (where changes in biomarkers are detectable but effects on AML mortality are not) helps inform the description of the AML response at lower exposures. This work provides a quantitative approach for linking changes in biomarkers of effect both to exposure information and to changes in disease response. Such linkage can provide a scientifically valid point of departure that incorporates precursor dose-response information without being dependent on the difficult issue of a definition of adversity for precursors.

  7. Early diagnosis of complex diseases by molecular biomarkers, network biomarkers, and dynamical network biomarkers.

    PubMed

    Liu, Rui; Wang, Xiangdong; Aihara, Kazuyuki; Chen, Luonan

    2014-05-01

    Many studies have been carried out for early diagnosis of complex diseases by finding accurate and robust biomarkers specific to respective diseases. In particular, recent rapid advance of high-throughput technologies provides unprecedented rich information to characterize various disease genotypes and phenotypes in a global and also dynamical manner, which significantly accelerates the study of biomarkers from both theoretical and clinical perspectives. Traditionally, molecular biomarkers that distinguish disease samples from normal samples are widely adopted in clinical practices due to their ease of data measurement. However, many of them suffer from low coverage and high false-positive rates or high false-negative rates, which seriously limit their further clinical applications. To overcome those difficulties, network biomarkers (or module biomarkers) attract much attention and also achieve better performance because a network (or subnetwork) is considered to be a more robust form to characterize diseases than individual molecules. But, both molecular biomarkers and network biomarkers mainly distinguish disease samples from normal samples, and they generally cannot ensure to identify predisease samples due to their static nature, thereby lacking ability to early diagnosis. Based on nonlinear dynamical theory and complex network theory, a new concept of dynamical network biomarkers (DNBs, or a dynamical network of biomarkers) has been developed, which is different from traditional static approaches, and the DNB is able to distinguish a predisease state from normal and disease states by even a small number of samples, and therefore has great potential to achieve "real" early diagnosis of complex diseases. In this paper, we comprehensively review the recent advances and developments on molecular biomarkers, network biomarkers, and DNBs in particular, focusing on the biomarkers for early diagnosis of complex diseases considering a small number of samples and high

  8. Learning Biomarkers of Pluripotent Stem Cells in Mouse

    PubMed Central

    Scheubert, Lena; Schmidt, Rainer; Repsilber, Dirk; Luštrek, Mitja; Fuellen, Georg

    2011-01-01

    Pluripotent stem cells are able to self-renew, and to differentiate into all adult cell types. Many studies report data describing these cells, and characterize them in molecular terms. Machine learning yields classifiers that can accurately identify pluripotent stem cells, but there is a lack of studies yielding minimal sets of best biomarkers (genes/features). We assembled gene expression data of pluripotent stem cells and non-pluripotent cells from the mouse. After normalization and filtering, we applied machine learning, classifying samples into pluripotent and non-pluripotent with high cross-validated accuracy. Furthermore, to identify minimal sets of best biomarkers, we used three methods: information gain, random forests and a wrapper of genetic algorithm and support vector machine (GA/SVM). We demonstrate that the GA/SVM biomarkers work best in combination with each other; pathway and enrichment analyses show that they cover the widest variety of processes implicated in pluripotency. The GA/SVM wrapper yields best biomarkers, no matter which classification method is used. The consensus best biomarker based on the three methods is Tet1, implicated in pluripotency just recently. The best biomarker based on the GA/SVM wrapper approach alone is Fam134b, possibly a missing link between pluripotency and some standard surface markers of unknown function processed by the Golgi apparatus. PMID:21791477

  9. Identification of Serum Biomarkers for Gastric Cancer Diagnosis Using a Human Proteome Microarray.

    PubMed

    Yang, Lina; Wang, Jingfang; Li, Jianfang; Zhang, Hainan; Guo, Shujuan; Yan, Min; Zhu, Zhenggang; Lan, Bin; Ding, Youcheng; Xu, Ming; Li, Wei; Gu, Xiaonian; Qi, Chong; Zhu, Heng; Shao, Zhifeng; Liu, Bingya; Tao, Sheng-Ce

    2016-02-01

    We aimed to globally discover serum biomarkers for diagnosis of gastric cancer (GC). GC serum autoantibodies were discovered and validated using serum samples from independent patient cohorts encompassing 1,401 participants divided into three groups, i.e. healthy, GC patients, and GC-related disease group. To discover biomarkers for GC, the human proteome microarray was first applied to screen specific autoantibodies in a total of 87 serum samples from GC patients and healthy controls. Potential biomarkers were identified via a statistical analysis protocol. Targeted protein microarrays with only the potential biomarkers were constructed and used to validate the candidate biomarkers using 914 samples. To provide further validation, the abundance of autoantibodies specific to the biomarker candidates was analyzed using enzyme-linked immunosorbent assays. Receiver operating characteristic curves were generated to evaluate the diagnostic accuracy of the serum biomarkers. Finally, the efficacy of prognosis efficacy of the final four biomarkers was evaluated by analyzing the clinical records. The final panel of biomarkers consisting of COPS2, CTSF, NT5E, and TERF1 provides high diagnostic power, with 95% sensitivity and 92% specificity to differentiate GC patients from healthy individuals. Prognosis analysis showed that the panel could also serve as independent predictors of the overall GC patient survival. The panel of four serum biomarkers (COPS2, CTSF, NT5E, and TERF1) could serve as a noninvasive diagnostic index for GC, and the combination of them could potentially be used as a predictor of the overall GC survival rate. PMID:26598640

  10. Interpretation of fish biomarker data for identification, classification, risk assessment and testing of endocrine disrupting chemicals.

    PubMed

    Dang, ZhiChao

    2016-01-01

    Chemical induced changes in fish biomarkers vitellogenin (VTG), secondary sex characteristics (SSC), and sex ratio indicate modes/mechanisms of action (MOAs) of EAS (estrogen, androgen and steroidogenesis) pathways. These biomarkers could be used for defining MOAs and the causal link between MOAs and adverse effects in fish for the identification of endocrine disrupting chemicals (EDCs). This paper compiled data sets of 150 chemicals for VTG, 57 chemicals for SSC and 38 chemicals for sex ratio in fathead minnow, medaka and zebrafish. It showed 1) changes in fish biomarkers can indicate the MOAs as anticipated; 2) in addition to EAS pathways, chemicals with non-EAS pathways induced changes in fish biomarkers; 3) responses of fish biomarkers did not always follow the anticipated patterns of EAS pathways. These responses may result from the interaction of chemical-induced multiple MOAs and confounding factors like fish diet, infection, culture conditions, general toxicity and stress response. The complex response of fish biomarkers to a chemical of interest requires EDC testing at multiple biological levels. Interpretation of fish biomarker data should be combined with relevant information at different biological levels, which is critical for defining chemical specific MOAs. The utility of fish biomarker data for identification, classification, PBT assessment, risk assessment, and testing of EDCs in the regulatory context was discussed. This paper emphasizes the importance of fish biomarker data in the regulatory context, a weight of evidence approach for the interpretation of fish biomarker data and the need for defining levels of evidence for the identification of EDCs.

  11. Biomarkers in Prostate Cancer Epidemiology

    PubMed Central

    Verma, Mukesh; Patel, Payal; Verma, Mudit

    2011-01-01

    Understanding the etiology of a disease such as prostate cancer may help in identifying populations at high risk, timely intervention of the disease, and proper treatment. Biomarkers, along with exposure history and clinical data, are useful tools to achieve these goals. Individual risk and population incidence of prostate cancer result from the intervention of genetic susceptibility and exposure. Biochemical, epigenetic, genetic, and imaging biomarkers are used to identify people at high risk for developing prostate cancer. In cancer epidemiology, epigenetic biomarkers offer advantages over other types of biomarkers because they are expressed against a person's genetic background and environmental exposure, and because abnormal events occur early in cancer development, which includes several epigenetic alterations in cancer cells. This article describes different biomarkers that have potential use in studying the epidemiology of prostate cancer. We also discuss the characteristics of an ideal biomarker for prostate cancer, and technologies utilized for biomarker assays. Among epigenetic biomarkers, most reports indicate GSTP1 hypermethylation as the diagnostic marker for prostate cancer; however, NKX2-5, CLSTN1, SPOCK2, SLC16A12, DPYS, and NSE1 also have been reported to be regulated by methylation mechanisms in prostate cancer. Current challenges in utilization of biomarkers in prostate cancer diagnosis and epidemiologic studies and potential solutions also are discussed. PMID:24213111

  12. Biomarker Identification Using Text Mining

    PubMed Central

    Li, Hui; Liu, Chunmei

    2012-01-01

    Identifying molecular biomarkers has become one of the important tasks for scientists to assess the different phenotypic states of cells or organisms correlated to the genotypes of diseases from large-scale biological data. In this paper, we proposed a text-mining-based method to discover biomarkers from PubMed. First, we construct a database based on a dictionary, and then we used a finite state machine to identify the biomarkers. Our method of text mining provides a highly reliable approach to discover the biomarkers in the PubMed database. PMID:23197989

  13. The microfluidics of the eccrine sweat gland, including biomarker partitioning, transport, and biosensing implications

    PubMed Central

    Sonner, Z.; Wilder, E.; Heikenfeld, J.; Kasting, G.; Beyette, F.; Swaile, D.; Sherman, F.; Joyce, J.; Hagen, J.; Kelley-Loughnane, N.; Naik, R.

    2015-01-01

    Non-invasive and accurate access of biomarkers remains a holy grail of the biomedical community. Human eccrine sweat is a surprisingly biomarker-rich fluid which is gaining increasing attention. This is especially true in applications of continuous bio-monitoring where other biofluids prove more challenging, if not impossible. However, much confusion on the topic exists as the microfluidics of the eccrine sweat gland has never been comprehensively presented and models of biomarker partitioning into sweat are either underdeveloped and/or highly scattered across literature. Reported here are microfluidic models for eccrine sweat generation and flow which are coupled with review of blood-to-sweat biomarker partition pathways, therefore providing insights such as how biomarker concentration changes with sweat flow rate. Additionally, it is shown that both flow rate and biomarker diffusion determine the effective sampling rate of biomarkers at the skin surface (chronological resolution). The discussion covers a broad class of biomarkers including ions (Na+, Cl−, K+, NH4+), small molecules (ethanol, cortisol, urea, and lactate), and even peptides or small proteins (neuropeptides and cytokines). The models are not meant to be exhaustive for all biomarkers, yet collectively serve as a foundational guide for further development of sweat-based diagnostics and for those beginning exploration of new biomarker opportunities in sweat. PMID:26045728

  14. Serum biomarker panels for diagnosis of gastric cancer

    PubMed Central

    Tong, Weihua; Ye, Fei; He, Liang; Cui, Lifeng; Cui, Miao; Hu, Yuan; Li, Wei; Jiang, Jing; Zhang, David Y; Suo, Jian

    2016-01-01

    Purpose Currently, serum biomarkers that are sufficiently sensitive and specific for early detection and risk classification of gastric adenocarcinomas are not known. In this study, ten serum markers were assessed using the Luminex system and enzyme-linked immunosorbent assay for the diagnosis of gastric cancer and analysis of the relation between prognosis and metastases. Patients and methods A training set consisting of 228 gastric adenocarcinoma and 190 control samples was examined. A Luminex multiplex panel with nine biomarkers, consisting of three proteins discovered through our previous studies and six proteins previously reported to be cancer-associated, was constructed. One additional biomarker was detected using a commercial kit containing EDTA. Logistic regression, random forest (RF), and support vector machine (SVM) were used to identify the panel of discriminatory biomarkers in the training set. After selecting five proteins as candidate biomarkers, multivariate classification analyses were used to identify algorithms for diagnostic biomarker combinations. These algorithms were independently validated using a set of 57 gastric adenocarcinoma and 48 control samples. Results Serum pepsinogen I, serum pepsinogen II, A Disintegrin And Metalloproteinase domain-containing protein 8 (ADAM8), vascular endothelial growth factor (VEGF), and serum IgG to Helicobacter pylori were selected as classifiers in the three algorithms. These algorithms differentiated between the majority of gastric adenocarcinoma and control serum samples in the training/test set with high accuracy (RF 79.0%, SVM 83.8%, logistic regression 76.2%). These algorithms also differentiated the samples in the validation set (accuracy: RF 82.5%, SVM 86.1%, logistic regression 78.7%). Conclusion A panel of combinatorial biomarkers comprising VEGF, ADAM8, IgG to H. pylori, serum pepsinogen I, and pepsinogen II were developed. The use of biomarkers is a less invasive method for the diagnosis of

  15. Chiral Biomarkers in Meteorites

    NASA Technical Reports Server (NTRS)

    Hoover, Richard B.

    2010-01-01

    The chirality of organic molecules with the asymmetric location of group radicals was discovered in 1848 by Louis Pasteur during his investigations of the rotation of the plane of polarization of light by crystals of sodium ammonium paratartrate. It is well established that the amino acids in proteins are exclusively Levorotary (L-aminos) and the sugars in DNA and RNA are Dextrorotary (D-sugars). This phenomenon of homochirality of biological polymers is a fundamental property of all life known on Earth. Furthermore, abiotic production mechanisms typically yield recemic mixtures (i.e. equal amounts of the two enantiomers). When amino acids were first detected in carbonaceous meteorites, it was concluded that they were racemates. This conclusion was taken as evidence that they were extraterrestrial and produced by abiologically. Subsequent studies by numerous researchers have revealed that many of the amino acids in carbonaceous meteorites exhibit a significant L-excess. The observed chirality is much greater than that produced by any currently known abiotic processes (e.g. Linearly polarized light from neutron stars; Circularly polarized ultraviolet light from faint stars; optically active quartz powders; inclusion polymerization in clay minerals; Vester-Ulbricht hypothesis of parity violations, etc.). This paper compares the measured chirality detected in the amino acids of carbonaceous meteorites with the effect of these diverse abiotic processes. IT is concluded that the levels observed are inconsistent with post-arrival biological contamination or with any of the currently known abiotic production mechanisms. However, they are consistent with ancient biological processes on the meteorite parent body. This paper will consider these chiral biomarkers in view of the detection of possible microfossils found in the Orgueil and Murchison carbonaceous meteorites. Energy dispersive x-ray spectroscopy (EDS) data obtained on these morphological biomarkers will be

  16. Biomarkers in Cervical Cancer

    PubMed Central

    Yim, Eun-Kyoung; Park, Jong-Sup

    2006-01-01

    Cervical cancer, a potentially preventable disease, remains the second most common malignancy in women worldwide. Human papillomavirus (HPV) is the single most important etiological agent in cervical cancer, contributing to neoplastic progression through the action of viral oncoproteins, mainly E6 and E7. Cervical screening programs using Pap smear testing have dramatically improved cervical cancer incidence and reduced deaths, but cervical cancer still remains a global health burden. The biomarker discovery for accurate detection and diagnosis of cervical carcinoma and its malignant precursors (collectively referred to as high-grade cervical disease) represents one of the current challenges in clinical medicine and cytopathology. PMID:19690652

  17. Linking Service-Learning Opportunities and Domestic Immersion Experiences in US Latino Communities: A Case Study of the "En Nuestra Lengua" Project

    ERIC Educational Resources Information Center

    Tijunelis, Viktorija; Satterfield, Teresa; Benki, Jose R.

    2013-01-01

    We report on the service-learning component of a Spanish-language Saturday school in Ann Arbor, Michigan, for elementary-aged Spanish-language heritage learners and also examine the newly forming Latino community served by this innovative program. The US Spanish-speaking population is growing throughout the country, resulting in greatly increased…

  18. The Arts--A Missing Link in the Basic Curriculum. A Process Manual to Integrate the Arts into the Elementary School Curriculum for Administrators, Teachers and Community Members.

    ERIC Educational Resources Information Center

    Link, Kathryn Gerlach

    Cited as a model project for the state of Vermont, this process model helps administrators, teachers, and community members integrate the arts into the elementary school curriculum. Arranged into 10 sections, the introduction in part 1 outlines the development of the program. Three major project goals are stated in section 2 and section 3 is an…

  19. Biomarkers in melanoma.

    PubMed

    Griewank, Klaus G

    2016-01-01

    Malignant melanoma remains the skin cancer with the highest number of mortalities worldwide. While early diagnosis and complete surgical excision remain the best possibility for curing disease, prognosis at the stage of metastasis is still poor. Recent years have brought about considerable advances in terms of understanding the pathogenesis of melanoma and treating advanced disease. The discovery of activating BRAF mutations in around 50% of tumors has led to the introduction of targeted therapies downregulating BRAF signaling output. These have been further refined as combination therapies, which by targeting multiple targets have further improved the clinical outcome. A comparable, potentially even superior therapeutic alternative has been the introduction of immunotherapeutic approaches, including PD-1 and CTLA-4 checkpoint blockade therapies. Despite all genetic knowledge acquired in recent years, a clearly applicable prognostic signature of clinical value has not been established. General prognostic assessment of cutaneous melanoma remains based on clinical and pathological criteria (most importantly tumor thickness). The main challenges lying ahead are to establish a reliable prognostic test effectively determining which tumors will metastasize. Additionally establishing biomarkers which will allow patients to be stratified according to the most promising systemic therapy (immunotherapies and/or BRAF inhibitor therapies) is of utmost importance for patients with metastasized disease. Identifying serum biomarkers enabling disease to be monitored as well as determining tumor properties (i.e. resistance) would also be of great value. While initial results have proven promising, there remains much work to be done. PMID:27467728

  20. Biomarkers in cancer screening: a public health perspective.

    PubMed

    Srivastava, Sudhir; Gopal-Srivastava, Rashmi

    2002-08-01

    definitive technology, such as CT scan. The National Cancer Institute's Early Detection Research Network (EDRN) has begun an innovative, investigator-initiated project to improve methods for detecting the biomarkers of cancer cells. The EDRN is a consortium of more than 32 institutions to link discovery of biomarkers to the next steps in the process of developing early detection tests. These discoveries will lead to early clinical validation of tests with improved accuracy and reliability. PMID:12163714

  1. Urinary Biomarkers of Oxidative Status

    PubMed Central

    Il’yasova, Dora; Scarbrough, Peter; Spasojevic, Ivan

    2012-01-01

    Oxidative damage produced by reactive oxygen species (ROS) has been implicated in the etiology and pathology of many health conditions, including a large number of chronic diseases. Urinary biomarkers of oxidative status present a great opportunity to study redox balance in human populations. With urinary biomarkers, specimen collection is non-invasive and the organic/metal content is low, which minimizes the artifactual formation of oxidative damage to molecules in specimens. Also, urinary levels of the biomarkers present intergraded indices of redox balance over a longer period of time compared to blood levels. This review summarizes the criteria for evaluation of biomarkers applicable to epidemiological studies and evaluation of several classes of biomarkers that are formed non-enzymatically: oxidative damage to lipids, proteins, DNA, and allantoin, an oxidative product of uric acid. The review considers formation, metabolism, and exertion of each biomarker, available data on validation in animal and clinical models of oxidative stress, analytical approaches, and their intra- and inter-individual variation. The recommended biomarkers for monitoring oxidative status over time are F2-isoprostanes and 8-oxodG. For inter-individual comparisons, F2-isoprostanes are recommended, whereas urinary 8-oxodG levels may be confounded by differences in the DNA repair capacity. Promising urinary biomarkers include allantoin, acrolein-lysine, and dityrosine. PMID:22683781

  2. Biomarkers of tobacco smoke exposure.

    PubMed

    Mattes, William; Yang, Xi; Orr, Michael S; Richter, Patricia; Mendrick, Donna L

    2014-01-01

    Diseases and death caused by exposure to tobacco smoke have become the single most serious preventable public health concern. Thus, biomarkers that can monitor tobacco exposure and health effects can play a critical role in tobacco product regulation and public health policy. Biomarkers of exposure to tobacco toxicants are well established and have been used in population studies to establish public policy regarding exposure to second-hand smoke, an example being the nicotine metabolite cotinine, which can be measured in urine. Biomarkers of biological response to tobacco smoking range from those indicative of inflammation to mRNA and microRNA patterns related to tobacco use and/or disease state. Biomarkers identifying individuals with an increased risk for a pathological response to tobacco have also been described. The challenge for any novel technology or biomarker is its translation to clinical and/or regulatory application, a process that requires first technical validation of the assay and then careful consideration of the context the biomarker assay may be used in the regulatory setting. Nonetheless, the current efforts to investigate new biomarker of tobacco smoke exposure promise to offer powerful new tools in addressing the health hazards of tobacco product use. This review will examine such biomarkers, albeit with a focus on those related to cigarette smoking. PMID:25735858

  3. Epigenetic biomarkers in liver cancer.

    PubMed

    Banaudha, Krishna K; Verma, Mukesh

    2015-01-01

    Liver cancer (hepatocellular carcinoma or HCC) is a major cancer worldwide. Research in this field is needed to identify biomarkers that can be used for early detection of the disease as well as new approaches to its treatment. Epigenetic biomarkers provide an opportunity to understand liver cancer etiology and evaluate novel epigenetic inhibitors for treatment. Traditionally, liver cirrhosis, proteomic biomarkers, and the presence of hepatitis viruses have been used for the detection and diagnosis of liver cancer. Promising results from microRNA (miRNA) profiling and hypermethylation of selected genes have raised hopes of identifying new biomarkers. Some of these epigenetic biomarkers may be useful in risk assessment and for screening populations to identify who is likely to develop cancer. Challenges and opportunities in the field are discussed in this chapter.

  4. Emerging biomarkers in psoriatic arthritis.

    PubMed

    Paek, So Yeon; Han, Ling; Weiland, Matthew; Lu, Chuan-Jian; McKinnon, Kathleen; Zhou, Li; Lim, Henry W; Elder, James T; Mi, Qing-Sheng

    2015-12-01

    Psoriasis is an immune-mediated skin disease which affects 2-4% of the worldwide population. Approximately 20-30% of patients with psoriasis develop psoriatic arthritis (PsA), a frequently destructive and disabling condition. As skin manifestations precede joint symptoms in nearly all patients with PsA, identification of biomarkers for early prediction of joint damage is an important clinical need. Because not all patients with PsA respond to treatment in the same fashion, identification of biomarkers capable of predicting therapeutic response is also imperative. Here, we review existing literature and discuss current investigations to identify potential biomarkers for PsA disease activity, with particular emphasis on microRNAs as novel markers of interest. Serum (soluble) biomarkers, peripheral osteoclast precursor as cellular biomarkers, and genetic loci associated with skin and joint disease are also reviewed. PMID:26602058

  5. The Genetics Underlying Natural Variation in the Biotic Interactions of Arabidopsis thaliana: The Challenges of Linking Evolutionary Genetics and Community Ecology.

    PubMed

    Roux, F; Bergelson, J

    2016-01-01

    In the context of global change, predicting the responses of plant communities in an ever-changing biotic environment calls for a multipronged approach at the interface of evolutionary genetics and community ecology. However, our understanding of the genetic basis of natural variation involved in mediating biotic interactions, and associated adaptive dynamics of focal plants in their natural communities, is still in its infancy. Here, we review the genetic and molecular bases of natural variation in the response to biotic interactions (viruses, bacteria, fungi, oomycetes, herbivores, and plants) in the model plant Arabidopsis thaliana as well as the adaptive value of these bases. Among the 60 identified genes are a number that encode nucleotide-binding site leucine-rich repeat (NBS-LRR)-type proteins, consistent with early examples of plant defense genes. However, recent studies have revealed an extensive diversity in the molecular mechanisms of defense. Many types of genetic variants associate with phenotypic variation in biotic interactions, even among the genes of large effect that tend to be identified. In general, we found that (i) balancing selection rather than directional selection explains the observed patterns of genetic diversity within A. thaliana and (ii) the cost/benefit tradeoffs of adaptive alleles can be strongly dependent on both genomic and environmental contexts. Finally, because A. thaliana rarely interacts with only one biotic partner in nature, we highlight the benefit of exploring diffuse biotic interactions rather than tightly associated host-enemy pairs. This challenge would help to improve our understanding of coevolutionary quantitative genetics within the context of realistic community complexity. PMID:27282025

  6. Use of Biomarkers in Oil Spill Risk Assessment in the marine environment

    SciTech Connect

    Anderson, Jack W.; Lee, Richard F.

    2006-12-01

    Numerous molecular, cellular and physiological biomarkers have been used to assess the responses of marine animals to petroleum compounds. To be used in ecological risk assessment after an oil spill, a biomarker response needs to be linked to petroleum exposure and not strongly influenced by internal and external confounding factors. Biomarker responses to petroleum PAH, dominated by alkylated two- and three-ringed aromatics, can be quite different than responses to pyrogenic PAH, dominated by four- and five-ringed aromatics. In many field sites there is a mixture of petrogenic and pyrogenic PAH, along with other contaminant, making it difficult to relate biomarker responses to a particular contaminant class. Biomarkers used to assess marine animal responses in the field include the cytochrome P450 system, heat stress protein, histopathology and bile fluorescent compounds (FAC). Other biomarkers, including DNA/chromosomal damage and phase 2 enzymes, have been shown to respond after laboratory exposure, but more works needs to be done to demonstrate their usefulness in the field. One of the most useful biomarkers of petroleum exposure are the FAC responses in fish, which can be used to distinguish between petrogenic and pyrogenic PAH exposure. Few of the presently used biomarkers are linked to higher order biological effects, e.g toxicity, reproductive failure.

  7. Linking Microbial Community and Catabolic Gene Structures during the Adaptation of Three Contaminated Soils under Continuous Long-Term Pollutant Stress

    PubMed Central

    Lima-Morales, Daiana; Jáuregui, Ruy; Camarinha-Silva, Amelia; Geffers, Robert; Vilchez-Vargas, Ramiro

    2016-01-01

    Three types of contaminated soil from three geographically different areas were subjected to a constant supply of benzene or benzene/toluene/ethylbenzene/xylenes (BTEX) for a period of 3 months. Different from the soil from Brazil (BRA) and Switzerland (SUI), the Czech Republic (CZE) soil which was previously subjected to intensive in situ bioremediation displayed only negligible changes in community structure. BRA and SUI soil samples showed a clear succession of phylotypes. A rapid response to benzene stress was observed, whereas the response to BTEX pollution was significantly slower. After extended incubation, actinobacterial phylotypes increased in relative abundance, indicating their superior fitness to pollution stress. Commonalities but also differences in the phylotypes were observed. Catabolic gene surveys confirmed the enrichment of actinobacteria by identifying the increase of actinobacterial genes involved in the degradation of pollutants. Proteobacterial phylotypes increased in relative abundance in SUI microcosms after short-term stress with benzene, and catabolic gene surveys indicated enriched metabolic routes. Interestingly, CZE soil, despite staying constant in community structure, showed a change in the catabolic gene structure. This indicates that a highly adapted community, which had to adjust its gene pool to meet novel challenges, has been enriched. PMID:26850298

  8. Microbial community stratification linked to utilization of carbohydrates and phosphorus limitation in a boreal peatland at Marcell Experimental Forest, Minnesota, USA.

    PubMed

    Lin, Xueju; Tfaily, Malak M; Steinweg, J Megan; Chanton, Patrick; Esson, Kaitlin; Yang, Zamin K; Chanton, Jeffrey P; Cooper, William; Schadt, Christopher W; Kostka, Joel E

    2014-06-01

    This study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance of Acidobacteria and the Syntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance of Archaea (primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at

  9. Microbial Community Stratification Linked to Utilization of Carbohydrates and Phosphorus Limitation in a Boreal Peatland at Marcell Experimental Forest, Minnesota, USA

    PubMed Central

    Tfaily, Malak M.; Steinweg, J. Megan; Chanton, Patrick; Esson, Kaitlin; Yang, Zamin K.; Chanton, Jeffrey P.; Cooper, William; Schadt, Christopher W.

    2014-01-01

    This study investigated the abundance, distribution, and composition of microbial communities at the watershed scale in a boreal peatland within the Marcell Experimental Forest (MEF), Minnesota, USA. Through a close coupling of next-generation sequencing, biogeochemistry, and advanced analytical chemistry, a biogeochemical hot spot was revealed in the mesotelm (30- to 50-cm depth) as a pronounced shift in microbial community composition in parallel with elevated peat decomposition. The relative abundance of Acidobacteria and the Syntrophobacteraceae, including known hydrocarbon-utilizing genera, was positively correlated with carbohydrate and organic acid content, showing a maximum in the mesotelm. The abundance of Archaea (primarily crenarchaeal groups 1.1c and 1.3) increased with depth, reaching up to 60% of total small-subunit (SSU) rRNA gene sequences in the deep peat below the 75-cm depth. Stable isotope geochemistry and potential rates of methane production paralleled vertical changes in methanogen community composition to indicate a predominance of acetoclastic methanogenesis mediated by the Methanosarcinales in the mesotelm, while hydrogen-utilizing methanogens predominated in the deeper catotelm. RNA-derived pyrosequence libraries corroborated DNA sequence data to indicate that the above-mentioned microbial groups are metabolically active in the mid-depth zone. Fungi showed a maximum in rRNA gene abundance above the 30-cm depth, which comprised only an average of 0.1% of total bacterial and archaeal rRNA gene abundance, indicating prokaryotic dominance. Ratios of C to P enzyme activities approached 0.5 at the acrotelm and catotelm, indicating phosphorus limitation. In contrast, P limitation pressure appeared to be relieved in the mesotelm, likely due to P solubilization by microbial production of organic acids and C-P lyases. Based on path analysis and the modeling of community spatial turnover, we hypothesize that P limitation outweighs N limitation at

  10. Stable Isotope Ratios as Biomarkers of Diet for Health Research.

    PubMed

    O'Brien, Diane M

    2015-01-01

    Diet is a leading modifiable risk factor for chronic disease, but it remains difficult to measure accurately due to the error and bias inherent in self-reported methods of diet assessment. Consequently, there is a pressing need for more objective biomarkers of diet for use in health research. The stable isotope ratios of light elements are a promising set of candidate biomarkers because they vary naturally and reproducibly among foods, and those variations are captured in molecules and tissues with high fidelity. Recent studies have identified valid isotopic measures of short- and long-term sugar intake, meat intake, and fish intake in specific populations. These studies provide a strong foundation for validating stable isotopic biomarkers in the general US population. Approaches to improve specificity for specific foods are needed; for example, by modeling intake using multiple stable isotope ratios or by isolating and measuring specific molecules linked to foods of interest. PMID:26048703

  11. Stable Isotope Ratios as Biomarkers of Diet for Health Research.

    PubMed

    O'Brien, Diane M

    2015-01-01

    Diet is a leading modifiable risk factor for chronic disease, but it remains difficult to measure accurately due to the error and bias inherent in self-reported methods of diet assessment. Consequently, there is a pressing need for more objective biomarkers of diet for use in health research. The stable isotope ratios of light elements are a promising set of candidate biomarkers because they vary naturally and reproducibly among foods, and those variations are captured in molecules and tissues with high fidelity. Recent studies have identified valid isotopic measures of short- and long-term sugar intake, meat intake, and fish intake in specific populations. These studies provide a strong foundation for validating stable isotopic biomarkers in the general US population. Approaches to improve specificity for specific foods are needed; for example, by modeling intake using multiple stable isotope ratios or by isolating and measuring specific molecules linked to foods of interest.

  12. Biomarkers in Alpha-1 Antitrypsin Deficiency Chronic Obstructive Pulmonary Disease.

    PubMed

    Turino, Gerard M; Ma, Shuren; Cantor, Jerome O; Lin, Yong Y

    2016-08-01

    Biomarkers of pathogenesis in chronic obstructive pulmonary disease (COPD) can significantly accelerate drug development. In COPD related to alpha-1 antitrypsin deficiency, the role of neutrophil elastase and its inhibition by alpha-1 antitrypsin protein focused interest on elastin degradation and the development of pulmonary emphysema. Amino acids desmosine and isodesmosine are unique cross-links in mature elastin fibers and can serve as biomarkers of elastin degradation when measured in body fluids. This review gives a perspective on what has been learned by the earliest measurements of desmosine and isodesmosine followed by later studies using methods of increased sensitivity and specificity and the meaning for developing new therapies. Also included are brief statements on the biomarkers fibrinogen, CC-16, and Aa-Val-360 in COPD. PMID:27564670

  13. Stable Isotope Ratios as Biomarkers of Diet for Health Research

    PubMed Central

    O’Brien, Diane M.

    2016-01-01

    Diet is a leading modifiable risk factor for chronic disease, but it remains difficult to measure accurately due to the error and bias inherent in self-reported methods of diet assessment. Consequently there is a pressing need for more objective biomarkers of diet for use in health research. The stable isotope ratios of light elements are a promising set of candidate biomarkers because they vary naturally and reproducibly among foods, and those variations are captured in molecules and tissues with high fidelity. Recent studies have identified valid isotopic measures of short and long-term sugar intake, meat intake, and fish intake in specific populations. These studies provide a strong foundation for validating stable isotopic biomarkers in the general United States population. Approaches to improve specificity for specific foods are needed, for example, by modeling intake using multiple stable isotope ratios, or by isolating and measuring specific molecules linked to foods of interest. PMID:26048703

  14. Circulating tumors cells as biomarkers: progress toward biomarker qualification.

    PubMed

    Danila, Daniel C; Pantel, Klaus; Fleisher, Martin; Scher, Howard I

    2011-01-01

    Personalized cancer medicine requires the development of tumor-specific biomarkers to optimize selection of targeted therapies and to better assess response to therapy. Current efforts in several tumor types have shown that patients in whom circulating tumor cells (CTCs) are detected have an inferior prognosis relative to those in whom CTCs are not detected and that the elimination or decrease of CTCs following treatment is associated with improved clinical outcomes. Technological advances in the detection, isolation, capture, and characterization of CTCs from phlebotomy samples obtained in a routine clinical practice setting have enabled the evaluation of different CTC biomarkers. Unmet needs in cancer diagnosis and treatment where CTC biomarkers have been studied include determining prognosis, assessing the effects of treatment, and as a source of tumor for the biologic identification and characterization of determinants to predict sensitivity to one form of treatment versus another and to understand mechanisms of treatment resistance.At present, there is no single definition of a CTC and no single CTC "biomarker." Rather, multiple assays (tests) are in development for CTC biomarkers. However, before the role of any biomarker in medical decision making can be determined, it is essential that the assays used to measure the biomarker are analytically validated in a sequence of trials to generate the evidence to support the biomarker's use in the given context of use. It is against this background that this review focuses on the process of developing CTC biomarker assays, with the objective of outlining the necessary steps to qualify specific CTC tests for medical decision making in clinical practice or drug development. The potential for point-of-care tests is clear.

  15. Imaging Biomarkers in Immunotherapy

    PubMed Central

    Juergens, Rosalyn A.; Zukotynski, Katherine A.; Singnurkar, Amit; Snider, Denis P.; Valliant, John F.; Gulenchyn, Karen Y.

    2016-01-01

    Immune-based therapies have been in use for decades but recent work with immune checkpoint inhibitors has now changed the landscape of cancer treatment as a whole. While these advances are encouraging, clinicians still do not have a consistent biomarker they can rely on that can accurately select patients or monitor response. Molecular imaging technology provides a noninvasive mechanism to evaluate tumors and may be an ideal candidate for these purposes. This review provides an overview of the mechanism of action of varied immunotherapies and the current strategies for monitoring patients with imaging. We then describe some of the key researches in the preclinical and clinical literature on the current uses of molecular imaging of the immune system and cancer. PMID:26949344

  16. Biomarkers for lymphoma

    DOEpatents

    Zangar, Richard C.; Varnum, Susan M.

    2014-09-02

    A biomarker, method, test kit, and diagnostic system for detecting the presence of lymphoma in a person are disclosed. The lymphoma may be Hodgkin's lymphoma or non-Hodgkin's lymphoma. The person may be a high-risk subject. In one embodiment, a plasma sample from a person is obtained. The level of at least one protein listed in Table S3 in the plasma sample is measured. The level of at least one protein in the plasma sample is compared with the level in a normal or healthy subject. The lymphoma is diagnosed based upon the level of the at least one protein in the plasma sample in comparison to the normal or healthy level.

  17. Molecular Pathology and Biomarkers.

    PubMed

    Ha, Patrick K; Stenman, Göran

    2016-01-01

    The field of salivary gland tumor biology is quite broad, given the numerous subtypes of both benign and malignant tumors originating from the major and minor salivary glands. Knowledge about the molecular pathology of these lesions is still limited, and there are few clinically useful diagnostic and prognostic biomarkers. However, recent discoveries of certain key genomic alterations, such as chromosome translocations, copy number alterations, and mutations, provide new insights into the molecular pathogenesis of these lesions and may help to better define them. It is also hoped that this new knowledge can help to guide therapy, but this translation has been somewhat slow to develop, perhaps due to the rarity of these tumors and the lack of large, randomized studies. However, because of the limitations inherent in what surgery and radiation can provide, there is an urgent need for understanding of the mechanisms of carcinogenesis in these tumors individually, so that chemotherapy and/or targeted therapy can be rationally selected.

  18. Biomarkers of manganese intoxication.

    PubMed

    Zheng, Wei; Fu, Sherleen X; Dydak, Ulrike; Cowan, Dallas M

    2011-01-01

    Manganese (Mn), upon absorption, is primarily sequestered in tissue and intracellular compartments. For this reason, blood Mn concentration does not always accurately reflect Mn concentration in the targeted tissue, particularly in the brain. The discrepancy between Mn concentrations in tissue or intracellular components means that blood Mn is a poor biomarker of Mn exposure or toxicity under many conditions and that other biomarkers must be established. For group comparisons of active workers, blood Mn has some utility for distinguishing exposed from unexposed subjects, although the large variability in mean values renders it insensitive for discriminating one individual from the rest of the study population. Mn exposure is known to alter iron (Fe) homeostasis. The Mn/Fe ratio (MIR) in plasma or erythrocytes reflects not only steady-state concentrations of Mn or Fe in tested individuals, but also a biological response (altered Fe homeostasis) to Mn exposure. Recent human studies support the potential value for using MIR to distinguish individuals with Mn exposure. Additionally, magnetic resonance imaging (MRI), in combination with noninvasive assessment of γ-aminobutyric acid (GABA) by magnetic resonance spectroscopy (MRS), provides convincing evidence of Mn exposure, even without clinical symptoms of Mn intoxication. For subjects with long-term, low-dose Mn exposure or for those exposed in the past but not the present, neither blood Mn nor MRI provides a confident distinction for Mn exposure or intoxication. While plasma or erythrocyte MIR is more likely a sensitive measure, the cut-off values for MIR among the general population need to be further tested and established. Considering the large accumulation of Mn in bone, developing an X-ray fluorescence spectroscopy or neutron-based spectroscopy method may create yet another novel non-invasive tool for assessing Mn exposure and toxicity. PMID:20946915

  19. Link Analysis

    NASA Astrophysics Data System (ADS)

    Donoho, Steve

    Link analysis is a collection of techniques that operate on data that can be represented as nodes and links. This chapter surveys a variety of techniques including subgraph matching, finding cliques and K-plexes, maximizing spread of influence, visualization, finding hubs and authorities, and combining with traditional techniques (classification, clustering, etc). It also surveys applications including social network analysis, viral marketing, Internet search, fraud detection, and crime prevention.

  20. Biomarkers and prognostic indicators in pulmonary arterial hypertension.

    PubMed

    Jardim, Carlos; Souza, Rogerio

    2015-06-01

    Our understanding of the pathophysiology of pulmonary arterial hypertension (PAH) has increased substantially in the past decades. More accurate diagnosis and increased options for treatment have given researchers the opportunity to better explore the response to medical therapy and prognosis. As a result, the use of biomarkers and prognostic indicators for this devastating disease has been widely investigated. Biomarkers and prognostic indicators have also been more frequently incorporated into the design of new clinical trials. This approach has helped the pulmonary hypertension (PH) community step forward in the search for effective treatments for PAH. However, no single biomarker has shown significant superiority in predicting prognosis or patient response and an integrative approach is necessary to understand which combination of markers should be used in each of the clinical scenarios that characterize the management of PAH.

  1. Impact of gravel mining on benthic invertebrate communities in a highly dynamic gravel-bed river: an integrated methodology to link geomorphic disturbances and ecological status

    NASA Astrophysics Data System (ADS)

    Béjar, María; Gibbins, Chris; Vericat, Damià; Batalla, Ramon J.; Buendia, Cristina; Lobera, Gemma

    2014-05-01

    Water and sediments are transported along river channels. Their supply, transport and deposition control river morphology and sedimentary characteristics, which in turn support habitat. Floods disturb river channels naturally although anthropogenic impacts may also contribute. River channel disturbance is considered the main factor affecting the organization of riverine communities and contributes to key ecological processes. In this paper we present an integrated methodology designed to analyze the impacts of in-channel gravel mining on benthic invertebrate communities. The study is conducted in the Upper River Cinca (Southern Pyrenees). A 11 km river reach is being monitored in order to understand the effects of floods and gravel mining on channel morphodynamics and invertebrate communities. The study reach is located in and upland gravel-bed system historically and currently affected by periodical episodes of in-channel sediment mining. This methodology has been developed in the background of the research project MorphSed. An integrated methodology of four components (Co) has been designed and is being implemented: (Co1) acquisition of high resolution imagery to generate topographic models before and after channel disturbances. Floods and in-channel gravel mining are considered natural and anthropogenic disturbances, respectively. Topographic models are obtained by means of combining automated digital photogrammetry (SfM) and optical bathymetric models. Event-scale models are used to assess the spatial extent and magnitude of bed disturbance. (Co2) Invertebrate sampling in 5 representative reaches along the study site. Invertebrate surber samples are providing data to define assemblages and their characteristics (composition, density, distribution, traits). These data is used to assess the spatial extent of channel disturbance impacts on the taxonomic and trait structure of communities. (Co3) Monitoring flow and sediment transport in the upstream and downstream

  2. [Novel biomarkers for diabetic nephropathy].

    PubMed

    Araki, Shin-ichi

    2014-02-01

    Diabetic nephropathy is a leading cause of end-stage renal disease worldwide. An early clinical sign of this complication is an increase of urinary albumin excretion, called microalbuminuria, which is not only a predictor of the progression of nephropathy, but also an independent risk factor for cardiovascular disease. Although microalbuminuria is clinically important to assess the prognosis of diabetic patients, it may be insufficient as an early and specific biomarker of diabetic nephropathy because of a large day-to-day variation and lack of a good correlation of microalbuminuria with renal dysfunction and pathohistological changes. Thus, more sensitive and specific biomarkers are needed to improve the diagnostic capability of identifying patients at high risk. The factors involved in renal tubulo-interstitial damage, the production and degradation of extracellular matrix, microinflammation, etc., are investigated as candidate molecules. Despite numerous efforts so far, the assessment of these biomarkers is still a subject of ongoing investigations. Recently, a variety of omics and quantitative techniques in systems biology are rapidly emerging in the field of biomarker discovery, including proteomics, transcriptomics, and metabolomics, and they have been applied to search for novel putative biomarkers of diabetic nephropathy. Novel biomarkers or their combination with microalbuminuria provide a better diagnostic accuracy than microalbuminuria alone, and may be useful for establishing personal medicine. Furthermore, the identification of novel biomarkers may provide insight into the mechanisms underlying diabetic nephropathy.

  3. MOLECULAR CHARACTERIZATION OF MICROBIAL COMMUNITIES IN A JP-4 FUEL CONTAMINATED SOIL

    EPA Science Inventory

    In this study, lipid biomarker characterization of the bacterial and eukaryotic communities was combined with PCR-DGGE analysis of the eubacterial community to evaluate correlation between JP-4 fuel concentration and community structure shifts. Vadose, capillary fringe and satur...

  4. Buds from the tree of life: linking compartmentalized prokaryotes and eukaryotes by a non-hyperthermophile common ancestor and implications for understanding Archaean microbial communities

    NASA Astrophysics Data System (ADS)

    Fuerst, John A.; Nisbet, Euan G.

    2004-07-01

    The origin of the first nucleated eukaryote and the nature of the last common ancestor of the three domains of life are major questions in the evolutionary biology of cellular life on Earth, the solutions to which may be linked. Planctomycetes are unusual compartmentalized bacteria that include a membrane-bounded nucleoid. The possibility that they constitute a very deep branch of the domain Bacteria suggests a model for the evolution of the three domains of life from a last common ancestor that was a mesophile or moderate thermophile with a compartmentalized eukaryote-like cell plan. Planctomycetes and some members of the domain Archaea may have retained cell compartmentalization present in an original eukaryote-like last common ancestor of the three domains of life. The implications of this model for possible habitats of the early evolution of domains of cellular life and for interpretation of geological evidence relating to those habitats and the early emergence of life are examined here.

  5. Biomarkers as tracers for life on early earth and Mars

    NASA Technical Reports Server (NTRS)

    Simoneit, B. R.; Summons, R. E.; Jahnke, L. L.

    1998-01-01

    Biomarkers in geological samples are products derived from biochemical (natural product) precursors by reductive and oxidative processes (e.g., cholestanes from cholesterol). Generally, lipids, pigments and biomembranes are preserved best over longer geological times and labile compounds such as amino acids, sugars, etc. are useful biomarkers for recent times. Thus, the detailed characterization of biomarker compositions permits the assessment of the major contributing species of extinct and/or extant life. In the case of the early Earth, work has progressed to elucidate molecular structure and carbon isotropic signals preserved in ancient sedimentary rocks. In addition, the combination of bacterial biochemistry with the organic geochemistry of contemporary and ancient hydrothermal ecosystems permits the modeling of the nature, behavior and preservation potential of primitive microbial communities. This approach uses combined molecular and isotopic analyses to characterize lipids produced by cultured bacteria (representative of ancient strains) and to test a variety of culture conditions which affect their biosynthesis. On considering Mars, the biomarkers from lipids and biopolymers would be expected to be preserved best if life flourished there during its early history (3.5-4 x 10(9) yr ago). Both oxidized and reduced products would be expected. This is based on the inferred occurrence of hydrothermal activity during that time with the concomitant preservation of biochemically-derived organic matter. Both known biomarkers (i.e., as elucidated for early terrestrial samples and for primitive terrestrial microbiota) and novel, potentially unknown compounds should be characterized.

  6. Can Molecular Biomarkers Change the Paradigm of Pancreatic Cancer Prognosis?

    PubMed Central

    Garcia-Foncillas, Jesus

    2016-01-01

    Pancreatic ductal adenocarcinoma is one of the most lethal types of tumour, and its incidence is rising worldwide. Although survival can be improved when these tumours are detected at an early stage, this cancer is usually asymptomatic, and the disease only becomes apparent after metastasis. The only prognostic biomarker approved by the FDA to date is carbohydrate antigen 19-9 (CA19-9); however, the specificity of this biomarker has been called into question, and diagnosis is usually based on clinical parameters. Tumour size, degree of differentiation, lymph node status, presence of distant metastasis at diagnosis, protein levels of KI-67 or C-reactive protein, and mutational status of P53, KRAS, or BRCA2 are the most useful biomarkers in clinical practice. In addition to these, recent translational research has provided evidence of new biomarkers based on different molecules involved in endoplasmic reticulum stress, epithelial-to-mesenchymal transition, and noncoding RNA panels, especially microRNAs and long noncoding RNAs. These new prospects open new paths to tumour detection using minimally or noninvasive techniques such as liquid biopsies. To find sensitive and specific biomarkers to manage these patients constitutes a challenge for the research community and for public health policies.

  7. Disease Biomarker Query from RNA-Seq Data

    PubMed Central

    Han, Henry; Jiang, Xiaoqian

    2014-01-01

    As a revolutionary way to unveil transcription, RNA-Seq technologies are challenging bioinformatics for its large data volumes and complexities. A large number of computational models have been proposed for differential expression (DE) analysis and normalization from different standing points. However, there were no studies available yet to conduct disease biomarker discovery for this type of high-resolution digital gene expression data, which will actually be essential to explore its potential in clinical bioinformatics. Although there were many biomarker discovery algorithms available in traditional omics communities, they cannot be applied to RNA-Seq count data to seek biomarkers directly for its special characteristics. In this work, we have presented a biomarker discovery algorithm, SEQ-Marker for RNA-Seq data, which is built on a novel data-driven feature selection algorithm, nonnegative singular value approximation (NSVA), which contributes to the robustness and sensitivity of the following DE analysis by taking advantages of the built-in characteristics of RNA-Seq count data. As a biomarker discovery algorithm built on network marker topology, the proposed SEQ-Marker not only bridges transcriptomics and systems biology but also contributes to clinical diagnostics. PMID:25392686

  8. Biomarkers as tracers for life on early earth and Mars.

    PubMed

    Simoneit, B R; Summons, R E; Jahnke, L L

    1998-10-01

    Biomarkers in geological samples are products derived from biochemical (natural product) precursors by reductive and oxidative processes (e.g., cholestanes from cholesterol). Generally, lipids, pigments and biomembranes are preserved best over longer geological times and labile compounds such as amino acids, sugars, etc. are useful biomarkers for recent times. Thus, the detailed characterization of biomarker compositions permits the assessment of the major contributing species of extinct and/or extant life. In the case of the early Earth, work has progressed to elucidate molecular structure and carbon isotropic signals preserved in ancient sedimentary rocks. In addition, the combination of bacterial biochemistry with the organic geochemistry of contemporary and ancient hydrothermal ecosystems permits the modeling of the nature, behavior and preservation potential of primitive microbial communities. This approach uses combined molecular and isotopic analyses to characterize lipids produced by cultured bacteria (representative of ancient strains) and to test a variety of culture conditions which affect their biosynthesis. On considering Mars, the biomarkers from lipids and biopolymers would be expected to be preserved best if life flourished there during its early history (3.5-4 x 10(9) yr ago). Both oxidized and reduced products would be expected. This is based on the inferred occurrence of hydrothermal activity during that time with the concomitant preservation of biochemically-derived organic matter. Both known biomarkers (i.e., as elucidated for early terrestrial samples and for primitive terrestrial microbiota) and novel, potentially unknown compounds should be characterized.

  9. Can Molecular Biomarkers Change the Paradigm of Pancreatic Cancer Prognosis?

    PubMed Central

    Garcia-Foncillas, Jesus

    2016-01-01

    Pancreatic ductal adenocarcinoma is one of the most lethal types of tumour, and its incidence is rising worldwide. Although survival can be improved when these tumours are detected at an early stage, this cancer is usually asymptomatic, and the disease only becomes apparent after metastasis. The only prognostic biomarker approved by the FDA to date is carbohydrate antigen 19-9 (CA19-9); however, the specificity of this biomarker has been called into question, and diagnosis is usually based on clinical parameters. Tumour size, degree of differentiation, lymph node status, presence of distant metastasis at diagnosis, protein levels of KI-67 or C-reactive protein, and mutational status of P53, KRAS, or BRCA2 are the most useful biomarkers in clinical practice. In addition to these, recent translational research has provided evidence of new biomarkers based on different molecules involved in endoplasmic reticulum stress, epithelial-to-mesenchymal transition, and noncoding RNA panels, especially microRNAs and long noncoding RNAs. These new prospects open new paths to tumour detection using minimally or noninvasive techniques such as liquid biopsies. To find sensitive and specific biomarkers to manage these patients constitutes a challenge for the research community and for public health policies. PMID:27689078

  10. Ethical Issues in Measuring Biomarkers in Children’s Environmental Health

    PubMed Central

    Sly, Peter D.; Eskenazi, Brenda; Pronczuk, Jenny; Šrám, Radim; Diaz-Barriga, Fernando; Machin, Diego Gonzalez; Carpenter, David O.; Surdu, Simona; Meslin, Eric M.

    2009-01-01

    Background Studying the impact of environmental exposures is important in children because they are more vulnerable to adverse effects on growth, development, and health. Assessing exposure in children is difficult, and measuring biomarkers is potentially useful. Research measuring biomarkers in children raises a number of ethical issues, some of which relate to children as research subjects and some of which are specific to biomarker research. Objective As an international group with experience in pediatric research, biomarkers, and the ethics of research in children, we highlight the ethical issues of undertaking biomarker research in children in these environments. Discussion Significant issues include undertaking research in vulnerable communities, especially in developing countries; managing community expectations; obtaining appropriate consent to conduct the research; the potential conflicts of obtaining permission from an ethics review board in an economically developed country to perform research in a community that may have different cultural values; returning research results to participants and communities when the researchers are uncertain of how to interpret the results; and the conflicting ethical obligations of maintaining participant confidentiality when information about harm or illegal activities mandate reporting to authorities. Conclusion None of these challenges are insurmountable and all deserve discussion. Pediatric biomarker research is necessary for advancing child health. PMID:19672395

  11. Analysis of in situ manganese(II) oxidation in the Columbia River and offshore plume: linking Aurantimonas and the associated microbial community to an active biogeochemical cycle.

    PubMed

    Anderson, C R; Davis, R E; Bandolin, N S; Baptista, A M; Tebo, B M

    2011-06-01

    The Columbia River is a major source of dissolved nutrients and trace metals for the west coast of North America. A large proportion of these nutrients are sourced from the Columbia River Estuary, where coastal and terrestrial waters mix and resuspend particulate matter within the water column. As estuarine water is discharged off the coast, it transports the particulate matter, dissolved nutrients and microorganisms forming nutrient-rich and metabolically dynamic plumes. In this study, bacterial manganese oxidation within the plume and estuary was investigated during spring and neap tides. The microbial community proteome was fractionated and assayed for Mn oxidation activity. Proteins from the outer membrane and the loosely bound outer membrane fractions were separated using size exclusion chromatography and Mn(II)-oxidizing eluates were analysed with tandem mass spectrometry to identify potential Mn oxidase protein targets. Multi-copper oxidase (MCO) and haem-peroxidase enzymes were identified in active fractions. T-RFLP profiles and cluster analysis indicates that organisms and bacterial communities capable of oxidizing Mn(II) can be sourced from the Columbia River estuary and nearshore coastal ocean. These organisms are producing up to 10 fM MnO₂ cell⁻¹ day⁻¹. Evidence for the presence of Mn(II)-oxidizing bacterial isolates from the genera Aurantimonas, Rhodobacter, Bacillus and Shewanella was found in T-RFLP profiles. Specific Q-PCR probes were designed to target potential homologues of the Aurantimonas manganese oxidizing peroxidase (Mop). By comparing total Mop homologues, Aurantimonas SSU rRNA and total bacterial SSU rRNA gene copies, it appears that Aurantimonas can only account for ~1.7% of the peroxidase genes quantified. Under the broad assumption that at least some of the peroxidase homologues quantified are involved in manganese oxidation, it is possible that other organisms oxidize manganese via peroxidases. PMID:21418498

  12. Biomarker in archaeological soils

    NASA Astrophysics Data System (ADS)

    Wiedner, Katja; Glaser, Bruno; Schneeweiß, Jens

    2015-04-01

    The use of biomarkers in an archaeological context allow deeper insights into the understanding of anthropogenic (dark) earth formation and from an archaeological point of view, a completely new perspective on cultivation practices in the historic past. During an archaeological excavation of a Slavic settlement (10th/11th C. A.D.) in Brünkendorf (Wendland region in Northern Germany), a thick black soil (Nordic Dark Earth) was discovered that resembled the famous terra preta phenomenon. For the humid tropics, terra preta could act as model for sustainable agricultural practices and as example for long-term CO2-sequestration into terrestrial ecosystems. The question was whether this Nordic Dark Earth had similar properties and genesis as the famous Amazonian Dark Earth in order to find a model for sustainable agricultural practices and long term CO2-sequestration in temperate zones. For this purpose, a multi-analytical approach was used to characterize the sandy-textured Nordic Dark Earth in comparison to less anthropogenically influenced soils in the adjacent area in respect of ecological conditions (e.g. amino sugar), input materials (faeces) and the presence of stable soil organic matter (black carbon). Amino sugar analyses showed that Nordic Dark Earth contained higher amounts of microbial residues being dominated by soil fungi. Faecal biomarkers such as stanols and bile acids indicated animal manure from omnivores and herbivores but also human excrements. Black carbon content of about 30 Mg ha-1 in the Nordic Dark Earth was about four times higher compared to the adjacent soil and in the same order of magnitude compared to terra preta. Our data strongly suggest parallels to anthropogenic soil formation in Amazonia and in Europe by input of organic wastes, faecal material and charred organic matter. An obvious difference was that in terra preta input of human-derived faecal material dominated while in NDE human-derived faecal material played only a minor role

  13. A Robust Biomarker

    NASA Technical Reports Server (NTRS)

    Westall, F.; Steele, A.; Toporski, J.; Walsh, M. M.; Allen, C. C.; Guidry, S.; McKay, D. S.; Gibson, E. K.; Chafetz, H. S.

    2000-01-01

    containing fossil biofilm, including the 3.5 b.y..-old carbonaceous cherts from South Africa and Australia. As a result of the unique compositional, structural and "mineralisable" properties of bacterial polymer and biofilms, we conclude that bacterial polymers and biofilms constitute a robust and reliable biomarker for life on Earth and could be a potential biomarker for extraterrestrial life.

  14. Urinary Biomarkers of Brain Diseases

    PubMed Central

    An, Manxia; Gao, Youhe

    2016-01-01

    Biomarkers are the measurable changes associated with a physiological or pathophysiological process. Unlike blood, urine is not subject to homeostatic mechanisms. Therefore, greater fluctuations could occur in urine than in blood, better reflecting the changes in human body. The roadmap of urine biomarker era was proposed. Although urine analysis has been attempted for clinical diagnosis, and urine has been monitored during the progression of many diseases, particularly urinary system diseases, whether urine can reflect brain disease status remains uncertain. As some biomarkers of brain diseases can be detected in the body fluids such as cerebrospinal fluid and blood, there is a possibility that urine also contain biomarkers of brain diseases. This review summarizes the clues of brain diseases reflected in the urine proteome and metabolome. PMID:26751805

  15. Biomarkers in localized prostate cancer.

    PubMed

    Ferro, Matteo; Buonerba, Carlo; Terracciano, Daniela; Lucarelli, Giuseppe; Cosimato, Vincenzo; Bottero, Danilo; Deliu, Victor M; Ditonno, Pasquale; Perdonà, Sisto; Autorino, Riccardo; Coman, Ioman; De Placido, Sabino; Di Lorenzo, Giuseppe; De Cobelli, Ottavio

    2016-02-01

    Biomarkers can improve prostate cancer diagnosis and treatment. Accuracy of prostate-specific antigen (PSA) for early diagnosis of prostate cancer is not satisfactory, as it is an organ- but not cancer-specific biomarker, and it can be improved by using models that incorporate PSA along with other test results, such as prostate cancer antigen 3, the molecular forms of PSA (proPSA, benign PSA and intact PSA), as well as kallikreins. Recent reports suggest that new tools may be provided by metabolomic studies as shown by preliminary data on sarcosine. Additional molecular biomarkers have been identified by the use of genomics, proteomics and metabolomics. We review the most relevant biomarkers for early diagnosis and management of localized prostate cancer.

  16. Translational progress on tumor biomarkers

    PubMed Central

    Guo, Hongwei; Zhou, Xiaolin; Lu, Yi; Xie, Liye; Chen, Qian; Keller, Evan T; Liu, Qian; Zhou, Qinghua; Zhang, Jian

    2015-01-01

    There is an urgent need to apply basic research achievements to the clinic. In particular, mechanistic studies should be developed by bench researchers, depending upon clinical demands, in order to improve the survival and quality of life of cancer patients. To date, translational medicine has been addressed in cancer biology, particularly in the identification and characterization of novel tumor biomarkers. This review focuses on the recent achievements and clinical application prospects in tumor biomarkers based on translational medicine. PMID:26557902

  17. Clinical biomarkers in metabolic syndrome.

    PubMed

    Barazzoni, Rocco; Silva, Veronica; Singer, Pierre

    2014-04-01

    A biomarker can be defined as a measurable variable that may be used as an indicator of a given biological state or condition. Biomarkers have been used in health and disease for diagnostic purposes, as tools to assess effectiveness of nutritional or drug intervention, or as risk markers to predict the development of certain diseases. In nutrition studies, selecting appropriate biomarkers is important to assess compliance, or incidence of a particular dietary component in the biochemistry of the organism, and in the diagnosis and prognosis of nutrition-related diseases. Metabolic syndrome is a cluster of cardiovascular risk factors that occur simultaneously in the same individual, and it is associated with systemic alterations that may involve several organs and tissues. Given its close association with obesity and the increasing prevalence of obesity worldwide, identifying obese individuals at risk for metabolic syndrome is a major clinical priority. Biomarkers for metabolic syndrome are therefore potential important tools to maximize the effectiveness of treatment in subjects who would likely benefit the most. Choice of biomarkers may be challenging due to the complexity of the syndrome, and this article will mainly focus on nutrition biomarkers related to the diagnosis and prognosis of the metabolic syndrome.

  18. Linking watershed terrain and hydrology to soil chemical properties, microbial communities and impacts on soil organic C in a humid mid-latitude forested watershed

    NASA Astrophysics Data System (ADS)

    Watson, D. B.; Brooks, S. C.; Schadt, C. W.; Tang, G.; Collier, N.; Earles, J. E.; Mehlhorn, T. L.; Lowe, K. A.; Brandt, C. C.; koo Yang, Z.; Phillips, D.; Li, P.; Yuan, F.

    2014-12-01

    Understanding the response of humid mid-latitude forests to changes in precipitation, temperature, nutrient cycling, and disturbance is critical to improving our predictive understanding of changes in the surface-subsurface energy balance due to climate change. Mechanistic understanding of the effects of long-term and transient moisture conditions are needed to quantify linkages between changing redox conditions, microbial activity, and soil mineral and nutrient interactions on C cycling and greenhouse gas releases. To illuminate relationships between the soil chemistry, microbial communities and organic C we established transects across hydraulic and topographic gradients in a small watershed with transient moisture conditions. Valley bottoms tend to be more frequently saturated than ridge tops and side slopes which generally are only saturated when shallow storm flow zones are active. Fifty shallow (~36") soil cores were collected during timeframes representative of low CO2, soil winter conditions and high CO2, soil summer conditions. Cores were subdivided into 240 samples based on pedology and analyses of the geochemical (moisture content, metals, pH, Fe species, N, C, CEC, AEC) and microbial (16S rRNA gene amplification with Illumina MiSeq sequencing) characteristics were conducted and correlated to watershed terrain and hydrology. To associate microbial metabolic activity with greenhouse gas emissions we installed 17 soil gas probes, collected gas samples for 16 months and analyzed them for CO2 and other fixed and greenhouse gasses. Parallel to the experimental efforts our data is being used to support hydrobiogeochemical process modeling by coupling the Community Land Model (CLM) with a subsurface process model (PFLOTRAN) to simulate processes and interactions from the molecular to watershed scales. Including above ground processes (biogeophysics, hydrology, and vegetation dynamics), CLM provides mechanistic water, energy, and organic matter inputs to the

  19. Linking Environmental Exposure with Public Health: Dichlorodiphenyltrichloroethane Extracted from Soils and Water of Recently Exposed Communities of Selected Locations in Zambia

    PubMed Central

    Sipilanyambe Munyinda, Nosiku; Michelo, Charles; Sichilongo, Kwenga

    2015-01-01

    Background. In 2000, a Zambian private mining company reintroduced the use of dichlorodiphenyltrichloroethane (DDT) to control malaria in two districts. From 2000 to 2010, DDT had been applied in homes without any studies conducted to ascertain its fate in the environment. We aimed to quantify the presence of DDT and its metabolites in the soil and water around communities where it was recently used. Methods. We collected superficial soil and water samples from drinking sources of three study areas. DDT was extracted by QuEChERS method and solid phase extraction for soils and water, respectively. Analysis was by gas chromatography-mass spectrometry. A revalidated method with limits of detection ranging from 0.034 to 0.04 ppb was used. Results. Median levels of total DDT were found at 100.4 (IQR 90.9–110) and 725.4 ng/L (IQR 540–774.5) for soils and water, respectively. No DDT above detection limits was detected in the reference area. These results are clinically significant given the persistent characteristics of DDT. Conclusion. DDT presence in these media suggests possible limitations in the environmental safeguards during IRS. Such occurrence could have potential effects on humans, especially children; hence, there is a need to further examine possible associations between this exposure and humans. PMID:26579199

  20. Linking microbial comunity composition and soil processes in acalifornia annual grassland and mixed-conifer forest

    SciTech Connect

    Balser, T.C.; Firestone, M.K.

    2003-07-21

    To investigate the potential role of microbial community composition in soil carbon and nitrogen cycling, we transplanted soil cores between a grassland and a conifer ecosystem in the Sierra Nevada California and measured soil process rates (N-mineralization, nitrous oxide and carbon dioxide flux, nitrification potential), soil water and temperature, and microbial community parameters (PLFA and substrate utilization profiles) over a 2 year period. Our goal was to assess whether microbial community composition could be related to soil process rates independent of soil temperature and water content. We performed multiple regression analyses using microbial community parameters and soil water and temperature as X-variables and soil process rates and inorganic N concentrations as Y-variables. We found that field soil temperature had the strongest relationship with CO2 production and soil NH4+ concentration, while microbial community characteristics correlated with N2O production, nitrification potential, gross N-mineralization, and soil NO3 concentration, independent of environmental controllers. We observed a relationship between specific components of the microbial community (as determined by PLFA) and soil processes, particularly processes tightly linked to microbial phylogeny (e.g. nitrification). The most apparent change in microbial community composition in response to the 2 year transplant was a change in relative abundance of fungi (there was only one significant change in PLFA biomarkers for bacteria during 2years). The relationship between microbial community composition and soil processes suggests that prediction of ecosystem response to environmental change may be improved by recognizing and accounting for changes in microbial community composition and physiological ecology.

  1. Regional Approach for Managing for Resilience Linking Ecosystem Services and Livelihood Strategies for Agro-Pastoral Communities in the Mongolian Steppe Ecosystem

    NASA Astrophysics Data System (ADS)

    Ojima, D. S.; Togtohyn, C.; Qi, J.; Galvin, K.

    2011-12-01

    Dramatic changes due to climate and land use dynamics in the Mongolian Plateau are affecting ecosystem services and agro-pastoral livelihoods in Mongolia and China. Recently, evaluation of pastoral systems, where humans depend on livestock and grassland ecosystem services, have demonstrated the vulnerability of the social-ecological system to climate change. Current social-ecological changes in ecosystem services are affecting land productivity and carrying capacity, land-atmosphere interactions, water resources, and livelihood strategies. Regional dust events, changes in hydrological cycle, and land use changes contribute to changing interactions between ecosystem and landscape processes which then affect social-ecological systems. The general trend involves greater intensification of resource exploitation at the expense of traditional patterns of extensive range utilization. Thus we expect climate-land use-land cover relationships to be crucially modified by the socio-economic forces. The analysis incorporates information of the socio-economic transitions taking place in the region which affect land-use, food security, and ecosystem dynamics. The region of study extends from the Mongolian plateau in Mongolia and China to the fertile northeast China plain. Sustainability of agro-pastoral systems in the region needs to integrate the impact of climate change on ecosystem services with socio-economic changes shaping the livelihood strategies of pastoral systems in the region. Adaptation strategies which incorporate landscape management provides a potential framework to link ecosystem services across space and time more effectively to meet the needs of agro-pastoral land use, herd quality, and herder's living standards. Under appropriate adaptation strategies agro-pastoralists will have the opportunity to utilize seasonal resources and enhance their ability to process and manufacture products from the available ecosystem services in these dynamic social

  2. The use of biomarkers to trace carbon transformations and input in soils

    NASA Astrophysics Data System (ADS)

    Jansen, Boris; Kalbitz, Karsten

    2015-04-01

    Tracing the origin of soil organic matter is an important tool to unravel mechanisms that lead to (de)stabilization of organic carbon in soil systems. To this end biomarkers, i.e. (groups of) specific molecules that can be linked to (groups of) specific plant species or plant parts are often used. A good example is the use of suberin and cutin as biomarkers to distinguish organic matter with a root origin from organic matter with a leaf origin. However, the use of biomarkers to trace the origin of soil organic matter is also subject of fierce scientific debate. On the one extreme end there are those colleagues who see biomarkers as a cure-all solution to all organic matter tracing problems. On the other end of the spectrum there are experts who claim that the concept of biomarkers is so intrinsically flawed that it can never yield meaningful information about carbon transformations except in the most specific cases. We believe that neither vision is correct. In our presentation we discuss the merits and drawbacks of using biomarkers to trace root versus leaf derived organic matter in soils. For this we use a 1-year incubation experiment with fine root and leaf material of six temperate tree species as a case study. We discuss the abundance, or lack thereof, of root and leaf derived biomarkers and the development of their concentration over time. Specifically, we found that the specificity of root and leaf specific biomarkers depended strongly on the amount and diversity of studied species. For instance, four molecules were identified to be leaf biomarkers for some species, while serving as root biomarkers for others. This could result in serious misjudgment of root and leaf specific biomarkers if the boundary conditions, including species of interest, are not well known. On the other hand, our results show that cutin and suberin derived biomarkers can indeed be successfully used to distinguish root from leaf input in certain situations, such as an ecosystem

  3. Preemptive tumor profiling for biomarker-stratified early clinical drug development in metastatic breast cancer patients.

    PubMed

    Welt, Anja; Tewes, Mitra; Aktas, Bahriye; O Hoffmann, Oliver; Wiesweg, Marcel; Ting, Saskia; Reis, Henning; Worm, Karl; Richly, Heike; Hense, Jörg; Palmer, Michael R; Lee, Benjamin H; Wendling, Johanna; Kossow, Josef; Scheulen, Max E; Lehnerdt, Cathrin; Kohl, Marzena; Derks, Cordula; Skottky, Silke; Haus, Ulrike; Schmid, Kurt W; Kimmig, Rainer; Schuler, Martin; Kasper, Stefan

    2013-11-01

    Biomarker-stratified cancer pharmacotherapy was pioneered in the care of breast cancer patients. The utility of agents modulating hormone receptors, synthesis of steroid hormones, or HER2-targeting agents has been greatly enhanced by the detection of predictive biomarkers in diagnostic tumor samples. Based on deeper understanding of breast cancer biology multiple drug candidates have been developed to modulate additional molecular targets which may associate with specific biomarker profiles. Accordingly, exploratory biomarkers are increasingly incorporated in early clinical trials, thus demanding a new process of patient selection. Here, we describe the implementation of preemptive, multiplexed biomarker profiling linked to standard diagnostic algorithms for metastatic breast cancer patients treated at the West German Cancer Center. Profiling for experimental biomarkers was prospectively offered to patients with metastatic breast cancer who met generic clinical trial inclusion criteria. Formalin-fixed, paraffin-embedded tumor samples were retrieved and studied for potentially “actionable” biomarkers related to active clinical trials by immunohistochemistry, amplicon sequencing, and in situ hybridization. The clinical course of those “profiled” patients was closely monitored to offer trial participation whenever applicable. Here, we report results from the first 131 patients enrolled in this program. PIK3CA mutations (23 %) and amplifications (2 %), loss of PTEN expression (13 %), and FGFR1 amplifications (8 %) were detected next to established biomarkers such as estrogen (67 %) and progesterone receptor expression (52 %), and HER2 overexpression or amplification (23 %). So far 16 “profiled” patients (12 %) have been enrolled in biomarker-stratified early clinical trials. Preemptive profiling of investigational biomarkers can be integrated into the diagnostic algorithm of a large Comprehensive Cancer Center. Extensive administrative efforts are required

  4. Deep biomarkers of human aging: Application of deep neural networks to biomarker development.

    PubMed

    Putin, Evgeny; Mamoshina, Polina; Aliper, Alexander; Korzinkin, Mikhail; Moskalev, Alexey; Kolosov, Alexey; Ostrovskiy, Alexander; Cantor, Charles; Vijg, Jan; Zhavoronkov, Alex

    2016-05-01

    One of the major impediments in human aging research is the absence of a comprehensive and actionable set of biomarkers that may be targeted and measured to track the effectiveness of therapeutic interventions. In this study, we designed a modular ensemble of 21 deep neural networks (DNNs) of varying depth, structure and optimization to predict human chronological age using a basic blood test. To train the DNNs, we used over 60,000 samples from common blood biochemistry and cell count tests from routine health exams performed by a single laboratory and linked to chronological age and sex. The best performing DNN in the ensemble demonstrated 81.5 % epsilon-accuracy r = 0.90 with R(2) = 0.80 and MAE = 6.07 years in predicting chronological age within a 10 year frame, while the entire ensemble achieved 83.5% epsilon-accuracy r = 0.91 with R(2) = 0.82 and MAE = 5.55 years. The ensemble also identified the 5 most important markers for predicting human chronological age: albumin, glucose, alkaline phosphatase, urea and erythrocytes. To allow for public testing and evaluate real-life performance of the predictor, we developed an online system available at http://www.aging.ai. The ensemble approach may facilitate integration of multi-modal data linked to chronological age and sex that may lead to simple, minimally invasive, and affordable methods of tracking integrated biomarkers of aging in humans and performing cross-species feature importance analysis. PMID:27191382

  5. Deep biomarkers of human aging: Application of deep neural networks to biomarker development

    PubMed Central

    Putin, Evgeny; Mamoshina, Polina; Aliper, Alexander; Korzinkin, Mikhail; Moskalev, Alexey; Kolosov, Alexey; Ostrovskiy, Alexander; Cantor, Charles; Vijg, Jan; Zhavoronkov, Alex

    2016-01-01

    One of the major impediments in human aging research is the absence of a comprehensive and actionable set of biomarkers that may be targeted and measured to track the effectiveness of therapeutic interventions. In this study, we designed a modular ensemble of 21 deep neural networks (DNNs) of varying depth, structure and optimization to predict human chronological age using a basic blood test. To train the DNNs, we used over 60,000 samples from common blood biochemistry and cell count tests from routine health exams performed by a single laboratory and linked to chronological age and sex. The best performing DNN in the ensemble demonstrated 81.5 % epsilon-accuracy r = 0.90 with R2 = 0.80 and MAE = 6.07 years in predicting chronological age within a 10 year frame, while the entire ensemble achieved 83.5% epsilon-accuracy r = 0.91 with R2 = 0.82 and MAE = 5.55 years. The ensemble also identified the 5 most important markers for predicting human chronological age: albumin, glucose, alkaline phosphatase, urea and erythrocytes. To allow for public testing and evaluate real-life performance of the predictor, we developed an online system available at http://www.aging.ai. The ensemble approach may facilitate integration of multi-modal data linked to chronological age and sex that may lead to simple, minimally invasive, and affordable methods of tracking integrated biomarkers of aging in humans and performing cross-species feature importance analysis. PMID:27191382

  6. A review on oral cancer biomarkers: Understanding the past and learning from the present.

    PubMed

    Santosh, Arvind Babu Rajendra; Jones, Thaon; Harvey, John

    2016-01-01

    Biomarkers are broadly classified as genomic, proteomic, or metabolomic. Molecular biology and oncology research studies on oral cancer biomarkers focus on identifying key biological molecules or markers that could be linked to cancer development, risk assessment, screening, recurrence prediction, indicating prognosis, indicating invasion/metastasis and monitoring therapeutic responses of cancer. Cluster of differentiation factor 34 is a salivary biomarker that can identify recurrence potential of oral squamous cell carcinoma (OSCC). Integrin α3 and integrin β4 are genomic biomarkers that are helpful in estimating the risk of regional and hematogenous dissemination of malignant oral squamous cells. Other examples are vascular endothelial growth factor, B-cell lymphoma-2, claudin 4, yes-associated protein 1 and MET proto-oncogene, and receptor tyrosine kinase, which are genomic biomarkers that are used to predict radio-resistance in OSCC tissue. The present article reviews the clinical application, methodologies and steps in developing candidate biomarkers, protocols in reporting, evaluating candidate biomarkers, and challenges in biomarker research with a focus OSCC.

  7. Temporal Trends in Syngenetic Lipid Biomarker Signals from Proterozoic Sedimentary Organic Matter

    NASA Astrophysics Data System (ADS)

    Love, G. D.; Li, C.; Summons, R. E.

    2008-12-01

    The development of continuous-flow catalytic hydropyrolysis (HyPy) for reproducible recovery of biomarker lipid skeletons covalently-bound within kerogen has proved to be an important analytical breakthrough for ancient lipid biomarker research. The parallel analyses of free (solvent-extractable) and kerogen-bound biomarkers affords more confidence that we have correctly identified syngenetic compounds. Combining HyPy with detailed biomarker product analyzes using metastable reaction monitoring-gas chromatography mass spectrometry (MRM-GC-MS) allows detection of a large suite of biomarker compounds which are usually too low in abundance to be analyzed in detail using conventional GC-MS. Here we compare free and bound lipid biomarker records generated from Paleoproterozoic (ca. 1.7 Ga) to Late Ediacaran age (ca. 542 Ma) strata from marine basins from North and South China, Australia and Oman. Fundamental changes in eukaryotic community structure are evident after the Sturtian glaciation (ca. 713 Ma) from distinctive sterane distributions. In particular, radiations in basal animals (sponges) and chlorophyte microalgae are first apparent in Huqf sedimentary rocks from South Oman Salt Basin. Marine microbial communities were not globally homogenous in contemporaneous Proterozoic settings from comparison of biomarker profiles and this could reflect differences in ocean chemistry, affecting nutrient supply, from basin to basin.

  8. Prostate cancer biomarkers: an update.

    PubMed

    Romero Otero, Javier; Garcia Gomez, Borja; Campos Juanatey, Felix; Touijer, Karim A

    2014-04-01

    Many aspects of prostate cancer diagnosis and treatment could be greatly advanced with new, effective biomarkers. Prostate-specific antigen (PSA) has multiple weaknesses as a biomarker, such as not distinguishing well between cancer and benign prostatic hyperplasia or between indolent and aggressive cancers, thus leading to overtreatment, especially unnecessary biopsies. PSA also often fails to indicate accurately which patients are responding to a given treatment. Yet PSA is the only prostate cancer biomarker routinely used by urologists. Here, we provide updated information on the most relevant of the other biomarkers currently in use or in development for prostate cancer. Recent research shows improvement over using PSA alone by comparing total PSA (tPSA) or free PSA (fPSA) with new, related markers, such as prostate cancer antigen (PCA) 3, the individual molecular forms of PSA (proPSA, benign PSA, and intact PSA), and kallikreins other than PSA. Promising results have also been seen with the use of the fusion gene TMPRSS2:ERG and with various forms of the urokinase plasminogen activation receptor. Initially, there were high hopes for early PCA, but those data were not reproducible and thus research on early PCA has been abandoned. Much work remains to be done before any of these biomarkers are fully validated and accepted. Currently, the only markers discussed in this paper with Food and Drug Administration-approved tests are PCA 3 and an isoform of proPSA, [-2]proPSA. Assays are in development for most of the other biomarkers described in this paper. While the biomarker validation process can be long and filled with obstacles, the rewards will be great-in terms of both patient care and costs to the health care system.

  9. Linking Human Health and Livestock Health: A “One-Health” Platform for Integrated Analysis of Human Health, Livestock Health, and Economic Welfare in Livestock Dependent Communities

    PubMed Central

    Thumbi, S. M.; Njenga, M. Kariuki; Marsh, Thomas L.; Noh, Susan; Otiang, Elkanah; Munyua, Peninah; Ochieng, Linus; Ogola, Eric; Yoder, Jonathan; Audi, Allan; Montgomery, Joel M.; Bigogo, Godfrey; Breiman, Robert F.; Palmer, Guy H.; McElwain, Terry F.

    2015-01-01

    Background For most rural households in sub-Saharan Africa, healthy livestock play a key role in averting the burden associated with zoonotic diseases, and in meeting household nutritional and socio-economic needs. However, there is limited understanding of the complex nutritional, socio-economic, and zoonotic pathways that link livestock health to human health and welfare. Here we describe a platform for integrated human health, animal health and economic welfare analysis designed to address this challenge. We provide baseline epidemiological data on disease syndromes in humans and the animals they keep, and provide examples of relationships between human health, animal health and household socio-economic status. Method We designed a study to obtain syndromic disease data in animals along with economic and behavioral information for 1500 rural households in Western Kenya already participating in a human syndromic disease surveillance study. Data collection started in February 2013, and each household is visited bi-weekly and data on four human syndromes (fever, jaundice, diarrhea and respiratory illness) and nine animal syndromes (death, respiratory, reproductive, musculoskeletal, nervous, urogenital, digestive, udder disorders, and skin disorders in cattle, sheep, goats and chickens) are collected. Additionally, data from a comprehensive socio-economic survey is collected every 3 months in each of the study households. Findings Data from the first year of study showed 93% of the households owned at least one form of livestock (55%, 19%, 41% and 88% own cattle, sheep, goats and chickens respectively). Digestive disorders, mainly diarrhea episodes, were the most common syndromes observed in cattle, goats and sheep, accounting for 56% of all livestock syndromes, followed by respiratory illnesses (18%). In humans, respiratory illnesses accounted for 54% of all illnesses reported, followed by acute febrile illnesses (40%) and diarrhea illnesses (5%). While controlling

  10. Biomarkers and Microbial Fossils In Antarctic Rocks

    NASA Astrophysics Data System (ADS)

    Wierzchos, J.; Ascaso, C.

    Lithobiontic microbial communities living within Antarctic rocks are an example of survival in an extremely cold and dry environment. Any unfavourable change in ex- ternal conditions can result in the death and disappearance of microscopic organisms, and this may be followed by the appearance of trace biomarkers and microbial fossils. The extinction of these microorganisms in some zones of the Ross Desert, probably provoked by the hostile environment, might be considered a good terrestrial analogue of the first stage of the disappearance of possible life on early Mars. Granite samples from maritime Antarctica (Granite Harbour) and sandstone rocks from the continental Ross Desert were collected with the aim of searching for biomarkers and microbial fossils at the microscopic level of observation. To this end, a novel in situ applica- tion of scanning electron microscopy with backscattered electron imaging was com- bined with the simultaneous use of X-ray energy dispersive spectroscopy techniques. Our findings confirm the existence of inorganic biomarkers in the form of physico- chemically bioweathered minerals within the granitic rocks. The presence of Fe-rich diagenetic minerals, such as iron hydroxide nanocrystals and biogenic clays around chasmoendolithic hyphae and bacterial cells was also observed. Others biomarkers, including inorganic deposits such as calcium oxalates and silica accumulations, are clear signs of endolithic microorganism activity. The interior of the sandstone rocks (Ross Desert, Mt. Fleming) reveal the presence of microbial fossils of algae and other endolithic microorganisms. These microbial fossils, detected for the first time within Antarctic rocks, contain well preserved and morphologically distinguishable relics of ultrastructural cytoplasm elements, such as cell walls, chloroplast membranes, and oc- casionally, pyrenoids and traces of organic matter. These structures are similar to those observed in live cells also found in Antarctic

  11. Analytical Aspects of the Implementation of Biomarkers in Clinical Transplantation.

    PubMed

    Shipkova, Maria; López, Olga Millán; Picard, Nicolas; Noceti, Ofelia; Sommerer, Claudia; Christians, Uwe; Wieland, Eberhard

    2016-04-01

    In response to the urgent need for new reliable biomarkers to complement the guidance of the immunosuppressive therapy, a huge number of biomarker candidates to be implemented in clinical practice have been introduced to the transplant community. This includes a diverse range of molecules with very different molecular weights, chemical and physical properties, ex vivo stabilities, in vivo kinetic behaviors, and levels of similarity to other molecules, etc. In addition, a large body of different analytical techniques and assay protocols can be used to measure biomarkers. Sometimes, a complex software-based data evaluation is a prerequisite for appropriate interpretation of the results and for their reporting. Although some analytical procedures are of great value for research purposes, they may be too complex for implementation in a clinical setting. Whereas the proof of "fitness for purpose" is appropriate for validation of biomarker assays used in exploratory drug development studies, a higher level of analytical validation must be achieved and eventually advanced analytical performance might be necessary before diagnostic application in transplantation medicine. A high level of consistency of results between laboratories and between methods (if applicable) should be obtained and maintained to make biomarkers effective instruments in support of therapeutic decisions. This overview focuses on preanalytical and analytical aspects to be considered for the implementation of new biomarkers for adjusting immunosuppression in a clinical setting and highlights critical points to be addressed on the way to make them suitable as diagnostic tools. These include but are not limited to appropriate method validation, standardization, education, automation, and commercialization.

  12. Biomarkers of ageing in Drosophila

    PubMed Central

    Jacobson, Jake; Portero-Otín, Manuel; Pamplona, Reinald; Magwere, Tapiwanashe; Miwa, Satomi; Driege, Yasmine; Brand, Martin D.; Partridge, Linda

    2015-01-01

    Summary Low environmental temperature and dietary restriction (DR) extend lifespan in diverse organisms. In the fruit fly Drosophila, switching flies between temperatures alters the rate at which mortality subsequently increases with age but does not reverse mortality rate. In contrast, DR acts acutely to lower mortality risk; flies switched between control feeding and DR show a rapid reversal of mortality rate. DR thus does not slow accumulation of ageing-related damage. Molecular species that track the effects of temperatures on mortality but are unaltered with switches in diet are therefore potential biomarkers of ageing-related damage. However, molecular species that switch upon instigation or withdrawal of DR are thus potential biomarkers of mechanisms underlying risk of mortality, but not of ageing-related damage. Using this approach, we assessed several commonly used biomarkers of ageing-related damage. Accumulation of fluorescent advanced glycation end products (AGEs) correlated strongly with mortality rate of flies at different temperatures but was independent of diet. Hence fluorescent AGEs are biomarkers of ageing-related damage in flies. In contrast, five oxidised and glycated protein adducts accumulated with age, but were reversible with both temperature and diet, and are therefore not markers either of acute risk of dying or of ageing-related damage. Our approach provides a powerful method for identification of biomarkers of ageing. PMID:20367621

  13. Salivary biomarkers for clinical applications.

    PubMed

    Zhang, Lei; Xiao, Hua; Wong, David T

    2009-01-01

    For clinical applications such as monitoring health status, disease onset and progression, and treatment outcome, there are three necessary prerequisites: (i) a simple method for collecting biologic samples, ideally noninvasively; (ii) specific biomarkers associated with health or disease; and (iii) a technology platform to rapidly utilize the biomarkers. Saliva, often regarded as the 'mirror of the body', is a perfect surrogate medium to be applied for clinical diagnostics. Saliva is readily accessible via a totally noninvasive method. Salivary biomarkers, whether produced by healthy individuals or by individuals affected by specific diseases, are sentinel molecules that could be used to scrutinize health and disease surveillance. The visionary investment by the US National Institute of Dental and Craniofacial Research, the discovery of salivary biomarkers, and the ongoing development of salivary diagnostic technologies have addressed its diagnostic value for clinical applications. The availability of more sophisticated analytic techniques gives optimism that saliva can eventually be placed as a biomedium for clinical diagnostics. This review presents current salivary biomarker research and technology developmental efforts for clinical applications.

  14. Exploring Biomarkers for Alzheimer's Disease.

    PubMed

    Sharma, Neeti; Singh, Anshika Nikita

    2016-07-01

    Alzheimer's Disease (AD) is one of the most common form of dementia occurring in elderly population worldwide. Currently Aβ42, tau and p-tau in the cerebrospinal fluid is estimated for confirmation of AD. CSF which is being used as the potent source for biomarker screening is obtained by invasive lumbar punctures. Thus, there is an urgent need of minimal invasive methods for identification of diagnostic markers for early detection of AD. Blood serum and plasma serves as an appropriate source, due to minimal discomfort to the patients, promoting frequent testing, better follow-up and better consent to clinical trials. Hence, the need of the hour demands discovery of diagnostic and prognostic patient specific signature biomarkers by using emerging technologies of mass spectrometry, microarrays and peptidomics. In this review we summarize the present scenario of AD biomarkers such as circulatory biomarkers, blood based amyloid markers, inflammatory markers and oxidative stress markers being investigated and also some of the potent biomarkers which might be able to predict early onset of Alzheimer's and delay cognitive impairment. PMID:27630867

  15. Urothelial Bladder Cancer Urinary Biomarkers

    PubMed Central

    Noon, Aidan P

    2014-01-01

    Abstract Urothelial bladder cancer is the fourth most prevalent male malignancy in the United States and also one of the ten most lethal. Superficial or non-muscle-invasive bladder cancer has a high rate of recurrence and can progress to muscle invasive disease. Conventional surveillance requires regular cystoscopy and is used often with urinary cytology. Unfortunately, the cystoscopy procedure is invasive for patients and costly for health care providers. Urinary biomarkers have the potential to improve bladder cancer diagnosis, the efficiency and also the cost-effectiveness of follow up. It may also be possible for urinary biomarkers to help prognosticate particularly for patients with high-grade bladder cancer who may want enhanced assessment of their risk of disease progression. In this review the important historical urinary biomarkers and the newly emerging biomarkers are discussed. As will be presented, although many of the tests have good performance characteristics, unfortunately no single test can fulfill all the roles currently provided by cystoscopy and cytology. It is likely that in the future, urinary biomarker testing will be used selectively in a personalized manner to try and improve prognostication or reduce the necessity for invasive cystoscopy in patients understanding the limits of the test.

  16. Biomarkers in acute heart failure.

    PubMed

    Mallick, Aditi; Januzzi, James L

    2015-06-01

    The care of patients with acutely decompensated heart failure is being reshaped by the availability and understanding of several novel and emerging heart failure biomarkers. The gold standard biomarkers in heart failure are B-type natriuretic peptide and N-terminal pro-B-type natriuretic peptide, which play an important role in the diagnosis, prognosis, and management of acute decompensated heart failure. Novel biomarkers that are increasingly involved in the processes of myocardial injury, neurohormonal activation, and ventricular remodeling are showing promise in improving diagnosis and prognosis among patients with acute decompensated heart failure. These include midregional proatrial natriuretic peptide, soluble ST2, galectin-3, highly-sensitive troponin, and midregional proadrenomedullin. There has also been an emergence of biomarkers for evaluation of acute decompensated heart failure that assist in the differential diagnosis of dyspnea, such as procalcitonin (for identification of acute pneumonia), as well as markers that predict complications of acute decompensated heart failure, such as renal injury markers. In this article, we will review the pathophysiology and usefulness of established and emerging biomarkers for the clinical diagnosis, prognosis, and management of acute decompensated heart failure.

  17. Biomarker Identification by Feature Wrappers

    PubMed Central

    Xiong, Momiao; Fang, Xiangzhong; Zhao, Jinying

    2001-01-01

    Gene expression studies bridge the gap between DNA information and trait information by dissecting biochemical pathways into intermediate components between genotype and phenotype. These studies open new avenues for identifying complex disease genes and biomarkers for disease diagnosis and for assessing drug efficacy and toxicity. However, the majority of analytical methods applied to gene expression data are not efficient for biomarker identification and disease diagnosis. In this paper, we propose a general framework to incorporate feature (gene) selection into pattern recognition in the process to identify biomarkers. Using this framework, we develop three feature wrappers that search through the space of feature subsets using the classification error as measure of goodness for a particular feature subset being “wrapped around”: linear discriminant analysis, logistic regression, and support vector machines. To effectively carry out this computationally intensive search process, we employ sequential forward search and sequential forward floating search algorithms. To evaluate the performance of feature selection for biomarker identification we have applied the proposed methods to three data sets. The preliminary results demonstrate that very high classification accuracy can be attained by identified composite classifiers with several biomarkers. PMID:11691853

  18. Leaf Litter Mixtures Alter Microbial Community Development: Mechanisms for Non-Additive Effects in Litter Decomposition

    PubMed Central

    Chapman, Samantha K.; Newman, Gregory S.; Hart, Stephen C.; Schweitzer, Jennifer A.; Koch, George W.

    2013-01-01

    To what extent microbial community composition can explain variability in ecosystem processes remains an open question in ecology. Microbial decomposer communities can change during litter decomposition due to biotic interactions and shifting substrate availability. Though relative abundance of decomposers may change due to mixing leaf litter, linking these shifts to the non-additive patterns often recorded in mixed species litter decomposition rates has been elusive, and links community composition to ecosystem function. We extracted phospholipid fatty acids (PLFAs) from single species and mixed species leaf litterbags after 10 and 27 months of decomposition in a mixed conifer forest. Total PLFA concentrations were 70% higher on litter mixtures than single litter types after 10 months, but were only 20% higher after 27 months. Similarly, fungal-to-bacterial ratios differed between mixed and single litter types after 10 months of decomposition, but equalized over time. Microbial community composition, as indicated by principal components analyses, differed due to both litter mixing and stage of litter decomposition. PLFA biomarkers a15∶0 and cy17∶0, which indicate gram-positive and gram-negative bacteria respectively, in particular drove these shifts. Total PLFA correlated significantly with single litter mass loss early in decomposition but not at later stages. We conclude that litter mixing alters microbial community development, which can contribute to synergisms in litter decomposition. These findings advance our understanding of how changing forest biodiversity can alter microbial communities and the ecosystem processes they mediate. PMID:23658639

  19. Protein biomarkers of alcohol abuse

    PubMed Central

    Torrente, Mariana P; Freeman, Willard M; Vrana, Kent E

    2012-01-01

    Alcohol abuse can lead to a number of health and social issues. Our current inability to accurately assess long-term drinking behaviors is an important obstacle to its diagnosis and treatment. Biomarkers for chronic alcohol consumption have made a number of important advances but have yet to become highly accurate and as accepted as objective tests for other diseases. Thus, there is a crucial need for the development of more sensitive and specific markers of alcohol abuse. Recent advancements in proteomic technologies have greatly increased the potential for alcohol abuse biomarker discovery. Here, the authors review established and novel protein biomarkers for long-term alcohol consumption and the proteomic technologies that have been used in their study. PMID:22967079

  20. Quantitative Imaging Biomarkers of NAFLD

    PubMed Central

    Kinner, Sonja; Reeder, Scott B.

    2016-01-01

    Conventional imaging modalities, including ultrasonography (US), computed tomography (CT), and magnetic resonance (MR), play an important role in the diagnosis and management of patients with nonalcoholic fatty liver disease (NAFLD) by allowing noninvasive diagnosis of hepatic steatosis. However, conventional imaging modalities are limited as biomarkers of NAFLD for various reasons. Multi-parametric quantitative MRI techniques overcome many of the shortcomings of conventional imaging and allow comprehensive and objective evaluation of NAFLD. MRI can provide unconfounded biomarkers of hepatic fat, iron, and fibrosis in a single examination—a virtual biopsy has become a clinical reality. In this article, we will review the utility and limitation of conventional US, CT, and MR imaging for the diagnosis NAFLD. Recent advances in imaging biomarkers of NAFLD are also discussed with an emphasis in multi-parametric quantitative MRI. PMID:26848588

  1. Linked Ocean Data

    NASA Astrophysics Data System (ADS)

    Leadbetter, Adam; Arko, Robert; Chandler, Cynthia; Shepherd, Adam

    2014-05-01

    Data repositories. The benefits of this approach include: increased interoperability between the metadata created by projects; improved data discovery as users of SeaDataNet, R2R and BCO-DMO terms can find data using labels with which they are familiar both standard tools and newly developed custom tools may be used to explore the data; and using standards means the custom tools are easier to develop Linked Data is a concept which has been in existence for nearly a decade, and has a simple set of formal best practices associated with it. Linked Data is increasingly being seen as a driver of the next generation of "community science" activities. While many data providers in the oceanographic domain may be unaware of Linked Data, they may also be providing it at one of its lower levels. Here we have shown that it is possible to deliver the highest standard of Linked Oceanographic Data, and some of the benefits of the approach.

  2. DMS-prefiltered mass spectrometry for the detection of biomarkers

    NASA Astrophysics Data System (ADS)

    Coy, Stephen L.; Krylov, Evgeny V.; Nazarov, Erkinjon G.

    2008-04-01

    Technologies based on Differential Mobility Spectrometry (DMS) are ideally matched to rapid, sensitive, and selective detection of chemicals like biomarkers. Biomarkers linked to exposure to radiation, exposure to CWA's, exposure to toxic materials (TICs and TIMs) and to specific diseases are being examined in a number of laboratories. Screening for these types of exposure can be improved in accuracy and greatly speeded up by using DMS-MS instead of slower techniques like LC-MS and GC-MS. We have performed an extensive series of tests with nanospray-DMS-mass spectroscopy and standalone nanospray-DMS obtaining extensive information on chemistry and detectivity. DMS-MS systems implemented with low-resolution, low-cost, portable mass-spectrometry systems are very promising. Lowresolution mass spectrometry alone would be inadequate for the task, but with DMS pre-filtration to suppress interferences, can be quite effective, even for quantitative measurement. Bio-fluids and digests are well suited to ionization by electrospray and detection by mass-spectrometry, but signals from critical markers are overwhelmed by chemical noise from unrelated species, making essential quantitative analysis impossible. Sionex and collaborators have presented data using DMS to suppress chemical noise, allowing detection of cancer biomarkers in 10,000-fold excess of normal products 1,2. In addition, a linear dynamic range of approximately 2,000 has been demonstrated with accurate quantitation 3. We will review the range of possible applications and present new data on DMS-MS biomarker detection.

  3. Interpretation of fish biomarker data for identification, classification, risk assessment and testing of endocrine disrupting chemicals.

    PubMed

    Dang, ZhiChao

    2016-01-01

    Chemical induced changes in fish biomarkers vitellogenin (VTG), secondary sex characteristics (SSC), and sex ratio indicate modes/mechanisms of action (MOAs) of EAS (estrogen, androgen and steroidogenesis) pathways. These biomarkers could be used for defining MOAs and the causal link between MOAs and adverse effects in fish for the identification of endocrine disrupting chemicals (EDCs). This paper compiled data sets of 150 chemicals for VTG, 57 chemicals for SSC and 38 chemicals for sex ratio in fathead minnow, medaka and zebrafish. It showed 1) changes in fish biomarkers can indicate the MOAs as anticipated; 2) in addition to EAS pathways, chemicals with non-EAS pathways induced changes in fish biomarkers; 3) responses of fish biomarkers did not always follow the anticipated patterns of EAS pathways. These responses may result from the interaction of chemical-induced multiple MOAs and confounding factors like fish diet, infection, culture conditions, general toxicity and stress response. The complex response of fish biomarkers to a chemical of interest requires EDC testing at multiple biological levels. Interpretation of fish biomarker data should be combined with relevant information at different biological levels, which is critical for defining chemical specific MOAs. The utility of fish biomarker data for identification, classification, PBT assessment, risk assessment, and testing of EDCs in the regulatory context was discussed. This paper emphasizes the importance of fish biomarker data in the regulatory context, a weight of evidence approach for the interpretation of fish biomarker data and the need for defining levels of evidence for the identification of EDCs. PMID:27155823

  4. Translational implications of inflammatory biomarkers and cytokine networks in psychoneuroimmunology.

    PubMed

    Yan, Qing

    2012-01-01

    Developments in psychoneuroimmunology (PNI) need to be translated into personalized medicine to achieve better clinical outcomes. One of the most critical steps in this translational process is to identify systemic biomarkers for better diagnosis and treatment. Applications of systems biology approaches in PNI would enable the insights into the correlations among various systems and different levels for the identification of the basic elements of the psychophysiological framework. Among the potential PNI biomarkers, inflammatory markers deserve special attention as they play a pivotal role linking various health conditions and disorders. The elucidation of inflammatory markers, cytokine networks, and immune-brain-behavior interactions may help establish PNI profiles for the identification of potential targets for personalized interventions in at risk populations. The understanding of the general systemic pathways among different disorders may contribute to the transition from the disease-centered medicine to patient-centered medicine. Integrative strategies targeting these factors and pathways would be useful for the prevention and treatment of a spectrum of diseases that share the common links. Examples of the translational implications of potential PNI biomarkers and networks in diseases including depression, Alzheimer's disease, obesity, cardiovascular disease, stroke, and HIV are discussed in details.

  5. Scaling up Learning Communities: The Experience of Six Community Colleges

    ERIC Educational Resources Information Center

    Visher, Mary G.; Schneider, Emily; Wathington, Heather; Collado, Herbert

    2010-01-01

    The Learning Communities Demonstration is a large-scale, random assignment evaluation of learning community programs at six community colleges. During the first year of the demonstration, all six colleges expanded their learning community programs and, in the process, faced similar challenges in selecting courses to link, recruiting and supporting…

  6. Biomarkers to guide clinical therapeutics in rheumatology?

    PubMed Central

    Robinson, William H.; Mao, Rong

    2016-01-01

    Purpose of review The use of biomarkers in rheumatology can help identify disease risk, improve diagnosis and prognosis, target therapy, assess response to treatment, and further our understanding of the underlying pathogenesis of disease. Here, we discuss the recent advances in biomarkers for rheumatic disorders, existing impediments to progress in this field, and the potential of biomarkers to enable precision medicine and thereby transform rheumatology. Recent findings Although significant challenges remain, progress continues to be made in biomarker discovery and development for rheumatic diseases. The use of next-generation technologies, including large-scale sequencing, proteomic technologies, metabolomic technologies, mass cytometry, and other single-cell analysis and multianalyte analysis technologies, has yielded a slew of new candidate biomarkers. Nevertheless, these biomarkers still require rigorous validation and have yet to make their way into clinical practice and therapeutic development. This review focuses on advances in the biomarker field in the last 12 months as well as the challenges that remain. Summary Better biomarkers, ideally mechanistic ones, are needed to guide clinical decision making in rheumatology. Although the use of next-generation techniques for biomarker discovery is making headway, it is imperative that the roadblocks in our search for new biomarkers are overcome to enable identification of biomarkers with greater diagnostic and predictive utility. Identification of biomarkers with robust diagnostic and predictive utility would enable precision medicine in rheumatology. PMID:26720904

  7. Toxicogenomic Biomarkers for Liver Toxicity

    PubMed Central

    Kiyosawa, Naoki; Ando, Yosuke; Manabe, Sunao; Yamoto, Takashi

    2009-01-01

    Toxicogenomics (TGx) is a widely used technique in the preclinical stage of drug development to investigate the molecular mechanisms of toxicity. A number of candidate TGx biomarkers have now been identified and are utilized for both assessing and predicting toxicities. Further accumulation of novel TGx biomarkers will lead to more efficient, appropriate and cost effective drug risk assessment, reinforcing the paradigm of the conventional toxicology system with a more profound understanding of the molecular mechanisms of drug-induced toxicity. In this paper, we overview some practical strategies as well as obstacles for identifying and utilizing TGx biomarkers based on microarray analysis. Since clinical hepatotoxicity is one of the major causes of drug development attrition, the liver has been the best documented target organ for TGx studies to date, and we therefore focused on information from liver TGx studies. In this review, we summarize the current resources in the literature in regard to TGx studies of the liver, from which toxicologists could extract potential TGx biomarker gene sets for better hepatotoxicity risk assessment. PMID:22271975

  8. Biomarkers of space radiation risk.

    PubMed

    Durante, Marco

    2005-10-01

    Radiation risk estimates are based on epidemiological data obtained on Earth for cohorts exposed predominantly to acute doses of gamma rays, and the extrapolation to the space environment is highly problematic and error-prone. The uncertainty can be reduced if risk estimates are compared directly to space radiation-induced biological alterations, i.e. by detecting biomarkers in astronauts. Chromosomal aberrations in peripheral blood lymphocytes are the only biomarker that can provide simultaneous information on dose, dose equivalent and risk, and they have been measured extensively in astronauts during the past 10 years. Individual relative risks calculated from chromosomal aberration measurements in crew members after single space missions in low-Earth orbit fall in the same range as the estimates derived from physical dosimetry, suggesting that the current system for radiogenic risk evaluation is essentially sound. However, the output of the biomarker test is dependent upon the sampling time. Recent results show a fast time-dependent decay of chromosomal aberrations in blood lymphocytes after space flight and a lack of correlation between translocations and cumulative dose in astronauts involved in two to five space missions. This "time factor" may reflect individual variability and time dependence in the risk produced by exposure to cosmic radiation during the flight. Biomarkers may be superior to dose in predicting space radiation risk, pending technical improvements in sensitivity, and validation by epidemiological studies. PMID:16187751

  9. Biomarkers to Predict Antidepressant Response

    PubMed Central

    Cook, Ian A.; Hamilton, Steven P.; Narr, Katherine L.; Toga, Arthur; Hunter, Aimee M.; Faull, Kym; Whitelegge, Julian; Andrews, Anne M.; Loo, Joseph; Way, Baldwin; Nelson, Stanley F.; Horvath, Steven; Lebowitz, Barry D.

    2010-01-01

    During the past several years, we have achieved a deeper understanding of the etiology/pathophysiology of major depressive disorder (MDD). However, this improved understanding has not translated to improved treatment outcome. Treatment often results in symptomatic improvement, but not full recovery. Clinical approaches are largely trial-and-error, and when the first treatment does not result in recovery for the patient, there is little proven scientific basis for choosing the next. One approach to enhancing treatment outcomes in MDD has been the use of standardized sequential treatment algorithms and measurement-based care. Such treatment algorithms stand in contrast to the personalized medicine approach, in which biomarkers would guide decision making. Incorporation of biomarker measurements into treatment algorithms could speed recovery from MDD by shortening or eliminating lengthy and ineffective trials. Recent research results suggest several classes of physiologic biomarkers may be useful for predicting response. These include brain structural or functional findings, as well as genomic, proteomic, and metabolomic measures. Recent data indicate that such measures, at baseline or early in the course of treatment, may constitute useful predictors of treatment outcome. Once such biomarkers are validated, they could form the basis of new paradigms for antidepressant treatment selection. PMID:20963521

  10. Redox biomarkers in cardiovascular medicine.

    PubMed

    Karimi Galougahi, Keyvan; Antoniades, Charalambos; Nicholls, Stephen J; Channon, Keith M; Figtree, Gemma A

    2015-07-01

    The central role of oxidative signalling in cardiovascular pathophysiology positions biometric measures of redox state as excellent markers for research and clinical application. However, despite this tantalizing biological plausibility, no redox biomarker is currently in widespread clinical use. Major recent insights into the mechanistic complexities of redox signalling may yet provide the opportunity to identify markers that most closely reflect the underlying pathobiology. Such redox biomarkers may, in principle, quantify the integrated effects of various known and unknown pathophysiological drivers of cardiovascular disease processes. Recent advances with the greatest potential include assays measuring post-translational oxidative modifications that have significant cellular effects. However, analytical issues, including the relative instability of redox-modified products, remain a major technical obstacle. Appreciation of these challenges may facilitate future development of user-friendly markers with prognostic value in addition to traditional risk factors, and which could be used to guide personalized cardiovascular therapies. We review both established and recently identified biomarkers of redox signalling, and provide a realistic discussion of the many challenges that remain if they are to be incorporated into clinical practice. Despite the current lack of redox biomarkers in clinical application, the integral role of reactive oxygen species in pathogenesis of cardiovascular disease provides a strong incentive for continued efforts.

  11. Cholinesterase and glutathione-S-transferase activities in freshwater invertebrates as biomarkers to assess pesticide contamination.

    PubMed

    Domingues, Inês; Agra, Ana Raquel; Monaghan, Kieran; Soares, Amadeu M V M; Nogueira, António J A

    2010-01-01

    Studies investigating the use of biomarkers in pesticide risk assessment have greatly increased in recent years; however, issues concerning the ecological meaning of enzymatic responses have proved controversial. Ideally a good biomarker response should be modulated by the environmental contaminants alone and demonstrate a predictable behavior towards certain types of toxins. As these premises are rarely observed, the present study aims to outline research that has contributed to an understanding of the behavior of two widely used biomarkers, cholinesterase and glutathione-S-transferase, describing environmental and biotic factors that affect their response in freshwater invertebrates. Studies were performed in the main classes of aquatic invertebrates with these biomarkers and conclusions were reached concerning their behavior towards the main classes of pesticides. Links between biomarker responses and conventional endpoints were evaluated so that ecological relevance could be attributed to enzymatic responses. Toxicity of mixtures was investigated, and cases of synergism and antagonism were pointed out as factors changing the expected toxicity of aquatic systems and leading to misinterpretations of biomarker responses. Finally, the use of biomarkers as a tool for biomonitoring and in situ assays was investigated, with discussion of advantages and disadvantages of their use.

  12. Using artificial neural network tools to analyze microbial biomarker data

    SciTech Connect

    Brandt, C.C.; Schryver, J.C.; Almeida, J.S.; Pfiffner, S.M.; Palumbo, A.V.

    2004-03-17

    A major challenge in the successful implementation of bioremediation is understanding the structure of the indigenous microbial community and how this structure is affected by environmental conditions. Culture-independent approaches that use biomolecular markers have become the key to comparative microbial community analysis. However, the analysis of biomarkers from environmental samples typically generates a large number of measurements. The large number and complex nonlinear relationships among these measurements makes conventional linear statistical analysis of the data difficult. New data analysis tools are needed to help understand these data. We adapted artificial neural network (ANN) tools for relating changes in microbial biomarkers to geochemistry. ANNs are nonlinear pattern recognition methods that can learn from experience to improve their performance. We have successfully applied these techniques to the analysis of membrane lipids and nucleic acid biomarker data from both laboratory and field studies. Although ANNs typically outperform linear data analysis techniques, the user must be aware of several considerations and issues to ensure that analysis results are not misleading: (1) Overfitting, especially in small sample size data sets; (2) Model selection; (3) Interpretation of analysis results; and (4) Availability of tools (code). This poster summarizes approaches for addressing each of these issues. The objectives are: (1) Develop new nonlinear data analysis tools for relating microbial biomolecular markers to geochemical conditions; (2) Apply these nonlinear tools to field and laboratory studies relevant to the NABIR Program; and (3) Provide these tools and guidance in their use to other researchers.

  13. Biomarkers of (osteo)arthritis

    PubMed Central

    Mobasheri, Ali; Henrotin, Yves

    2015-01-01

    Abstract Arthritic diseases are a major cause of disability and morbidity, and cause an enormous burden for health and social care systems globally. Osteoarthritis (OA) is the most common form of arthritis. The key risk factors for the development of OA are age, obesity, joint trauma or instability. Metabolic and endocrine diseases can also contribute to the pathogenesis of OA. There is accumulating evidence to suggest that OA is a whole-organ disease that is influenced by systemic mediators, inflammaging, innate immunity and the low-grade inflammation induced by metabolic syndrome. Although all joint tissues are implicated in disease progression in OA, articular cartilage has received the most attention in the context of aging, injury and disease. There is increasing emphasis on the early detection of OA as it has the capacity to target and treat the disease more effectively. Indeed it has been suggested that this is the era of “personalized prevention” for OA. However, the development of strategies for the prevention of OA require new and sensitive biomarker tools that can detect the disease in its molecular and pre-radiographic stage, before structural and functional alterations in cartilage integrity have occurred. There is also evidence to support a role for biomarkers in OA drug discovery, specifically the development of disease modifying osteoarthritis drugs. This Special Issue of Biomarkers is dedicated to recent progress in the field of OA biomarkers. The papers in this Special Issue review the current state-of-the-art and discuss the utility of OA biomarkers as diagnostic and prognostic tools. PMID:26954784

  14. Systems biology and biomarker discovery

    SciTech Connect

    Rodland, Karin D.

    2010-12-01

    Medical practitioners have always relied on surrogate markers of inaccessible biological processes to make their diagnosis, whether it was the pallor of shock, the flush of inflammation, or the jaundice of liver failure. Obviously, the current implementation of biomarkers for disease is far more sophisticated, relying on highly reproducible, quantitative measurements of molecules that are often mechanistically associated with the disease in question, as in glycated hemoglobin for the diagnosis of diabetes [1] or the presence of cardiac troponins in the blood for confirmation of myocardial infarcts [2]. In cancer, where the initial symptoms are often subtle and the consequences of delayed diagnosis often drastic for disease management, the impetus to discover readily accessible, reliable, and accurate biomarkers for early detection is compelling. Yet despite years of intense activity, the stable of clinically validated, cost-effective biomarkers for early detection of cancer is pathetically small and still dominated by a handful of markers (CA-125, CEA, PSA) first discovered decades ago. It is time, one could argue, for a fresh approach to the discovery and validation of disease biomarkers, one that takes full advantage of the revolution in genomic technologies and in the development of computational tools for the analysis of large complex datasets. This issue of Disease Markers is dedicated to one such new approach, loosely termed the 'Systems Biology of Biomarkers'. What sets the Systems Biology approach apart from other, more traditional approaches, is both the types of data used, and the tools used for data analysis - and both reflect the revolution in high throughput analytical methods and high throughput computing that has characterized the start of the twenty first century.

  15. DNA Methylation as a Biomarker for Preeclampsia

    SciTech Connect

    Anderson, Cindy M.; Ralph, Jody L.; Wright, Michelle L.; Linggi, Bryan E.; Ohm, Joyce E.

    2014-10-01

    Background: Preeclampsia contributes significantly to pregnancy-associated morbidity and mortality as well as future risk of cardiovascular disease in mother and offspring, and preeclampsia in offspring. The lack of reliable methods for early detection limits the opportunities for prevention, diagnosis, and timely treatment. Purpose: The purpose of this study was to explore distinct DNA methylation patterns associated with preeclampsia in both maternal cells and fetal-derived tissue that represent potential biomarkers to predict future preeclampsia and inheritance in children. Method: A convenience sample of nulliparous women (N = 55) in the first trimester of pregnancy was recruited for this prospective study. Genome-wide DNA methylation was quantified in first-trimester maternal peripheral white blood cells and placental chorionic tissue from normotensive women and those with preeclampsia (n = 6/group). Results: Late-onset preeclampsia developed in 12.7% of women. Significant differences in DNA methylation were identified in 207 individual linked cytosine and guanine (CpG) sites in maternal white blood cells collected in the first trimester (132 sites with gain and 75 sites with loss of methylation), which were common to approximately 75% of the differentially methylated CpG sites identified in chorionic tissue of fetal origin. Conclusion: This study is the first to identify maternal epigenetic targets and common targets in fetal-derived tissue that represent putative biomarkers for early detection and heritable risk of preeclampsia. Findings may pave the way for diagnosis of preeclampsia prior to its clinical presentation and acute damaging effects, and the potential for prevention of the detrimental long-term sequelae.

  16. Novel Biomarkers for Renal Diseases? None for the Moment (but One).

    PubMed

    Gentile, Giorgio; Remuzzi, Giuseppe

    2016-08-01

    Recent years have witnessed the unprecedented development and integration of genomics, epigenetics, transcriptomics, proteomics, and metabolomics, as well as a growing interest in novel single biomarkers and process-specific biomarker panels in human renal diseases. In a scenario currently dominated by kidney biopsy and established biomarkers such as serum creatinine, albuminuria, and proteinuria, novel biomarkers could potentially provide vital diagnostic and prognostic information and help to predict response to treatment in several clinical settings, including acute kidney injury, renal transplant, autosomal dominant polycystic kidney disease, and glomerulopathies. However, it is still uncertain whether and to what extent novel biomarkers will succeed in this difficult task. To date, they have generally failed to provide relevant information over and above what is already granted by established, cheap, and easily available biomarkers such as proteinuria, while the complexity and costs of these technology platforms are an important obstacle to their wide adoption. On the other hand, the successful implementation of anti-phospholipase A2 receptor antibodies as a diagnostic and prognostic biomarker of membranous nephropathy, as well as the huge number of ongoing collaborative efforts worldwide, should induce the nephrology community to be rather optimistic about a potential breakthrough in the management of kidney diseases over the next few decades. PMID:26950928

  17. Biomarkers for nutrient intake with focus on alternative sampling techniques.

    PubMed

    Holen, T; Norheim, F; Gundersen, T E; Mitry, P; Linseisen, J; Iversen, P O; Drevon, C A

    2016-01-01

    Biomarkers of nutrient intake or nutrient status are important objective measures of foods/nutrients as one of the most important environmental factors people are exposed to. It is very difficult to obtain accurate data on individual food intake, and there is a large variation of nutrient composition of foods consumed in a population. Thus, it is difficult to obtain precise measures of exposure to different nutrients and thereby be able to understand the relationship between diet, health, and disease. This is the background for investing considerable resources in studying biomarkers of nutrients believed to be important in our foods. Modern technology with high sensitivity and specificity concerning many nutrient biomarkers has allowed an interesting development with analyses of very small amounts of blood or tissue material. In combination with non-professional collection of blood by finger-pricking and collection on filters or sticks, this may make collection of samples and analyses of biomarkers much more available for scientists as well as health professionals and even lay people in particular in relation to the marked trend of self-monitoring of body functions linked to mobile phone technology. Assuming standard operating procedures are used for collection, drying, transport, extraction, and analysis of samples, it turns out that many analytes of nutritional interest can be measured like metabolites, drugs, lipids, vitamins, minerals, and many types of peptides and proteins. The advantage of this alternative sampling technology is that non-professionals can collect, dry, and mail the samples; the samples can often be stored under room temperature in a dry atmosphere, requiring small amounts of blood. Another promising area is the potential relation between the microbiome and biomarkers that may be measured in feces as well as in blood.

  18. Biomarkers for nutrient intake with focus on alternative sampling techniques.

    PubMed

    Holen, T; Norheim, F; Gundersen, T E; Mitry, P; Linseisen, J; Iversen, P O; Drevon, C A

    2016-01-01

    Biomarkers of nutrient intake or nutrient status are important objective measures of foods/nutrients as one of the most important environmental factors people are exposed to. It is very difficult to obtain accurate data on individual food intake, and there is a large variation of nutrient composition of foods consumed in a population. Thus, it is difficult to obtain precise measures of exposure to different nutrients and thereby be able to understand the relationship between diet, health, and disease. This is the background for investing considerable resources in studying biomarkers of nutrients believed to be important in our foods. Modern technology with high sensitivity and specificity concerning many nutrient biomarkers has allowed an interesting development with analyses of very small amounts of blood or tissue material. In combination with non-professional collection of blood by finger-pricking and collection on filters or sticks, this may make collection of samples and analyses of biomarkers much more available for scientists as well as health professionals and even lay people in particular in relation to the marked trend of self-monitoring of body functions linked to mobile phone technology. Assuming standard operating procedures are used for collection, drying, transport, extraction, and analysis of samples, it turns out that many analytes of nutritional interest can be measured like metabolites, drugs, lipids, vitamins, minerals, and many types of peptides and proteins. The advantage of this alternative sampling technology is that non-professionals can collect, dry, and mail the samples; the samples can often be stored under room temperature in a dry atmosphere, requiring small amounts of blood. Another promising area is the potential relation between the microbiome and biomarkers that may be measured in feces as well as in blood. PMID:27551313

  19. Community Connections: Intergenerational Links in Art Education

    ERIC Educational Resources Information Center

    La Porte, Angela M., Ed.

    2004-01-01

    Intergenerational programs have become widespread since the mid-20th century, emphasizing "activities that increase cooperation and exchange between any two generations. Typically, they involve interaction between young and old in which there is a sharing of skills, knowledge, and experience" (Newman, 1986, p. 6). They developed in response to…

  20. Biofilms as “Connectors” for Oral and Systems Medicine: A New Opportunity for Biomarkers, Molecular Targets, and Bacterial Eradication

    PubMed Central

    Gürsoy, Ulvi Kahraman

    2016-01-01

    Abstract Oral health and systems medicine are intimately related but have remained, sadly, as isolated knowledge communities for decades. Are there veritable connector knowledge domains that can usefully link them together on the critical path to biomarker research and “one health”? In this context, it is noteworthy that bacteria form surface-attached communities on most biological surfaces, including the oral cavity. Biofilm-forming bacteria contribute to periodontal diseases and recent evidences point to roles of these bacteria in systemic diseases as well, with cardiovascular diseases, obesity, and cancer as notable examples. Interestingly, the combined mass of microorganisms such as bacteria are so large that when we combine all plants and animals on earth, the total biomass of bacteria is still bigger. They literally do colonize everywhere, not only soil and water but our skin, digestive tract, and even oral cavity are colonized by bacteria. Hence efforts to delineate biofilm formation mechanisms of oral bacteria and microorganisms and the development of small molecules to inhibit biofilm formation in the oral cavity is very timely for both diagnostics and therapeutics. Research on biofilms can benefit both oral and systems medicine. Here, we examine, review, and synthesize new knowledge on the current understanding of oral biofilm formation, the small molecule targets that can inhibit biofilm formation in the mouth. We suggest new directions for both oral and systems medicine, using various omics technologies such as SILAC and RNAseq, that could yield deeper insights, biomarkers, and molecular targets to design small molecules that selectively aim at eradication of pathogenic oral bacteria. Ultimately, devising new ways to control and eradicate bacteria in biofilms will open up novel diagnostic and therapeutic avenues for oral and systemic diseases alike. PMID:26583256

  1. Biofilms as "Connectors" for Oral and Systems Medicine: A New Opportunity for Biomarkers, Molecular Targets, and Bacterial Eradication.

    PubMed

    Sintim, Herman O; Gürsoy, Ulvi Kahraman

    2016-01-01

    Oral health and systems medicine are intimately related but have remained, sadly, as isolated knowledge communities for decades. Are there veritable connector knowledge domains that can usefully link them together on the critical path to biomarker research and "one health"? In this context, it is noteworthy that bacteria form surface-attached communities on most biological surfaces, including the oral cavity. Biofilm-forming bacteria contribute to periodontal diseases and recent evidences point to roles of these bacteria in systemic diseases as well, with cardiovascular diseases, obesity, and cancer as notable examples. Interestingly, the combined mass of microorganisms such as bacteria are so large that when we combine all plants and animals on earth, the total biomass of bacteria is still bigger. They literally do colonize everywhere, not only soil and water but our skin, digestive tract, and even oral cavity are colonized by bacteria. Hence efforts to delineate biofilm formation mechanisms of oral bacteria and microorganisms and the development of small molecules to inhibit biofilm formation in the oral cavity is very timely for both diagnostics and therapeutics. Research on biofilms can benefit both oral and systems medicine. Here, we examine, review, and synthesize new knowledge on the current understanding of oral biofilm formation, the small molecule targets that can inhibit biofilm formation in the mouth. We suggest new directions for both oral and systems medicine, using various omics technologies such as SILAC and RNAseq, that could yield deeper insights, biomarkers, and molecular targets to design small molecules that selectively aim at eradication of pathogenic oral bacteria. Ultimately, devising new ways to control and eradicate bacteria in biofilms will open up novel diagnostic and therapeutic avenues for oral and systemic diseases alike.

  2. Biomarkers of PTSD: military applications and considerations

    PubMed Central

    Lehrner, Amy; Yehuda, Rachel

    2014-01-01

    Background Although there are no established biomarkers for posttraumatic stress disorder (PTSD) as yet, biological investigations of PTSD have made progress identifying the pathophysiology of PTSD. Given the biological and clinical complexity of PTSD, it is increasingly unlikely that a single biomarker of disease will be identified. Rather, investigations will more likely identify different biomarkers that indicate the presence of clinically significant PTSD symptoms, associate with risk for PTSD following trauma exposure, and predict or identify recovery. While there has been much interest in PTSD biomarkers, there has been less discussion of their potential clinical applications, and of the social, legal, and ethical implications of such biomarkers. Objective This article will discuss possible applications of PTSD biomarkers, including the social, legal, and ethical implications of such biomarkers, with an emphasis on military applications. Method Literature on applications of PTSD biomarkers and on potential ethical and legal implications will be reviewed. Results Biologically informed research findings hold promise for prevention, assessment, treatment planning, and the development of prophylactic and treatment interventions. As with any biological indicator of disorder, there are potentially positive and negative clinical, social, legal, and ethical consequences of using such biomarkers. Conclusions Potential clinical applications of PTSD biomarkers hold promise for clinicians, patients, and employers. The search for biomarkers of PTSD should occur in tandem with an interdisciplinary discussion regarding the potential implications of applying biological findings in clinical and employment settings. PMID:25206945

  3. The cancer secretome: a reservoir of biomarkers

    PubMed Central

    Xue, Hua; Lu, Bingjian; Lai, Maode

    2008-01-01

    Biomarkers are pivotal for cancer detection, diagnosis, prognosis and therapeutic monitoring. However, currently available cancer biomarkers have the disadvantage of lacking specificity and/or sensitivity. Developing effective cancer biomarkers becomes a pressing and permanent need. The cancer secretome, the totality of proteins released by cancer cells or tissues, provides useful tools for the discovery of novel biomarkers. The focus of this article is to review the recent advances in cancer secretome analysis. We aim to elaborate the approaches currently employed for cancer secretome studies, as well as its applications in the identification of biomarkers and the clarification of carcinogenesis mechanisms. Challenges encountered in this newly emerging field, including sample preparation, in vivo secretome analysis and biomarker validation, are also discussed. Further improvements on strategies and technologies will continue to drive forward cancer secretome research and enable development of a wealth of clinically valuable cancer biomarkers. PMID:18796163

  4. Oral Fluids that Detect Cardiovascular Disease Biomarkers

    PubMed Central

    Foley, Joseph D.; Sneed, J. Darrell; Steinhubl, Steven R; Kolasa, Justin; Ebersole, Jeffrey L.; Lin, Yushun; Kryscio, Richard J.; McDevitt, John T.; Campbell, Charles L.; Miller, Craig S.

    2013-01-01

    Objective To determine the utility of oral fluids for assessment of coronary and cardiovascular (CVD) health. Study Design Twenty-nine patients with pre-existing CVD disease underwent an invasive cardiac procedure (alcohol septal ablation or percutaneous coronary intervention) and provided unstimulated whole saliva (UWS), sublingual swabs (LS), gingival swabs (GS) and serum at 0, 8, 16, 24, 48 hr. Concentrations of 13 relevant biomarkers were determined and correlated with levels in serum and the oral fluids. Results Concentrations of the majority of biomarkers were higher in UWS than LS and GS. Coronary and CVD disease biomarkers in UWS correlated better with serum than LS and GS based on group status and measures of time effect. Seven biomarkers demonstrated time effect changes consistent with serum biomarkers, including C-reactive protein and troponin I. Conclusions Changes in serum biomarker profiles are reflected in oral fluids suggesting that oral fluid biomarkers could aid in the assessment of cardiac ischemia/necrosis. PMID:22769406

  5. Parasite communities of the deep-sea fish Alepocephalus rostratus Risso, 1820 in the Balearic Sea (NW Mediterranean) along the slope and relationships with enzymatic biomarkers and health indicators

    NASA Astrophysics Data System (ADS)

    Pérez-i-García, D.; Constenla, M.; Padrós, F.; Soler-Membrives, A.; Solé, M.; Carrassón, M.

    2015-05-01

    This study examines the parasite communities of Alepocephalus rostratus and its influence on some fish biochemical markers and histological alterations. A. rostratus constitutes the second most important fish species, in terms of biomass, inhabiting the deep slope of the Catalan Sea (Balearic Sea, NW Mediterranean). The study revealed eight different parasite species in this host: one coccidian, one digenean, one monogenean, one cestode and four nematodes. The parasite fauna of A. rostratus was partially dominated by larval forms (four of the seven metazoan taxa found), which combined with low species richness corresponds to a parasite fauna pattern more typical of bathypelagic fish species rather than demersal ones. The larval tetraphyllideans and cucullanid nematodes were the predominant species. In relation to depth, differences in abundance of the nematodes Cucullaninae gen. sp. and Hysterothylacium aduncum were found, probably due to the dietary shift in the fish host at greater depth. Thus, Cucullaninae gen. sp. and H. aduncum could be regarded as indicators for discriminating populations of A. rostratus in relation to depth in NW Mediterranean waters. Of the biochemical markers examined, acetylcholinesterase (AChE) and lactate dehydrogenase (LDH) activities and lipid peroxidation (LP) levels, only LP showed significant differences between depths. A positive relationship was found between AChE activity and Tetraphyllidea fam. gen. sp., Anisakis physeteris and H. aduncum abundance and a negative one with the abundance of Cucullaninae gen. sp. LDH showed a positive relationship with the abundance of the parasites Paracyclocotyla cherbonnieri and Tetraphyllidea fam. gen. sp. At cyto-histological level, coccidians were detected in the pyloric caeca with a prevalence of 90% in Barcelona, but in the rest of organs almost no alterations were detected. The restricted macroplanktonic diet of A. rostratus, that maintains it distant from the sea-floor for longer periods

  6. Biomarkers in Pediatric Liver Disease.

    PubMed

    Kyrana, Eirini; Fitzpatrick, Emer; Dhawan, Anil

    2016-01-01

    The chronic nature of liver diseases in children and adults merits close follow-up for disease progression and/or treatment evaluation. Disease progression involves injury to liver cells resulting in cell death, varying degrees of inflammation, steatosis depending on the insult, oxidative stress, and eventually fibrosis and cirrhosis unless the process is modified with treatment or spontaneous recovery. Inflammation, cell death, and fibrosis are the three major processes that determine the outcome of liver disease irrespective of the etiology. Markers to measure the activity or status of these parameters in a dynamic way, particularly via noninvasive methods, are urgently required. In this chapter, we summarize recent advances in the identification of biomarkers of liver diseases: biomarkers corresponding to inflammation, cell death, fibrosis, and the development of malignancy.

  7. Biomarkers in acute lung injury.

    PubMed

    Mokra, Daniela; Kosutova, Petra

    2015-04-01

    Acute respiratory distress syndrome (ARDS) and its milder form acute lung injury (ALI) may result from various diseases and situations including sepsis, pneumonia, trauma, acute pancreatitis, aspiration of gastric contents, near-drowning etc. ALI/ARDS is characterized by diffuse alveolar injury, lung edema formation, neutrophil-derived inflammation, and surfactant dysfunction. Clinically, ALI/ARDS is manifested by decreased lung compliance, severe hypoxemia, and bilateral pulmonary infiltrates. Severity and further characteristics of ALI/ARDS may be detected by biomarkers in the plasma and bronchoalveolar lavage fluid (or tracheal aspirate) of patients. Changed concentrations of individual markers may suggest injury or activation of the specific types of lung cells-epithelial or endothelial cells, neutrophils, macrophages, etc.), and thereby help in diagnostics and in evaluation of the patient's clinical status and the treatment efficacy. This chapter reviews various biomarkers of acute lung injury and evaluates their usefulness in diagnostics and prognostication of ALI/ARDS.

  8. Novel Biomarkers in Glomerular Disease

    PubMed Central

    Caliskan, Yasar; Kiryluk, Krzysztof

    2014-01-01

    Glomerular diseases are major contributors to the global burden of end stage kidney disease. The clinical course and outcome of these disorders are extremely variable and difficult to predict. The clinical trajectories range from a benign and spontaneously remitting condition to a symptomatic and rapidly progressive disease. The diagnosis is based entirely on the evaluation of kidney biopsy, but this invasive procedure carries multiple risks and often fails to predict the clinical course or responsiveness to treatment. However, more recent advances in genetics and molecular biology facilitated elucidation of novel pathogenic mechanisms of these disorders. These discoveries fuel the development of novel biomarkers and offer prospects of non-invasive diagnosis and improved prognostication. Our review focuses on the most promising novel biomarkers that have recently emerged for the major types of glomerular diseases, including IgA nephropathy, membranous nephropathy, focal segmental glomerulosclerosis, and membranoproliferative glomerulonephritis. PMID:24602470

  9. Proteomics Discovery of Disease Biomarkers.

    PubMed

    Ahram, Mamoun; Petricoin, Emanuel F

    2008-01-01

    Recent technological developments in proteomics have shown promising initiatives in identifying novel biomarkers of various diseases. Such technologies are capable of investigating multiple samples and generating large amount of data end-points. Examples of two promising proteomics technologies are mass spectrometry, including an instrument based on surface enhanced laser desorption/ionization, and protein microarrays. Proteomics data must, however, undergo analytical processing using bioinformatics. Due to limitations in proteomics tools including shortcomings in bioinformatics analysis, predictive bioinformatics can be utilized as an alternative strategy prior to performing elaborate, high-throughput proteomics procedures. This review describes mass spectrometry, protein microarrays, and bioinformatics and their roles in biomarker discovery, and highlights the significance of integration between proteomics and bioinformatics.

  10. Biomarkers of immunotoxicity in man.

    PubMed

    Descotes, J; Nicolas, B; Vial, T; Nicolas, J F

    1996-01-01

    Abstract The immunotoxic consequences of chemical exposures include direct immunotoxicity (namely immunosuppression and immunostimulation), hypersensitivity and autoimmunity, and because the mechanisms involved are markedly different, no single immune parameter is likely to ever predict or assess all three types of immunotoxicity. A fairly large number of immunological endpoints have been proposed for use as biomarkers of immunotoxicity in man. Unfortunately, they are often not sensitive enough and/or poorly standardized, so that their relevance for assessing immunotoxic effects in humans is debatable, and actually debated. Immune-mediated sentinel events detected in individuals with a defined history of chemical exposure, may prove helpful until methodological advances, notably with the introduction of technologies derived from molecular biology, provide reliable parameters to be used as biomarkers of immunotoxicity. PMID:23888916

  11. Equity in development and access to health services in the Wild