Science.gov

Sample records for biological community baselines

  1. The Mpumalanga Men's Study (MPMS): Results of a Baseline Biological and Behavioral HIV Surveillance Survey in Two MSM Communities in South Africa

    PubMed Central

    Lane, Tim; Osmand, Thomas; Marr, Alexander; Shade, Starley B.; Dunkle, Kristin; Sandfort, Theodorus; Struthers, Helen; Kegeles, Susan; McIntyre, James A.

    2014-01-01

    The Mpumalanga Men's Study (MPMS) is the assessment of the Project Boithato HIV prevention intervention for South African MSM. Boithato aims to increase consistent condom use, regular testing for HIV-negative MSM, and linkage to care for HIV-positive MSM. The MPMS baseline examined HIV prevalence and associated risk behaviors, and testing, care, and treatment behaviors among MSM in Gert Sibande and Ehlanzeni districts in Mpumalanga province, South Africa in order to effectively target intervention activities. We recruited 307 MSM in Gert Sibande and 298 in Ehlanzeni through respondent-driven sampling (RDS) between September 2012-March 2013. RDS-adjusted HIV prevalence estimates are 28.3% (95% CI 21.1%–35.3%) in Gert Sibande, and 13.7% (95% CI 9.1%–19.6%) in Ehlanzeni. Prevalence is significantly higher among MSM over age 25 [57.8% (95% CI 43.1%–72.9%) vs. 17.9% (95% CI 10.6%–23.9%), P<0.001 in Gert Sibande; 34.5% (95%CI 20.5%–56.0%) vs. 9.1% (95% CI 4.6%–13.9%), P<0.001 in Ehlanzeni]. In Gert Sibande, prevalence is higher among self-identified gay and transgender MSM vs. other MSM [39.3% (95%CI, 28.3%–47.9%), P<0.01], inconsistent condom users [38.1% (18.1%–64.2%), P<0.05], those with a current regular male partner [35.0% (27.1%–46.4%), P<0.05], and those with lifetime experience of intimate partner violence with men [40.4%, (95%CI 28.9%–50.9%), P<0.05]. Prevalence of previous HIV testing was 65.8% (95%CI 58.8%–74.0%) in Gert Sibande, and 69.3% (95%CI 61.9%–76.8%) in Ehlanzeni. Regular HIV testing was uncommon [(34.6%, (95%CI 27.9%–41.4%) in Gert Sibande; 31.0% (95%CI 24.9%–37.8%) in Ehlanzeni]. Among HIV-positive participants, few knew their status (28.1% in Gert Sibande and 14.5% in Ehlanzeni), or were appropriately linked to care (18.2% and 11.3%, respectively), or taking antiretroviral therapy (13.6% and 9.6% respectively). MPMS results demonstrate the importance of implementing interventions for MSM to increase consistent condom use

  2. IDENTIFICATION OF BIOLOGICALLY RELEVANT GENES USING A DATABASE OF RAT LIVER AND KIDNEY BASELINE GENE EXPRESSION

    EPA Science Inventory

    Microarray data from independent labs and studies can be compared to potentially identify toxicologically and biologically relevant genes. The Baseline Animal Database working group of HESI was formed to assess baseline gene expression from microarray data derived from control or...

  3. Optimization of Raman-spectrum baseline correction in biological application.

    PubMed

    Guo, Shuxia; Bocklitz, Thomas; Popp, Jürgen

    2016-04-21

    In the last decade Raman-spectroscopy has become an invaluable tool for biomedical diagnostics. However, a manual rating of the subtle spectral differences between normal and abnormal disease states is not possible or practical. Thus it is necessary to combine Raman-spectroscopy with chemometrics in order to build statistical models predicting the disease states directly without manual intervention. Within chemometrical analysis a number of corrections have to be applied to receive robust models. Baseline correction is an important step of the pre-processing, which should remove spectral contributions of fluorescence effects and improve the performance and robustness of statistical models. However, it is demanding, time-consuming, and depends on expert knowledge to select an optimal baseline correction method and its parameters every time working with a new dataset. To circumvent this issue we proposed a genetic algorithm based method to automatically optimize the baseline correction. The investigation was carried out in three main steps. Firstly, a numerical quantitative marker was defined to evaluate the baseline estimation quality. Secondly, a genetic algorithm based methodology was established to search the optimal baseline estimation with the defined quantitative marker as evaluation function. Finally, classification models were utilized to benchmark the performance of the optimized baseline. For comparison, model based baseline optimization was carried out applying the same classifiers. It was proven that our method could provide a semi-optimal and stable baseline estimation without any chemical knowledge required or any additional spectral information used. PMID:26907832

  4. Systems biology of Microbial Communities

    SciTech Connect

    Navid, A; Ghim, C; Fenley, A; Yoon, S; Lee, S; Almaas, E

    2008-04-11

    Microbes exist naturally in a wide range of environments, spanning the extremes of high acidity and high temperature to soil and the ocean, in communities where their interactions are significant. We present a practical discussion of three different approaches for modeling microbial communities: rate equations, individual-based modeling, and population dynamics. We illustrate the approaches with detailed examples. Each approach is best fit to different levels of system representation, and they have different needs for detailed biological input. Thus, this set of approaches is able to address the operation and function of microbial communities on a wide range of organizational levels.

  5. Exposure pathways and biological receptors: baseline data for the canyon uranium mine, Coconino County, Arizona

    USGS Publications Warehouse

    Hinck, Jo E.; Linder, Greg L.; Darrah, Abigail J.; Drost, Charles A.; Duniway, Michael C.; Johnson, Matthew J.; Méndez-Harclerode, Francisca M.; Nowak, Erika M.; Valdez, Ernest W.; Van Riper, Charles, III; Wolff, S.W.

    2014-01-01

    Recent restrictions on uranium mining within the Grand Canyon watershed have drawn attention to scientific data gaps in evaluating the possible effects of ore extraction to human populations as well as wildlife communities in the area. Tissue contaminant concentrations, one of the most basic data requirements to determine exposure, are not available for biota from any historical or active uranium mines in the region. The Canyon Uranium Mine is under development, providing a unique opportunity to characterize concentrations of uranium and other trace elements, as well as radiation levels in biota, found in the vicinity of the mine before ore extraction begins. Our study objectives were to identify contaminants of potential concern and critical contaminant exposure pathways for ecological receptors; conduct biological surveys to understand the local food web and refine the list of target species (ecological receptors) for contaminant analysis; and collect target species for contaminant analysis prior to the initiation of active mining. Contaminants of potential concern were identified as arsenic, cadmium, chromium, copper, lead, mercury, nickel, selenium, thallium, uranium, and zinc for chemical toxicity and uranium and associated radionuclides for radiation. The conceptual exposure model identified ingestion, inhalation, absorption, and dietary transfer (bioaccumulation or bioconcentration) as critical contaminant exposure pathways. The biological survey of plants, invertebrates, amphibians, reptiles, birds, and small mammals is the first to document and provide ecological information on .200 species in and around the mine site; this study also provides critical baseline information about the local food web. Most of the species documented at the mine are common to ponderosa pine Pinus ponderosa and pinyon–juniper Pinus–Juniperus spp. forests in northern Arizona and are not considered to have special conservation status by state or federal agencies; exceptions

  6. Community College Biology Lesson Index.

    ERIC Educational Resources Information Center

    Manteuffel, Mary S., Comp.; Herrick, Kathie, Comp.

    This catalog contains lesson descriptions of the available biology lessons on PLATO IV, compiled to assist instructors in planning their curricula. Information is provided for 87 lessons in the following areas: introductory material on experimental tools and techniques; chemical basis of life; cellular structure and function; reproduction and…

  7. Community College Biology Lesson Catalogue.

    ERIC Educational Resources Information Center

    Herrick, Kathie G.

    This catalog contains descriptions of the available biology lessons on PLATO IV, compiled to assist instructors in planning their curricula. Information is provided for 87 lessons in the following areas: experimental tools and techniques; chemical basis of life; cellular structure and function; bioenergetics - enzymes and cellular metabolism;…

  8. Testing Communities That Care: The Rationale, Design and Behavioral Baseline Equivalence of the Community Youth Development Study

    PubMed Central

    Hawkins, J. David; Catalano, Richard F; Arthur, Michael W.; Egan, Elizabeth; Brown, Eric C.; Abbott, Robert D.; Murray, David M.

    2008-01-01

    Recent advances in prevention science provide evidence that adolescent health and behavior problems can be prevented by high-quality prevention services. However, many communities continue to use prevention strategies that have not been shown to be effective. Studying processes for promoting the dissemination and high-quality implementation of prevention strategies found to be effective in controlled research trials has become an important focus for prevention science. The Communities That Care prevention operating system provides manuals, tools, training, and technical assistance to activate communities to use advances in prevention science to plan and implement community prevention services to reduce adolescent substance use, delinquency, and related health and behavior problems. This paper describes the rationale, aims, intervention, and design of the Community Youth Development Study, a randomized controlled community trial of the Communities That Care system, and investigates the baseline comparability of the 12 intervention and 12 control communities in the study. Results indicate baseline similarity of the intervention and control communities in levels of adolescent drug use and antisocial behavior prior to the Communities That Care intervention. Strengths and limitations of the study’s design are discussed. PMID:18516681

  9. Conservation of Forest Birds: Evidence of a Shifting Baseline in Community Structure

    PubMed Central

    Rittenhouse, Chadwick D.; Pidgeon, Anna M.; Albright, Thomas P.; Culbert, Patrick D.; Clayton, Murray K.; Flather, Curtis H.; Huang, Chengquan; Masek, Jeffrey G.; Stewart, Susan I.; Radeloff, Volker C.

    2010-01-01

    Background Quantifying changes in forest bird diversity is an essential task for developing effective conservation actions. When subtle changes in diversity accumulate over time, annual comparisons may offer an incomplete perspective of changes in diversity. In this case, progressive change, the comparison of changes in diversity from a baseline condition, may offer greater insight because changes in diversity are assessed over longer periods of times. Our objectives were to determine how forest bird diversity has changed over time and whether those changes were associated with forest disturbance. Methodology/Principal Findings We used North American Breeding Bird Survey data, a time series of Landsat images classified with respect to land cover change, and mixed-effects models to associate changes in forest bird community structure with forest disturbance, latitude, and longitude in the conterminous United States for the years 1985 to 2006. We document a significant divergence from the baseline structure for all birds of similar migratory habit and nest location, and all forest birds as a group from 1985 to 2006. Unexpectedly, decreases in progressive similarity resulted from small changes in richness (<1 species per route for the 22-year study period) and modest losses in abundance (−28.7–−10.2 individuals per route) that varied by migratory habit and nest location. Forest disturbance increased progressive similarity for Neotropical migrants, permanent residents, ground nesting, and cavity nesting species. We also documented highest progressive similarity in the eastern United States. Conclusions/Significance Contemporary forest bird community structure is changing rapidly over a relatively short period of time (e.g., ∼22 years). Forest disturbance and forest regeneration are primary factors associated with contemporary forest bird community structure, longitude and latitude are secondary factors, and forest loss is a tertiary factor. Importantly, these

  10. Validation of Community Models: 2. Development of a Baseline, Using the Wang-Sheeley-Arge Model

    NASA Technical Reports Server (NTRS)

    MacNeice, Peter

    2009-01-01

    This paper is the second in a series providing independent validation of community models of the outer corona and inner heliosphere. Here I present a comprehensive validation of the Wang-Sheeley-Arge (WSA) model. These results will serve as a baseline against which to compare the next generation of comparable forecasting models. The WSA model is used by a number of agencies to predict Solar wind conditions at Earth up to 4 days into the future. Given its importance to both the research and forecasting communities, it is essential that its performance be measured systematically and independently. I offer just such an independent and systematic validation. I report skill scores for the model's predictions of wind speed and interplanetary magnetic field (IMF) polarity for a large set of Carrington rotations. The model was run in all its routinely used configurations. It ingests synoptic line of sight magnetograms. For this study I generated model results for monthly magnetograms from multiple observatories, spanning the Carrington rotation range from 1650 to 2074. I compare the influence of the different magnetogram sources and performance at quiet and active times. I also consider the ability of the WSA model to forecast both sharp transitions in wind speed from slow to fast wind and reversals in the polarity of the radial component of the IMF. These results will serve as a baseline against which to compare future versions of the model as well as the current and future generation of magnetohydrodynamic models under development for forecasting use.

  11. Asymptomatic Polyvascular Abnormalities in Community (APAC) Study in China: Objectives, Design and Baseline Characteristics

    PubMed Central

    Xu, Liang; Xu, Jie; Wang, Anxing; Gao, Xiang; Wu, Shouling; Wei, Wen Bin; Zhao, Xingquan; Jonas, Jost B.

    2013-01-01

    Objective The population-based “Asymptomatic Polyvascular Abnormalities in Community (APAC) Study was designed to examine prevalence and associations of asymptomatic polyvascular abnormalities (APA) in a general population. In this report, the objectives, design and baseline data of the APAC study are described. Methods The study included 5,440 participants (40.1% women) with an age of 40+ years who were randomly selected from the population of the Kailuan Study which included 101,510 employees and retirees of the Kailuan Co. Ltd, a large coal mine industry located in Tangshan, Hebei, China. Exclusion criteria were previous cerebral stroke, transient ischemic attacks and coronary heart disease. In 2010 and 2011, information on potential cardiovascular risk factors was collected and all participants underwent transcranial Doppler sonography, measurement of the ankle brachial index, and bilateral carotid duplex sonography. In a first follow-up examination in 2012/2013, retinal photography and spectral-domain optical coherence tomography were additionally performed. In a planned long-term follow-up, data from clinical examinations and laboratory tests and the occurrence of cardiovascular or cerebrovascular events will be collected to build up a predicting model for the risk of ischemic events. Results At baseline, mean age of the participants was 55.2±11.8 years, and men showed a significantly (P<0.001) higher prevalence of arterial hypertension (55.5% vs. 36.5%) and hyperlipidemia (50.7% vs. 46.0%) and a higher blood homocysteine concentration (18.68±10.28µmol/L versus 11.69±6.40µmol/L). Conclusions The APAC is the first study to prospectively evaluate the relationship between intracranial arterial stenosis, retinal nerve fiber layer changes, retinal microvascular signs, and the eventual development of cerebrovascular or cardiovascular events. PMID:24386406

  12. Genome Annotation in a Community College Cell Biology Lab

    ERIC Educational Resources Information Center

    Beagley, C. Timothy

    2013-01-01

    The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning…

  13. COMPARISON OF BIOLOGICAL COMMUNITIES: THE PROBLEM OF SAMPLE REPRESENTATIVENESS

    EPA Science Inventory

    Obtaining an adequate, representative sample of biological communities or assemblages to make richness or compositional comparisons among sites is a continuing challenge. Traditionally, sample size is based on numbers of replicates or area collected or numbers of individuals enum...

  14. How-to-Do-It. Community Biology.

    ERIC Educational Resources Information Center

    Stencel, John E.

    1990-01-01

    Described is a project in which students find a living population in their community and either study it in the field or bring it into the laboratory for study. Seven example projects are suggested. (CW)

  15. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

    PubMed

    Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

    2014-06-01

    The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow. PMID:24911500

  16. Oil, biological communities and contingency planning

    USGS Publications Warehouse

    Albers, P.H.

    1995-01-01

    The Oil Pollution Act of 1990 mandates the inclusion of a fish and wildlife response plan in the National Contingency Plan (NCP) and the creation of Area Committees that must develop an Area Contingency Plan (ACP). Area Contingency Plans must include a detailed annex containing a Fish and Wildlife and Sensitive Environments Plan. Tank vessels, offshore facilities, and certain onshore facilities must have response plans consistent with the requirements of the NCP and the ACP. New regulations to supersede the Type A and B procedures of the Natural Resources Damage Assessment Regulations are being developed for oil spills. Currently, four assessment methods have been proposed: (1) Type A, (2) comprehensive (Type B), (3) intermediate (between types A and B), and (4) compensation tables. The Oil Spill Liability Trust Fund is approaching its ceiling of $1 billion, but only $50 million has been appropriated. Effective biological contingency planning requires extensive knowledge of (1) the environmental fate of petroleum, (2) the effects of petroleum on organisms, (3) the existing biological resources, and (4) the establishment of a system of biological priorities. The characteristics and fate of petroleum and the biological effects of petroleum are reviewed. Assessment of biological resources includes plant and animal distributions, important habitat, endangered or threatened species, and economic considerations. The establishment by Area Committees of priorities for environmental protection, injury assessment, and restoration will promote efficient spill response. Three special issues are discussed: (1) improving our ability to restore natural resources, (2) the potential role of biological diversity in spill response planning, and (3) planning for animal rehabilitation.

  17. Ankylosing Spondylitis Patients Commencing Biologic Therapy Have High Baseline Levels of Comorbidity: A Report from the Australian Rheumatology Association Database

    PubMed Central

    Oldroyd, John; Schachna, Lionel; Buchbinder, Rachelle; Staples, Margaret; Murphy, Bridie; Bond, Molly; Briggs, Andrew; Lassere, Marissa; March, Lyn

    2009-01-01

    Aims. To compare the baseline characteristics of a population-based cohort of patients with ankylosing spondylitis (AS) commencing biological therapy to the reported characteristics of bDMARD randomised controlled trials (RCTs) participants. Methods. Descriptive analysis of AS participants in the Australian Rheumatology Association Database (ARAD) who were commencing bDMARD therapy. Results. Up to December 2008, 389 patients with AS were enrolled in ARAD. 354 (91.0%) had taken bDMARDs at some time, and 198 (55.9%) completed their entry questionnaire prior to or within 6 months of commencing bDMARDs. 131 (66.1%) had at least one comorbid condition, and 24 (6.8%) had a previous malignancy (15 nonmelanoma skin, 4 melanoma, 2 prostate, 1 breast, cervix, and bowel). Compared with RCT participants, ARAD participants were older, had longer disease duration and higher baseline disease activity. Conclusions. AS patients commencing bDMARDs in routine care are significantly different to RCT participants and have significant baseline comorbidities. PMID:20107564

  18. WATER QUALITY, MERCURY, AND HEAVY METAL DEPOSITION STUDIES IN BIOLOGICAL SPECIMENS AND SEDIMENTS FOR ECOLOGICAL BASELINE DATA IN THE ISLAND PARK WATERWAYS SYSTEM, 1973

    EPA Science Inventory

    The water quality, mercury, and heavy metal deposition in biological specimens from the Island Park waterways (17040202) were measured to establish ecological baseline data. Neutron activation analysis was used to identify quantitatively and qualitatively approximately 20 differ...

  19. Applying the community partnership approach to human biology research.

    PubMed

    Ravenscroft, Julia; Schell, Lawrence M; Cole, Tewentahawih'tha'

    2015-01-01

    Contemporary human biology research employs a unique skillset for biocultural analysis. This skillset is highly appropriate for the study of health disparities because disparities result from the interaction of social and biological factors over one or more generations. Health disparities research almost always involves disadvantaged communities owing to the relationship between social position and health in stratified societies. Successful research with disadvantaged communities involves a specific approach, the community partnership model, which creates a relationship beneficial for researcher and community. Paramount is the need for trust between partners. With trust established, partners share research goals, agree on research methods and produce results of interest and importance to all partners. Results are shared with the community as they are developed; community partners also provide input on analyses and interpretation of findings. This article describes a partnership-based, 20 year relationship between community members of the Akwesasne Mohawk Nation and researchers at the University at Albany. As with many communities facing health disparity issues, research with Native Americans and indigenous peoples generally is inherently politicized. For Akwesasne, the contamination of their lands and waters is an environmental justice issue in which the community has faced unequal exposure to, and harm by environmental toxicants. As human biologists engage in more partnership-type research, it is important to understand the long term goals of the community and what is at stake so the research circle can be closed and 'helicopter' style research avoided. PMID:25380288

  20. A Newtonian framework for community detection in undirected biological networks.

    PubMed

    Narayanan, Tejaswini; Subramaniam, Shankar

    2014-02-01

    Community detection is a key problem of interest in network analysis, with applications in a variety of domains such as biological networks, social network modeling, and communication pattern analysis. In this paper, we present a novel framework for community detection that is motivated by a physical system analogy. We model a network as a system of point masses, and drive the process of community detection, by leveraging the Newtonian interactions between the point masses. Our framework is designed to be generic and extensible relative to the model parameters that are most suited for the problem domain. We illustrate the applicability of our approach by applying the Newtonian Community Detection algorithm on protein-protein interaction networks of E. coli , C. elegans, and S. cerevisiae. We obtain results that are comparable in quality to those obtained from the Newman-Girvan algorithm, a widely employed divisive algorithm for community detection. We also present a detailed analysis of the structural properties of the communities produced by our proposed algorithm, together with a biological interpretation using E. coli protein network as a case study. A functional enrichment heat map is constructed with the Gene Ontology functional mapping, in addition to a pathway analysis for each community. The analysis illustrates that the proposed algorithm elicits communities that are not only meaningful from a topological standpoint, but also possess biological relevance. We believe that our algorithm has the potential to serve as a key computational tool for driving therapeutic applications involving targeted drug development for personalized care delivery. PMID:24681920

  1. Altered baseline brain activity differentiates regional mechanisms subserving biological and psychological alterations in obese men.

    PubMed

    Zhang, Bin; Tian, Derun; Yu, Chunshui; Li, Meng; Zang, Yufeng; Liu, Yijun; Walter, Martin

    2015-01-01

    Obesity as a chronic disease is a major factor for insulin resistance and Type 2 diabetes, which has become a global health problem. In the present study, we used resting state functional MRI to investigate the amplitude of low frequency fluctuations of spontaneous signal during both hunger and satiety states in 20 lean and 20 obese males. We found that, before food intake, obese men had significantly greater baseline activity in the precuneus and lesser activity in dorsal anterior cingulate cortex (dACC) relative to lean subjects. Furthermore, after food intake, obese males had significantly lesser activity in dACC than lean males. We further found a significant positive correlation between precuneus activation and hunger ratings before food intake, while dACC activity was negatively correlated with plasma insulin levels before and after food intake. These results indicated that both precuneus and dACC may play an important role in eating behavior. While precuneus rather seemed to mediate subjective satiety, dACC levels rather reflected indirect measures of glucose utilization. PMID:26099208

  2. Monitoring biological impacts of space shuttle launches from Vandenberg Air Force Base: Establishment of baseline conditions

    NASA Technical Reports Server (NTRS)

    Schmaizer, Paul A.; Hinkle, C. Ross

    1987-01-01

    Space shuttle launches produce environmental impacts resulting from the formation of an exhaust cloud containing hydrogen chloride aerosols and aluminum oxide particulates. Studies have shown that most impacts occur near-field (within 1.5 km) of the launch site while deposition from launches occurs far-field (as distant as 22 km). In order to establish baseline conditions of vegetation and soils in the areas likely to be impacted by shuttle launches from Vandenberg Air Force Base (VAFB), vegetation and soils in the vicinity of Space Launch Complex-6 (SLC-6) were sampled and a vegetation map prepared. The areas likely to be impacted by launches were determined considering the structure of the launch complex, the prevailing winds, the terrain, and predictions of the Rocket Exhaust Effluent Diffusion Model (REEDM). Fifty vegetation transects were established and sampled in March 1986 and resampled in September 1986. A vegetation map was prepared for six Master Planning maps surrounding SLC-6 using LANDSAT Thematic Mapper imagery as well as color and color infrared aerial photography. Soil samples were collected form the 0 to 7.5 cm layer at all transects in the wet season and at a subsample of the transects in the dry season and analyzed for pH, organic matter, conductivity, cation exchange capacity, exchangeable Ca, Mg, Na, K, and Al, available NH3-N, PO4-P, Cu, Fe, Mn, Zn, and TKN.

  3. Altered baseline brain activity differentiates regional mechanisms subserving biological and psychological alterations in obese men

    PubMed Central

    Zhang, Bin; Tian, Derun; Yu, Chunshui; Li, Meng; Zang, Yufeng; Liu, Yijun; Walter, Martin

    2015-01-01

    Obesity as a chronic disease is a major factor for insulin resistance and Type 2 diabetes, which has become a global health problem. In the present study, we used resting state functional MRI to investigate the amplitude of low frequency fluctuations of spontaneous signal during both hunger and satiety states in 20 lean and 20 obese males. We found that, before food intake, obese men had significantly greater baseline activity in the precuneus and lesser activity in dorsal anterior cingulate cortex (dACC) relative to lean subjects. Furthermore, after food intake, obese males had significantly lesser activity in dACC than lean males. We further found a significant positive correlation between precuneus activation and hunger ratings before food intake, while dACC activity was negatively correlated with plasma insulin levels before and after food intake. These results indicated that both precuneus and dACC may play an important role in eating behavior. While precuneus rather seemed to mediate subjective satiety, dACC levels rather reflected indirect measures of glucose utilization. PMID:26099208

  4. 1994 Baseline biological studies for the Device Assembly Facility at the Nevada Test Site

    SciTech Connect

    Townsend, Y.E.; Woodward, B.D.; Hunter, R.B.; Greger, P.D.; Saethre, M.B.

    1995-02-01

    This report describes environmental work performed at the Device Assembly Facility (DAF) in 1994 by the Basic Environmental Monitoring and Compliance Program (BECAMP). The DAF is located near the Mojave-Great Basin desert transition zone 27 km north of Mercury. The area immediately around the DAF building complex is a gentle slope cut by 1 to 3 m deep arroyos, and occupied by transitional vegetation. In 1994, construction activities were largely limited to work inside the perimeter fence. The DAF was still in a preoperational mode in 1994, and no nuclear materials were present. The DAF facilities were being occupied so there was water in the sewage settling pond, and the roads and lights were in use. Sampling activities in 1994 represent the first year in the proposed monitoring scheme. The proposed biological monitoring plan gives detailed experimental protocols. Plant, lizard, tortoise, small mammal, and bird surveys were performed in 1994. The authors briefly outline procedures employed in 1994. Studies performed on each taxon are reviewed separately then summarized in a concluding section.

  5. Developing a wintering waterfowl community baseline for environmental monitoring of Narragansett Bay, Rhode Island

    PubMed Central

    Kreakie, Betty J.; Winiarski, Kristopher; McKinney, Richard

    2015-01-01

    In 2004, the Atlantic Ecology Division of the US Environmental Protection Agency’s Office of Research and Development began an annual winter waterfowl survey of Rhode Island’s Narragansett Bay. Herein, we explore the survey data gathered from 2004 to 2011 in order to establish a benchmark understanding of our waterfowl communities and to establish a statistical framework for future environmental monitoring. The abundance and diversity of wintering waterfowl were relatively stable during the initial years of this survey, except in 2010 when there was a large spike in abundance and a reciprocal fall in diversity. There was no significant change in ranked abundance of most waterfowl species, with only Bufflehead ( Bucephala albeola) and Hooded Merganser ( Lophodytes cucllatus) showing a slight yet significant upward trend during the course of our survey period. Nonmetric multidimensional scaling (NMDS) was used to examine the community structure of wintering waterfowl. The results of the NMDS indicate that there is a spatial structure to the waterfowl communities of Narragansett Bay and this structure has remained relatively stable since the survey began. Our NMDS analysis helps to solidify what is known anecdotally about the bay’s waterfowl ecology, and provides a formalized benchmark for long-term monitoring of Narragansett Bay’s waterfowl communities. Birds, including waterfowl, are preferred bioindicators and we propose using our multivariate approach to monitor the future health of the bay. While this research focuses on a specific area of New England, these methods can be easily applied to novel areas of concern and provide a straightforward nonparametric approach to community-level monitoring. The methods provide a statistic test to examine potential drivers of community turnover and well-suited visualization tools. PMID:27019692

  6. Disentangling emotion processes in borderline personality disorder: physiological and self-reported assessment of biological vulnerability, baseline intensity, and reactivity to emotionally evocative stimuli.

    PubMed

    Kuo, Janice R; Linehan, Marsha M

    2009-08-01

    This study investigated M. Linehan's (1993) theory that individuals meeting criteria for borderline personality disorder (BPD) have high biological vulnerability to emotion dysregulation, including high baseline emotional intensity and high reactivity to emotionally evocative stimuli. Twenty individuals with BPD, 20 age-matched individuals with generalized social anxiety disorder (SAD), and 20 age-matched normal controls (NCs) participated in 2 separate emotion induction conditions, a standardized condition, and a personally relevant condition. Respiratory sinus arrhythmia (RSA), skin conductance response (SCR), and self-report measures were collected throughout the experiment. BPD participants displayed heightened biological vulnerability compared with NCs as indicated by reduced basal RSA. BPD participants also exhibited high baseline emotional intensity, characterized by heightened SCR and heightened self-reported negative emotions at baseline. However, the BPD group did not display heightened reactivity, as their physiological and self-reported changes from baseline to the emotion inductions tasks were not greater than the other 2 groups. PMID:19685950

  7. Bioerosion by chemosynthetic biological communities on Holocene submarine slide scars

    NASA Astrophysics Data System (ADS)

    Paull, C. K.; Ussler, W.; Greene, H. G.; Barry, J.; Keaten, R.

    2005-02-01

    Geomorphic, stratigraphic, and faunal observations of submarine slide scars that occur along the flanks of Monterey Canyon in 2.0 2.5 km water depths were made to identify the processes that continue to alter the surface of a submarine landslide scar after the initial slope failure. Deep-sea chemosynthetic biological communities and small caves are common on the sediment-free surfaces of the slide scars, especially along the headwall. The chemosynthetic organisms observed on slide scars in Monterey Canyon undergo a faunal succession based in part on their ability to maintain their access to the redox boundaries in the sediment on which they depend on as an energy source. By burrowing into the seafloor, these organisms are able to follow the retreating redox boundaries as geochemical re-equilibration occurs on the sole of the slide. As these organisms dig into the seafloor on the footwall, they often generate small caves and weaken the remaining seafloor. While chemosynthetic biological communities are typically used as indicators of fluid flow, these communities may be supported by methane and hydrogen sulfide that are diffusing out of the fresh seafloor exposed at the sole of the slide by the slope failure event. If so, these chemosynthetic biological communities may simply mark sites of recent seafloor exhumation, and are not reliable fluid seepage indicators.

  8. PREDICT-PD: Identifying risk of Parkinson's disease in the community: methods and baseline results

    PubMed Central

    Noyce, Alastair J; Bestwick, Jonathan P; Silveira-Moriyama, Laura; Hawkes, Christopher H; Knowles, Charles H; Hardy, John; Giovannoni, Gavin; Nageshwaran, Saiji; Osborne, Curtis; Lees, Andrew J; Schrag, Anette

    2014-01-01

    Objectives To present methods and baseline results for an online screening tool to identify increased risk for Parkinson's disease (PD) in the UK population. Methods Risk estimates for future PD were derived from the results of a systematic review of risk factors and early features of PD. Participants aged 60–80 years without PD were recruited by self-referral. They completed an online survey (including family history, non-motor symptoms and lifestyle factors), a keyboard-tapping task and the University of Pennsylvania Smell Identification Test. Risk scores were calculated based on survey answers. Preliminary support for the validity of this algorithm was assessed by comparing those estimated to be higher risk for PD with those at lower risk using proxies, including smell loss, REM-sleep behaviour disorder and reduced tapping speed, and by assessing associations in the whole group. Results 1324 eligible participants completed the survey and 1146 undertook the keyboard-tapping task. Smell tests were sent to 1065 participants. Comparing the 100 highest-risk participants and 100 lowest-risk participants, median University of Pennsylvania Smell Identification Test scores were 30/40 versus 33/40 (p<0.001), mean number of key taps in 30 s were 55 versus 58 (p=0.045), and 24% versus 10% scored above cut-off for REM-sleep behaviour disorder (p=0.008). Regression analyses showed increasing risk scores were associated with worse scores in the three proxies across the whole group (p≤0.001). Conclusions PREDICT-PD is the first study to systematically combine risk factors for PD in the general population. Validity to predict risk of PD will be tested through longitudinal follow-up of incident PD diagnosis. PMID:23828833

  9. Baseline Assessment of Fish Communities, Benthic Macroinvertebrate Communities, and Stream Habitat and Land Use, Big Thicket National Preserve, Texas, 1999-2001

    USGS Publications Warehouse

    Moring, J. Bruce

    2003-01-01

    The Big Thicket National Preserve comprises 39,300 hectares in the form of nine preserve units connected by four stream corridor units (with two more corridor units proposed) distributed over the lower Neches and Trinity River Basins of southeastern Texas. Fish and benthic macroinvertebrate data were collected at 15 stream sites (reaches) in the preserve during 1999?2001 for a baseline assessment and a comparison of communities among stream reaches. The fish communities in the preserve were dominated by minnows (family Cyprinidae) and sunfishes (family Centrarchidae). Reaches with smaller channel sizes generally had higher fish species richness than the larger reaches in the Neches River and Pine Island Bayou units of the preserve. Fish communities in geographically adjacent reaches were most similar in overall community structure. The blue sucker, listed by the State as a threatened species, was collected in only one reach?a Neches River reach a few miles downstream from the Steinhagen Lake Dam. Riffle beetles (family Elmidae) and midges (family Chironomidae) dominated the aquatic insect communities at the 14 reaches sampled for aquatic insects in the preserve. The Ephemeroptera, Plecoptera and Trichoptera (EPT) Index, an index sensitive to water-quality degradation, was smallest at the Little Pine Island Bayou near Beaumont reach that is in a State 303(d)-listed stream segment on Little Pine Island Bayou. Trophic structure of the aquatic insect communities is consistent with the river continuum concept with shredder and scraper insect taxa more abundant in reaches with smaller stream channels and filter feeders more abundant in reaches with larger channels. Aquatic insect community metrics were not significantly correlated to any of the stream-habitat or land-use explanatory variables. The percentage of 1990s urban land use in the drainage areas upstream from 12 bioassessment reaches were negatively correlated to the reach structure index, which indicates less

  10. Biological communities at the Florida Escarpment resemble hydrothermal vent taxa

    USGS Publications Warehouse

    Paull, C.K.; Hecker, Barbara; Commeau, R.; Freeman-Lynde, R. P.; Neumann, C.; Corso, W.P.; Golubic, S.; Hook, J.E.; Sikes, E.; Curray, J.

    1984-01-01

    Dense biological communities of large epifaunal taxa similar to those found along ridge crest vents at the East Pacific Rise were discovered in the abyssal Gulf of Mexico. These assemblages occur on a passive continental margin at the base of the Florida Escarpment, the interface between the relatively impermeable hemipelagic clays of the distal Mississippi Fan and the jointed Cretaceous limestone of the Florida Platform. The fauna apparently is nourished by sulfide rich hypersaline waters seeping out at near ambient temperatures onto the sea floor.

  11. Early-Phase Clinical Trials In The Community: Results From the National Cancer Institute Community Cancer Centers Program Early-Phase Working Group Baseline Assessment

    PubMed Central

    Zaren, Howard A.; Nair, Suresh; Go, Ronald S.; Enos, Rebecca A.; Lanier, Keith S.; Thompson, Michael A.; Zhao, Jinxiu; Fleming, Deborah L.; Leighton, John C.; Gribbin, Thomas E.; Bryant, Donna M.; Carrigan, Angela; Corpening, Jennifer C.; Csapo, Kimberly A.; Dimond, Eileen P.; Ellison, Christie; Gonzalez, Maria M.; Harr, Jodi L.; Wilkinson, Kathy; Denicoff, Andrea M.

    2013-01-01

    Purpose: The National Cancer Institute (NCI) Community Cancer Centers Program (NCCCP) formed an Early-Phase Working Group to facilitate site participation in early-phase (EP) trials. The Working Group conducted a baseline assessment (BA) to describe the sites' EP trial infrastructure and its association with accrual. Methods: EP accrual and infrastructure data for the sites were obtained for July 2010-June 2011 and 2010, respectively. Sites with EP accrual rates at or above the median were considered high-accruing sites. Analyses were performed to identify site characteristics associated with higher accrual onto EP trials. Results: Twenty-seven of the 30 NCCCP sites participated. The median number of EP trials open per site over the course of July 2010-June 2011 was 19. Median EP accrual per site was 14 patients in 1 year. Approximately half of the EP trials were Cooperative Group; most were phase II. Except for having a higher number of EP trials open (P = .04), high-accruing sites (n = 14) did not differ significantly from low-accruing sites (n = 13) in terms of any single site characteristic. High-accruing sites did have shorter institutional review board (IRB) turnaround time by 20 days, and were almost three times as likely to be a lead Community Clinical Oncology Program site (small sample size may have prevented statistical significance). Most sites had at least basic EP trial infrastructure. Conclusion: Community cancer centers are capable of conducting EP trials. Infrastructure and collaborations are critical components of success. This assessment provides useful information for implementing EP trials in the community. PMID:23814525

  12. Communities advancing the studies of Tribal nations across their lifespan: Design, methods, and baseline of the CoASTAL cohort

    PubMed Central

    Tracy, Kate; Boushey, Carol; Roberts, Sparkle M.; Morris, J.Glenn; Grattan, Lynn M.

    2015-01-01

    The CoASTAL cohort represents the first community cohort assembled to study a HAB related illness. It is comprised of three Native American tribes in the Pacific NW for the purpose of studying the health impacts of chronic, low level domoic acid (DA) exposure through razor clam consumption. This cohort is at risk of domoic acid (DA) toxicity by virtue of their geographic location (access to beaches with a history of elevated DA levels in razor clams) and the cultural and traditional significance of razor clams in their diet. In this prospective, longitudinal study, Wave 1 of the cohort is comprised of 678 members across the lifespan with both sexes represented within child, adult and geriatric age groups. All participants are followed annually with standard measures of medical and social history; neuropsychological functions, psychological status, and dietary exposure. DA concentration levels are measured at both public and reservation beaches where razor clams are sourced and multiple metrics have been piloted to further determine exposure. Baseline data indicates that all cognitive and psychological functions are within normal limits. In addition there is considerable variability in razor clam exposure. Therefore, the CoASTAL cohort offers a unique opportunity to investigate the potential health effects of chronic, low level exposure to DA over time.

  13. BioDEAL: community generation of biological annotations

    PubMed Central

    Breimyer, Paul; Green, Nathan; Kumar, Vinay; Samatova, Nagiza F

    2009-01-01

    Background Publication databases in biomedicine (e.g., PubMed, MEDLINE) are growing rapidly in size every year, as are public databases of experimental biological data and annotations derived from the data. Publications often contain evidence that confirm or disprove annotations, such as putative protein functions, however, it is increasingly difficult for biologists to identify and process published evidence due to the volume of papers and the lack of a systematic approach to associate published evidence with experimental data and annotations. Natural Language Processing (NLP) tools can help address the growing divide by providing automatic high-throughput detection of simple terms in publication text. However, NLP tools are not mature enough to identify complex terms, relationships, or events. Results In this paper we present and extend BioDEAL, a community evidence annotation system that introduces a feedback loop into the database-publication cycle to allow scientists to connect data-driven biological concepts to publications. Conclusion BioDEAL may change the way biologists relate published evidence with experimental data. Instead of biologists or research groups searching and managing evidence independently, the community can collectively build and share this knowledge. PMID:19891799

  14. Coastal Mapping for Baseline Geoscience Knowledge to Support Community Hazard Assessment and Sustainable Development, Eastern Baffin Island, Nunavut

    NASA Astrophysics Data System (ADS)

    Forbes, D. L.; Bell, T.; Campbell, D. C.; Cowan, B.; Deering, R. L.; Hatcher, S. V.; Hughes Clarke, J. E.; Irvine, M.; Manson, G. K.; Smith, I. R.; Edinger, E.

    2015-12-01

    reversal from falling to rising relative sea levels. Overall, the coastal mapping results constitute baseline geoscience knowledge infrastructure for navigation, fisheries, port engineering, municipal planning, and informing sustainability initiatives in the isolated coastal communities of this Arctic region.

  15. Baseline Differences and Trajectories of Change for Deceased, Placed, and Community Residing Alzheimer’s Disease Patients

    PubMed Central

    Schulz, Richard; Zdaniuk, Bozena; Belle, Steven H; Czaja, Sara J; Arrighi, H Michael; Zbrozek, Arthur S

    2009-01-01

    This study identifies predictors of placement or death in a large ethnically/racially diverse sample of moderately impaired Alzheimer’s disease (AD) patients residing in the community. Patients and caregivers were followed for 18 months with four assessments at six month intervals. Multinomial regression was used to identify caregiver and patient baseline characteristics and changes over time as predictors of patient placement in a long-term care facility (n=180), patient death (not preceded by placement, n=187), or remaining in the community at home (n=583). Our findings reveal important differences between death and placement when compared to continued home care. Both death and placement are significantly associated with increased ADL limitations (Exp(B)=1.285, p=.017; Exp(B)=0.1.202, p= 0.038, for death and placement, compared to home care, respectively), having a non-spouse caregiver (Exp(B)=0.325, p=0.026; Exp(B)=0.386, p=0.050, for death and placement respectively), and being a male patient (Exp(B)=0.367, p=.003;Exp(B)=0.439, p= 0.016, for death and placement, respectively). Death and placement differ with respect to health service use, race, and group assignment. Whites are more likely to be placed rather than remain at home when compared to African American (Ex(B)=.520, p=.028) or Hispanic (Exp(B)=0.338, p <.005) patients, whereas being assigned to the control condition as opposed to active treatment (Exp(B)=.515, p=.008), having a male caregiver (Exp(B)=0.482, p=.043), and increasing patient health service use (Exp(B)=1.105, p=.015) are associated with increased mortality. Placed and deceased patients are further differentiated from each other by the fact that caregivers of placed patients report an increase in being bothered by memory problems when compared to caregivers of deceased patients (Exp(B)=.577, p=.006). Patients who are placed, die, or remain at home have unique trajectories which vary as a function of the reference group used for comparison

  16. The 1993 baseline biological studies and proposed monitoring plan for the Device Assembly Facility at the Nevada Test Site

    SciTech Connect

    Woodward, B.D.; Hunter, R.B.; Greger, P.D.; Saethre, M.B.

    1995-02-01

    This report contains baseline data and recommendations for future monitoring of plants and animals near the new Device Assembly Facility (DAF) on the Nevada Test Site (NTS). The facility is a large structure designed for safely assembling nuclear weapons. Baseline data was collected in 1993, prior to the scheduled beginning of DAF operations in early 1995. Studies were not performed prior to construction and part of the task of monitoring operational effects will be to distinguish those effects from the extensive disturbance effects resulting from construction. Baseline information on species abundances and distributions was collected on ephemeral and perennial plants, mammals, reptiles, and birds in the desert ecosystems within three kilometers (km) of the DAF. Particular attention was paid to effects of selected disturbances, such as the paved road, sewage pond, and the flood-control dike, associated with the facility. Radiological monitoring of areas surrounding the DAF is not included in this report.

  17. Research in Community-Based Biological Education. 4 Case-Studies.

    ERIC Educational Resources Information Center

    Atchia, Michael, Ed.

    Several case studies of research into the biological needs of communities in developing countries were conducted and two strategies for relating biological education (in both formal and nonformal contexts) to community development were identified. Four of these case studies are presented. They are: (1) "From Biological Knowledge to Community…

  18. Occurrence and Potential Biological Effects of Amphetamine on Stream Communities.

    PubMed

    Lee, Sylvia S; Paspalof, Alexis M; Snow, Daniel D; Richmond, Erinn K; Rosi-Marshall, Emma J; Kelly, John J

    2016-09-01

    The presence of pharmaceuticals, including illicit drugs in aquatic systems, is a topic of environmental significance because of their global occurrence and potential effects on aquatic ecosystems and human health, but few studies have examined the ecological effects of illicit drugs. We conducted a survey of several drug residues, including the potentially illicit drug amphetamine, at 6 stream sites along an urban to rural gradient in Baltimore, Maryland, U.S.A. We detected numerous drugs, including amphetamine (3 to 630 ng L(-1)), in all stream sites. We examined the fate and ecological effects of amphetamine on biofilm, seston, and aquatic insect communities in artificial streams exposed to an environmentally relevant concentration (1 μg L(-1)) of amphetamine. The amphetamine parent compound decreased in the artificial streams from less than 1 μg L(-1) on day 1 to 0.11 μg L(-1) on day 22. In artificial streams treated with amphetamine, there was up to 45% lower biofilm chlorophyll a per ash-free dry mass, 85% lower biofilm gross primary production, 24% greater seston ash-free dry mass, and 30% lower seston community respiration compared to control streams. Exposing streams to amphetamine also changed the composition of bacterial and diatom communities in biofilms at day 21 and increased cumulative dipteran emergence by 65% and 89% during the first and third weeks of the experiment, respectively. This study demonstrates that amphetamine and other biologically active drugs are present in urban streams and have the potential to affect both structure and function of stream communities. PMID:27513635

  19. A natural experiment opportunity in two low-income urban food desert communities: research design, community engagement methods, and baseline results.

    PubMed

    Dubowitz, Tamara; Ncube, Collette; Leuschner, Kristin; Tharp-Gilliam, Shannah

    2015-04-01

    A growing body of evidence has highlighted an association between a lack of access to nutritious, affordable food (e.g., through full-service grocery stores [FSGs]), poor diet, and increased risk for obesity. In response, there has been growing interest among policy makers in encouraging the siting of supermarkets in "food deserts," that is, low-income geographic areas with low access to healthy food options. However, there is limited research to evaluate the impact of such efforts, and most studies to date have been cross-sectional. The Pittsburgh Hill/Homewood Research on Eating, Shopping, and Health (PHRESH) is a longitudinal quasi-experimental study of a dramatic change (i.e., a new FSG) in the food landscape of a low-income, predominantly Black neighborhood. The study is following a stratified random sample of households (n = 1,372), and all food venues (n = 60) in both intervention and control neighborhoods, and the most frequently reported food shopping venues outside both neighborhoods. This article describes the study design and community-based methodology, which focused simultaneously on the conduct of scientifically rigorous research and the development and maintenance of trust and buy-in from the involved neighborhoods. Early results have begun to define markers for success in creating a natural experiment, including strong community engagement. Baseline data show that the vast majority of residents already shop at a FSG and do not shop at the nearest one. Follow-up data collection will help determine whether and how a new FSG may change behaviors and may point to the need for additional interventions beyond new FSGs alone. PMID:25829122

  20. Relevance of ammonium oxidation within biological soil crust communities

    USGS Publications Warehouse

    Johnson, S.L.; Budinoff, C.R.; Belnap, J.; Garcia-Pichel, F.

    2005-01-01

    Thin, vertically structured topsoil communities that become ecologically important in arid regions (biological soil crusts or BSCs) are responsible for much of the nitrogen inputs into pristine arid lands. We studied N2 fixation and ammonium oxidation (AO) at subcentimetre resolution within BSCs from the Colorado Plateau. Pools of dissolved porewater nitrate/ nitrite, ammonium and organic nitrogen in wetted BSCs were high in comparison with those typical of aridosoils. They remained stable during incubations, indicating that input and output processes were of similar magnitude. Areal N2 fixation rates (6.5-48 ??mol C2H2 m-2 h -1) were high, the vertical distribution of N2 fixation peaking close to the surface if populations of heterocystous cyanobacteria were present, but in the subsurface if they were absent. Areal AO rates (19-46 ??mol N m-2 h-1) were commensurate with N2 fixation inputs. When considering oxygen availability, AO activity invariably peaked 2-3 mm deep and was limited by oxygen (not ammonium) supply. Most probable number (MPN)-enumerated ammonia-oxidizing bacteria (6.7-7.9 ?? 103 cells g-1 on average) clearly peaked at 2-3 mm depth. Thus, AO (hence nitrification) is a spatially restricted but important process in the nitrogen cycling of BSC, turning much of the biologically fixed nitrogen into oxidized forms, the fate of which remains to be determined.

  1. Enabling a next generation of synthetic biology community organization and leadership.

    PubMed

    Palmer, Megan J; Jewett, Michael C

    2014-03-21

    Synthetic biology seeks to make engineering of complex biological functions more efficient, reliable, and predictable. Advancing the process of engineering biology requires community organization and leadership. As synthetic biology matures into a globally significant enterprise, the community needs to enable a next generation of leaders to organize the field's responsible advancement. We discuss key points raised at a community meeting on these issues at SB6.0--the Sixth International Meeting on Synthetic Biology--and highlight opportunities to carry forward the conversation. PMID:24617412

  2. Baseline survey for rare plant species and native plant communities within the Kamehameha Schools 'Lupea Safe Harbor Planning Project Area, North Kona District, Island of Hawai'i

    USGS Publications Warehouse

    Jacobi, James; F. R. Warshauer, frwvolcano@hotmail.com; Jonathan Price, jpprice@hawaii.edu

    2010-01-01

    Non-zero baseline values are proposed for the one listed plant species found within the Lupea Project area, one species that is a candidate for listing, and the four other rare species we found that may be considered for listing in the future. Additionally, a zero baseline is proposed for 23 other species that were predicted, but not found within the project area. These include 14 Endangered species, one Threatened species, two candidates for listing, and six species of concern. Subsequent monitoring of the site will be necessary to determine if the populations of these species have increased or decreased relative to their baseline values. It is presumed that the management activities Kamehameha Schools has proposed for this area, particularly removal of the ungulates and weed control, will provide a benefit to the habitat as a whole and allow for natural regeneration and maintenance of the all elements of the plant communities found there.

  3. Community-driven computational biology with Debian Linux

    PubMed Central

    2010-01-01

    Background The Open Source movement and its technologies are popular in the bioinformatics community because they provide freely available tools and resources for research. In order to feed the steady demand for updates on software and associated data, a service infrastructure is required for sharing and providing these tools to heterogeneous computing environments. Results The Debian Med initiative provides ready and coherent software packages for medical informatics and bioinformatics. These packages can be used together in Taverna workflows via the UseCase plugin to manage execution on local or remote machines. If such packages are available in cloud computing environments, the underlying hardware and the analysis pipelines can be shared along with the software. Conclusions Debian Med closes the gap between developers and users. It provides a simple method for offering new releases of software and data resources, thus provisioning a local infrastructure for computational biology. For geographically distributed teams it can ensure they are working on the same versions of tools, in the same conditions. This contributes to the world-wide networking of researchers. PMID:21210984

  4. Biology in Context: Teachers' Professional Development in Learning Communities

    ERIC Educational Resources Information Center

    Elster, Doris

    2009-01-01

    Biology in Context ("bik") is a project that aims to improve biology teaching in lower secondary schools in Germany. Based on a theoretical framework derived from the National Educational Standards, four competence areas should be fostered in biology education: subject knowledge; inquiry acquisition; subject-related communication; and valuing and…

  5. Communities of the Biological Crossroads: An Extraordinary Outdoor Classroom.

    ERIC Educational Resources Information Center

    Maier, Charles R.

    1992-01-01

    Provides rich description of the biological diversity found in a 30-mile section of Nebraska known as the "biological crossroads." Argues that the seven major associations of the Niobrara River valley provide a great classroom. Includes a complete listing of plant species. (DDR)

  6. Re-evaluating the health of coral reef communities: baselines and evidence for human impacts across the central Pacific.

    PubMed

    Smith, Jennifer E; Brainard, Rusty; Carter, Amanda; Grillo, Saray; Edwards, Clinton; Harris, Jill; Lewis, Levi; Obura, David; Rohwer, Forest; Sala, Enric; Vroom, Peter S; Sandin, Stuart

    2016-01-13

    Numerous studies have documented declines in the abundance of reef-building corals over the last several decades and in some but not all cases, phase shifts to dominance by macroalgae have occurred. These assessments, however, often ignore the remainder of the benthos and thus provide limited information on the present-day structure and function of coral reef communities. Here, using an unprecedentedly large dataset collected within the last 10 years across 56 islands spanning five archipelagos in the central Pacific, we examine how benthic reef communities differ in the presence and absence of human populations. Using islands as replicates, we examine whether benthic community structure is associated with human habitation within and among archipelagos and across latitude. While there was no evidence for coral to macroalgal phase shifts across our dataset we did find that the majority of reefs on inhabited islands were dominated by fleshy non-reef-building organisms (turf algae, fleshy macroalgae and non-calcifying invertebrates). By contrast, benthic communities from uninhabited islands were more variable but in general supported more calcifiers and active reef builders (stony corals and crustose coralline algae). Our results suggest that cumulative human impacts across the central Pacific may be causing a reduction in the abundance of reef builders resulting in island scale phase shifts to dominance by fleshy organisms. PMID:26740615

  7. The Well London program - a cluster randomized trial of community engagement for improving health behaviors and mental wellbeing: baseline survey results

    PubMed Central

    2012-01-01

    Background The Well London program used community engagement, complemented by changes to the physical and social neighborhood environment, to improve physical activity levels, healthy eating, and mental wellbeing in the most deprived communities in London. The effectiveness of Well London is being evaluated in a pair-matched cluster randomized trial (CRT). The baseline survey data are reported here. Methods The CRT involved 20 matched pairs of intervention and control communities (defined as UK census lower super output areas (LSOAs); ranked in the 11% most deprived LSOAs in London by the English Indices of Multiple Deprivation) across 20 London boroughs. The primary trial outcomes, sociodemographic information, and environmental neighbourhood characteristics were assessed in three quantitative components within the Well London CRT at baseline: a cross-sectional, interviewer-administered adult household survey; a self-completed, school-based adolescent questionnaire; a fieldworker completed neighborhood environmental audit. Baseline data collection occurred in 2008. Physical activity, healthy eating, and mental wellbeing were assessed using standardized, validated questionnaire tools. Multiple imputation was used to account for missing data in the outcomes and other variables in the adult and adolescent surveys. Results There were 4,107 adults and 1,214 adolescent respondents in the baseline surveys. The intervention and control areas were broadly comparable with respect to the primary outcomes and key sociodemographic characteristics. The environmental characteristics of the intervention and control neighborhoods were broadly similar. There was greater between-cluster variation in the primary outcomes in the adult population compared to the adolescent population. Levels of healthy eating, smoking, and self-reported anxiety/depression were similar in the Well London adult population and the national Health Survey for England. Levels of physical activity were higher

  8. Historical macrobenthic community assemblages in the Avilés Canyon, N Iberian Shelf: Baseline biodiversity information for a marine protected area

    NASA Astrophysics Data System (ADS)

    Louzao, Maite; Anadón, Nuria; Arrontes, Julio; Álvarez-Claudio, Consuelo; Fuente, Dulce María; Ocharan, Francisco; Anadón, Araceli; Acuña, José Luis

    2010-02-01

    Deep-sea ecosystems are highly diverse, and European countries seek to protect these environments by identifying conservation targets. One of these is the Avilés Canyon, southern Bay of Biscay, NE Atlantic, Spain. We present the first analysis of historical benthic communities (1987-1988) of this canyon ecosystem, which is a valuable source of biodiversity baseline information. We found 810 taxa divided in five main macrobenthic assemblages, showing a highly diverse benthic community. Bathymetry was the major structuring agent of benthic community, separating shallow (assemblages I and II, 31 to 307 m depth) from deep stations (assemblages III, IV and V, 198 to 1400 m depth). Especially diverse was assemblage IV, located at the easternmost part of the continental slope (378-1100 m depth) where we found reef-forming corals Lophelia pertusa and Madrepora oculata. These and other communities (sea-pens [Order Pennatulacea, Phylum Cnidaria] and burrowing macrofauna) represent key habitats in NE Atlantic continental slopes, which are currently threatened. The present dataset has produced the most comprehensive assessment of diversity in this area to date, focusing on the taxonomic groups which may best reflect the health of the marine ecosystem and supporting previous studies which indicate that the continental slope of the southern Bay of Biscay hosts key benthic habitats.

  9. Coral community change on a turbid-zone reef complex: developing baseline records for the central Great Barrier Reef's nearshore coral reefs

    NASA Astrophysics Data System (ADS)

    Johnson, Jamie; Perry, Chris; Smithers, Scott; Morgan, Kyle; Johnson, Kenneth

    2016-04-01

    Understanding past coral community development and reef growth is crucial for placing contemporary ecological and environmental change within appropriate reef-building timescales. Coral reefs located within coastal inner-shelf zones are widely perceived to be most susceptible to declining water quality due to their proximity to modified river catchments. On the inner-shelf of Australia's Great Barrier Reef (GBR) the impacts and magnitude of declining water quality since European settlement (c. 1850 A.D.) still remain unclear. This relates to ongoing debates concerning the significance of increased sediment yields against the naturally high background sedimentary regimes and the paucity of long-term (>decadal) ecological datasets. To provide baseline records for interpreting coral community change within the turbid inner-shelf waters of the GBR, 21 cores were recovered from five nearshore reefs spanning an evolutionary spectrum of reef development. Discrete intervals pre- and post-dating European settlement, but deposited at equivalent water depths, were identified by radiocarbon dating, enabling the discrimination of extrinsic and intrinsic driven shifts within the coral palaeo-record. We report no discernible evidence of anthropogenically-driven disturbance on the coral community records at these sites. Instead, significant transitions in coral community assemblages relating to water depth and vertical reef accretion were observed. We suggest that these records may be used to contextualise observed contemporary ecological change within similar environments on the GBR.

  10. Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

    PubMed Central

    Emerson, Brent C.; Cicconardi, Francesco; Fanciulli, Pietro P.; Shaw, Peter J. A.

    2011-01-01

    There has been much recent interest and progress in the characterization of community structure and community assembly processes through the application of phylogenetic methods. To date most focus has been on groups of taxa for which some relevant detail of their ecology is known, for which community composition is reasonably easily quantified and where the temporal scale is such that speciation is not likely to feature. Here, we explore how we might apply a molecular genetic approach to investigate community structure and assembly at broad taxonomic and geographical scales, where we have little knowledge of species ecology, where community composition is not easily quantified, and where speciation is likely to be of some importance. We explore these ideas using the class Collembola as a focal group. Gathering molecular evidence for cryptic diversity suggests that the ubiquity of many species of Collembola across the landscape may belie greater community complexity than would otherwise be assumed. However, this morphologically cryptic species-level diversity poses a challenge for attempts to characterize diversity both within and among local species assemblages. Recent developments in high throughput parallel sequencing technology, combined with mtDNA barcoding, provide an advance that can bring together the fields of phylogenetic and phylogeographic analysis to bear on this problem. Such an approach could be standardized for analyses at any geographical scale for a range of taxonomic groups to quantify the formation and composition of species assemblages. PMID:21768154

  11. Proximate environmental drivers of coral communities at Palmyra Atoll: establishing baselines prior to removing a WWII military causeway.

    PubMed

    Williams, Gareth J; Knapp, Ingrid S; Maragos, James E; Davy, Simon K

    2011-08-01

    A management proposal aims to partly remove a WWII military causeway at Palmyra Atoll to improve lagoon water circulation and alleviate sedimentation stress on the southeast backreef, an area of high coral cover and diversity. This action could result in a shift in sedimentation across reef sites. To provide management advice, we quantified the proximate environmental factors driving scleractinian coral cover and community patterns at Palmyra. The proportion of fine sedimentation was the optimal predictor of coral cover and changes in community structure, explaining 23.7% and 24.7% of the variation between sites, respectively. Scleractinian coral cover was negatively correlated with increases in fine sedimentation. Removing the causeway could negatively affect the Montipora corals that dominate the western reef terrace, as this genus was negatively correlated with levels of fine sedimentation. The tolerance limits of corals, and sediment re-distribution patterns, should be determined prior to complete removal of the causeway. PMID:21632066

  12. BASELINE ASSESSMENT

    EPA Science Inventory

    Resource Purpose:The Baseline Assessment is a project to collect data on environmental conditions in Indian country from existing data sources using a geographic enabling system called the Oracle Spatial Data Cartridge.
    Legislation/Enabling Authority:None
    S...

  13. The Biology of HIV/AIDS: A Case Study in Community Engagement

    ERIC Educational Resources Information Center

    Caccavo, Frank, Jr.

    2008-01-01

    This article describes a project for the Biology of HIV/AIDS course for undergraduate biology majors. This project challenged science students to engage the community on two different levels. They first had to interact directly and personally with HIV/AIDS activists. The proposal then encouraged them to think about and describe ways of engaging a…

  14. Mutualistic Interactions and Community Structure in Biological Metacommunities

    NASA Astrophysics Data System (ADS)

    Rikvold, Per Arne; Filotas, Elise; Grant, Martin; Parrott, Lael

    2011-03-01

    The role of space in determining species coexistence and community structure is well established. However, previous studies mainly focus on simple competition and predation systems, and the role of mutualistic interspecies interactions is not well understood. Here we use a spatially explicit metacommunity model, in which new species enter by a mutation process, to study the effect of fitness-dependent dispersal on the structure of communities with interactions comprising mutualism, competition, and exploitation. We find that the diversity and interaction network undergo a nonequilibrium phase transition with increasing dispersal rate. Low dispersion rate favors spontaneous emergence of many dissimilar, strongly mutualistic and species-poor local communities. Due to the local dissimilarities, the global diversity is high. High dispersion rate promotes local biodiversity and supports similar, species-rich local communities with a wide range of interactions. The strong similarity between neighboring local communities leads to reduced global diversity. Supported by NSERC (Canada), FQRNT (Québec), NSF (U.S.A.)

  15. Vision and Change in the Biology Community: Snapshots of Change

    ERIC Educational Resources Information Center

    Vasaly, Helen L.; Feser, Jason; Lettrich, Matthew D.; Correa, Kevin; Denniston, Katherine J.

    2014-01-01

    When the authors were first invited to write these columns, the editors felt it would be an interesting way to give the readers of "CBE - Life Sciences Education" an agency's-eye view of its concerns, workings, and accomplishments. This column is written with that charge in mind. It is intended to inform the community about outreach…

  16. Spatial succession modeling of biological communities: a multi-model approach.

    PubMed

    Zhang, WenJun; Wei, Wu

    2009-11-01

    Strong spatial correlation may exist in the spatial succession of biological communities, and the spatial succession can be mathematically described. It was confirmed by our study on spatial succession of both plant and arthropod communities along a linear transect of natural grassland. Both auto-correlation and cross-correlation analyses revealed that the succession of plant and arthropod communities exhibited a significant spatial correlation, and the spatial correlation for plant community succession was stronger than arthropod community succession. Theoretically it should be reasonable to infer a site's community composition from the last site in the linear transect. An artificial neural network for state space modeling (ANNSSM) was developed in present study. An algorithm (i.e., Importance Detection Method (IDM)) for determining the relative importance of input variables was proposed. The relative importance for plant families Gramineae, Compositae and Leguminosae, and arthropod orders Homoptera, Diptera and Orthoptera, were detected and analyzed using IDM. ANNSSM performed better than multivariate linear regression and ordinary differential equation, while ordinary differential equation exhibited the worst performance in the simulation and prediction of spatial succession of biological communities. A state transition probability model (STPM) was proposed to simulate the state transition process of biological communities. STPM performed better than multinomial logistic regression in the state transition modeling. We suggested a novel multi-model framework, i.e., the joint use of ANNSSM and STPM, to predict the spatial succession of biological communities. In this framework, ANNSSM and STPM can be separately used to simulate the continuous and discrete dynamics. PMID:18850283

  17. Baseline program

    NASA Technical Reports Server (NTRS)

    Roberts, Barney B.; Vonputtkamer, Jesco

    1992-01-01

    This assumed program was developed from several sources of information and is extrapolated over future decades using a set of reasonable assumptions based on incremental growth. The assumptions for the NASA baseline program are as follows: balanced emphasis in four domains; a constant level of activity; low to moderate real budget growth; maximum use of commonality; and realistic and practical technology development. The first domain is low Earth Orbit (LEO). Activities there are concentrated on the space station but extend on one side to Earth-pointing sensors for unmanned platforms and on the other to the launch and staging of unmanned solar system exploration missions. The second domain is geosynchronous Earth orbit (GEO) and cislunar space. Activities here include all GEO missions and operations, both unmanned and manned, and all transport of materials and crews between LEO and the vicinity of the Moon. The third domain is the Moon itself. Lunar activities are to include both orbiting and landing missions; the landings may be either unmanned or manned. The last domain is Mars. Missions to Mars will initially be unmanned but they will eventually be manned. Program elements and descriptions are discussed as are critiques of the NASA baseline.

  18. Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative

    PubMed Central

    Hucka, Michael; Nickerson, David P.; Bader, Gary D.; Bergmann, Frank T.; Cooper, Jonathan; Demir, Emek; Garny, Alan; Golebiewski, Martin; Myers, Chris J.; Schreiber, Falk; Waltemath, Dagmar; Le Novère, Nicolas

    2015-01-01

    The Computational Modeling in Biology Network (COMBINE) is a consortium of groups involved in the development of open community standards and formats used in computational modeling in biology. COMBINE’s aim is to act as a coordinator, facilitator, and resource for different standardization efforts whose domains of use cover related areas of the computational biology space. In this perspective article, we summarize COMBINE, its general organization, and the community standards and other efforts involved in it. Our goals are to help guide readers toward standards that may be suitable for their research activities, as well as to direct interested readers to relevant communities where they can best expect to receive assistance in how to develop interoperable computational models. PMID:25759811

  19. Estimating size and composition of biological communities by modeling the occurrence of species

    USGS Publications Warehouse

    Dorazio, R.M.; Royle, J. Andrew

    2005-01-01

    We develop a model that uses repeated observations of a biological community to estimate the number and composition of species in the community. Estimators of community-level attributes are constructed from model-based estimators of occurrence of individual species that incorporate imperfect detection of individuals. Data from the North American Breeding Bird Survey are analyzed to illustrate the variety of ecologically important quantities that are easily constructed and estimated using our model-based estimators of species occurrence. In particular, we compute site-specific estimates of species richness that honor classical notions of species-area relationships. We suggest extensions of our model to estimate maps of occurrence of individual species and to compute inferences related to the temporal and spatial dynamics of biological communities.

  20. Marriage patterns in a Mesoamerican peasant community are biologically adaptive.

    PubMed

    Little, Bertis B; Malina, Robert M

    2010-12-01

    Differential investment in offspring by parental and progeny gender has been discussed and periodically analyzed for the past 80 years as an evolutionary adaptive strategy. Parental investment theory suggests that parents in poor condition have offspring in poor condition. Conversely, parents in good condition give rise to offspring in good condition. As formalized in the Trivers-Willard hypothesis (TWH), investment in daughters will be greater under poor conditions while sons receive greater parental investment under good conditions. Condition is ultimately equated to offspring reproductive fitness, with parents apparently using a strategy to maximize their genetic contribution to future generations. Analyses of sex ratio have been used to support parental investment theory and in many instances, though not all, results provide support for TWH. In the present investigation, economic strategies were analyzed in the context of offspring sex ratio and survival to reproductive age in a Zapotec-speaking community in the Valley of Oaxaca, southern Mexico. Growth status of children, adult stature, and agricultural resources were analyzed as proxies for parental and progeny condition in present and prior generations. Traditional marriage practice in Mesoamerican peasant communities is patrilocal postnuptial residence with investments largely favoring sons. The alternative, practiced by ∼25% of parents, is matrilocal postnuptial residence which is an investment favoring daughters. Results indicated that sex ratio of offspring survival to reproductive age was related to economic strategy and differed significantly between the patrilocal and matrilocal strategies. Variance in sex ratio was affected by condition of parents and significant differences in survival to reproductive age were strongly associated with economic strategy. While the results strongly support TWH, further studies in traditional anthropological populations are needed. PMID:21089106

  1. Assessing the Food Environment of a Rural Community: Baseline Findings From the Heart of New Ulm Project, Minnesota, 2010–2011

    PubMed Central

    Sidebottom, Abbey C.; Boucher, Jackie L.; Lindberg, Rebecca; Werner, Rebecca

    2014-01-01

    Introduction Changes in the food environment in the United States during the past few decades have contributed to increased rates of obesity, diabetes, and heart disease. Improving the food environment may be an effective primary prevention strategy to address these rising disease rates. The purpose of this study was to assess the consumer food environment of a rural community with high rates of obesity and low levels of fruit and vegetable consumption. Findings were used to identify food environment intervention strategies to be implemented as part of a larger community-based heart disease prevention program. Methods We used the Nutrition Environment Measures Survey for Restaurants (NEMS-R) and Stores (NEMS-S) to assess 34 restaurants, 3 grocery stores, and 5 convenience stores in New Ulm, Minnesota. Results At least half of the restaurants offered nonfried vegetables and 100% fruit juice. Only 32% had at least 1 entrée or 1 main dish salad that met standards for “healthy.” Fewer than half (41%) had fruit available and under one-third offered reduced-size portions (29%) or whole-grain bread (26%). Grocery stores had more healthful items available, but findings were mixed on whether these items were made available at a lower price than less healthful items. Convenience stores were less likely to have fruits and vegetables and less likely to carry more healthful products (except milk) than grocery stores. Conclusion Baseline findings indicated opportunities to improve availability, quality, and price of foods to support more healthful eating. A community-wide food environment assessment can be used to strategically plan targeted interventions. PMID:24602590

  2. Export flux and stability as regulators of community composition in pelagic marine biological communities: Implications for regime shifts [review article

    NASA Astrophysics Data System (ADS)

    Laws, Edward

    2004-02-01

    Regime shifts occur when a system transitions from one stable configuration to another. Such abrupt changes in biological communities may reflect small changes in environmental conditions such as temperature, oxygen concentration, or irradiance. Although it seems clear that biological communities are not randomly organized with respect to their functional components, there is disagreement concerning the factors that control that organization. In this paper, I examine the implications of assuming that the composition of pelagic marine biological communities evolves to a condition of maximum stability or resilience. At temperatures of 25 °C or less, a model based on this hypothesis predicts abrupt and discontinuous transitions from configurations associated with low export ratios to configurations associated with high export ratios as the rate of primary production increases. Comparison between field data and model predictions shows very good agreement at low and high production rates, but the field data do not support a step-function transition from low to high export ratios at intermediate rates of production. Instead, the field data are consistent with the assumption that food webs effect the transition between high and low ef ratio modes by reconfiguring themselves in a more-or-less continuous manner. The configurations associated with these transitions are at least locally more resilient than any similar food web structure.

  3. The rationale, design, and baseline characteristics of PREVENT-DM: A community-based comparative effectiveness trial of lifestyle intervention and metformin among Latinas with prediabetes.

    PubMed

    Perez, Alberly; Alos, Victor A; Scanlan, Adam; Maia, Catarina M; Davey, Adam; Whitaker, Robert C; Foster, Gary D; Ackermann, Ronald T; O'Brien, Matthew J

    2015-11-01

    Promotora Effectiveness Versus Metformin Trial (PREVENT-DM) is a randomized comparative effectiveness trial of a lifestyle intervention based on the Diabetes Prevention Program delivered by community health workers (or promotoras), metformin, and standard care. Eligibility criteria are Hispanic ethnicity, female sex, age ≥ 20 years, fluent Spanish-speaking status, BMI ≥ 23 kg/m(2), and prediabetes. We enrolled 92 participants and randomized them to one of the following three groups: standard care, DPP-based lifestyle intervention, or metformin. The primary outcome of the trial is the 12-month difference in weight between groups. Secondary outcomes include the following cardiometabolic markers: BMI, waist circumference, blood pressure, and fasting plasma glucose, hemoglobin A1C (HbA1c), total cholesterol, triglycerides, LDL cholesterol, HDL cholesterol, and insulin. PREVENT-DM participants are socioeconomically disadvantaged Latinas with a mean annual household income of $15,527 ± 9922 and educational attainment of 9.7 ± 3.6 years. Eighty-six percent of participants are foreign born, 20% have a prior history of gestational diabetes, and 71% have a first-degree relative with diagnosed diabetes. At baseline, PREVENT-DM participants had a mean age of 45.1 ± 12.5 years, weight of 178.8 ± 39.3 lbs, BMI of 33.3 ± 6.5 kg/m(2), HbA1c of 5.9 ± 0.2%, and waist circumference of 97.4 ± 11.1cm. Mean baseline levels of other cardiometabolic markers were normal. The PREVENT-DM study successfully recruited and randomized an understudied population of Latinas with prediabetes. This trial will be the first U.S. study to test the comparative effectiveness of metformin and lifestyle intervention versus standard care among prediabetic adults in a "real-world" setting. PMID:26597415

  4. Using lay counsellors to promote community-based voluntary counselling and HIV testing in rural northern Ghana: a baseline survey on community acceptance and stigma.

    PubMed

    Baiden, F; Akanlu, G; Hodgson, A; Akweongo, P; Debpuur, C; Binka, F

    2007-09-01

    Access to voluntary counselling and HIV testing (VCT) remains limited in most parts of Ghana with rural populations being the least served. Services remain facility-based and employ the use of an ever-dwindling number of health workers as counsellors. This study assessed approval for the use of lay counsellors to promote community-based voluntary counselling and testing for HIV and the extent of HIV/AIDS-related stigma in the Kassena-Nankana district of rural northern Ghana. A cross-sectional questionnaire survey was conducted. Logistic regression was used to identify predictors of the tendency to stigmatize people living with HIV/AIDS (PLWHAs). Focus group discussions were held and analytical coding of the data performed. The majority (91.1%) of the 403 respondents indicated a desire to know their HIV status. Most (88.1%) respondents considered locations outside of the health facility as preferred places for VCT. The majority (98.7%) of respondents approved the use of lay counsellors. About a quarter (24%) of respondents believed that it was possible to acquire HIV through sharing a drinking cup with a PLWHA. About half (52.1%) of the respondents considered that a teacher with HIV/AIDS should not be allowed to teach, while 77.2% would not buy vegetables from a PLWHA. Respondents who believed that sharing a drinking cup with a PLWHA could transmit HIV infection (OR 2.50, 95%CI 1.52-4.11) and respondents without formal education (OR 2.94, 95%CI 1.38-6.27) were more likely to stigmatize PLWHAs. In contrast, respondents with knowledge of the availability of antiretroviral (ARV) drugs were less likely to do so (OR 0.40, 95%CI 0.22-0.73). Findings from the thirteen focus group discussions reinforced approval for community-based VCT and lay counsellors but revealed concerns about stigma and confidentiality. In conclusion, community-based VCT and the use of lay counsellors may be acceptable options for promoting access. Interventional studies are required to assess

  5. Adolescents and parental caregivers as lay health advisers in a community-based risk reduction intervention for youth: baseline data from Teach One, Reach One.

    PubMed

    Ritchwood, Tiarney D; Dave, Gaurav; Carthron, Dana L; Isler, Malika Roman; Blumenthal, Connie; Wynn, Mysha; Odulana, Adebowale; Lin, Feng-Chang; Akers, Aletha Y; Corbie-Smith, Giselle

    2016-01-01

    The purpose of the current study is to describe the demographic, behavioral, and psychosocial characteristics of adolescent and caregiver lay health advisers (LHAs) participating in an intervention designed to reduce risk behaviors among rural African-American adolescents. Teach One, Reach One integrates constructs from the Theory of Planned Behavior and Social Cognitive Theory. It acknowledges that changing the sexual behaviors of African-American adolescents requires changing one's knowledge, attitudes, normative beliefs about the behavior of peers, and self-efficacy regarding adolescent sexual behavior, parent-teen communication about sex, and healthy dating relations among adolescents. Study participants completed baseline questionnaires assessing demographics and psychosocial determinants (knowledge, attitudes, perceived social norms, and self-efficacy) of sexual behaviors. Sixty-two adolescent and caregiver dyads participated. Caregivers included biological parents, legal guardians, or other parental figures. Strengths and areas in need of improvement were determined using median splits. Few adolescents had initiated sex. Their strengths included high levels of open parent-teen communication; positive attitudes and normative beliefs regarding both sex communication and healthy dating relationships; and high knowledge and self-efficacy for healthy dating behaviors. Areas needing improvement included low knowledge, unfavorable attitudes, poor normative beliefs, and low self-efficacy regarding condom use. Caregiver strengths included positive attitudes, normative beliefs, and self-efficacy for sex communication; positive attitudes and self-efficacy for condom use; and low acceptance of couple violence. Areas needing improvement included low levels of actual communication about sex and low knowledge about effective communication strategies and condom use. The current study highlights the value of assessing baseline characteristics of LHAs prior to intervention

  6. Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant.

    PubMed

    Flowers, Jason J; Cadkin, Tracey A; McMahon, Katherine D

    2013-12-01

    Activated sludge is one of the most abundant and effective wastewater treatment process used to treat wastewater, and has been used in developed countries for nearly a century. In all that time, several hundreds of studies have explored the bacterial communities responsible for treatment, but most studies were based on a handful of samples and did not consider temporal dynamics. In this study, we used the DNA fingerprinting technique called automated ribosomal intergenic spacer region analysis (ARISA) to study bacterial community dynamics over a two-year period in two different treatment trains. We also used quantitative PCR to measure the variation of five phylogenetically-defined clades within the Accumulibacter lineage, which is a model polyphosphate accumulating organism. The total bacterial community exhibited seasonal patterns of change reminiscent of those observed in lakes and oceans. Surprisingly, all five Accumulibacter clades were present throughout the study, and the total Accumulibacter community was relatively stable. However, the abundance of each clade did fluctuate through time. Clade IIA dynamics correlated positively with temperature (ρ = 0.65, p < 0.05) while Clade IA dynamics correlated negatively with temperature (ρ = -0.35, p < 0.05). This relationship with temperature hints at the mechanisms that may be driving the seasonal patterns in overall bacterial community dynamics and provides further evidence for ecological differentiation among clades within the Accumulibacter lineage. This work provides a valuable baseline for activated sludge bacterial community variation. PMID:24200007

  7. Seasonal bacterial community dynamics in a full-scale enhanced biological phosphorus removal plant

    PubMed Central

    Flowers, Jason J.; Cadkin, Tracey A.; McMahon, Katherine D.

    2014-01-01

    Activated sludge is one of the most abundant and effective wastewater treatment process used to treat wastewater, and has been used in developed countries for nearly a century. In all that time, several hundreds of studies have explored the bacterial communities responsible for treatment, but most studies were based on a handful of samples and did not consider temporal dynamics. In this study, we used the DNA fingerprinting technique called automated ribosomal intergenic spacer region analysis (ARISA) to study bacterial community dynamics over a two-year period in two different treatment trains. We also used quantitative PCR to measure the variation of five phylogenetically-defined clades within the Accumulibacter lineage, which is a model polyphosphate accumulating organism. The total bacterial community exhibited seasonal patterns of change reminiscent of those observed in lakes and oceans. Surprisingly, all five Accumulibacter clades were present throughout the study, and the total Accumulibacter community was relatively stable. However, the abundance of each clade did fluctuate through time. Clade IIA dynamics correlated positively with temperature (ρ = 0.65, p < 0.05) while Clade IA dynamics correlated negatively with temperature (ρ = –0.35, p < 0.05). This relationship with temperature hints at the mechanisms that may be driving the seasonal patterns in overall bacterial community dynamics and provides further evidence for ecological differentiation among clades within the Accumulibacter lineage. This work provides a valuable baseline for activated sludge bacterial community variation. PMID:24200007

  8. Effectiveness of Blended Cooperative Learning Environment in Biology Teaching: Classroom Community Sense, Academic Achievement and Satisfaction

    ERIC Educational Resources Information Center

    Yapici, I. Ümit

    2016-01-01

    The aim of this study was to examine the effect of Blended Cooperative Learning Environment (BCLE) in biology teaching on students' classroom community sense, their academic achievement and on their levels of satisfaction. In the study, quantitative and qualitative research methods were used together. The study was carried out with 30 students in…

  9. Hydrogeomorphology explains acidification-driven variation in aquatic biological communities in the Neversink Basin, USA.

    PubMed

    Harpold, Adrian A; Burns, Douglas A; Walter, M T; Steenhuis, Tammo S

    2013-06-01

    Describing the distribution of aquatic habitats and the health of biological communities can be costly and time-consuming; therefore, simple, inexpensive methods to scale observations of aquatic biota to watersheds that lack data would be useful. In this study, we explored the potential of a simple "hydrogeomorphic" model to predict the effects of acid deposition on macroinvertebrate, fish, and diatom communities in 28 sub-watersheds of the 176-km2 Neversink River basin in the Catskill Mountains of New York State. The empirical model was originally developed to predict stream-water acid neutralizing capacity (ANC) using the watershed slope and drainage density. Because ANC is known to be strongly related to aquatic biological communities in the Neversink, we speculated that the model might correlate well with biotic indicators of ANC response. The hydrogeomorphic model was strongly correlated to several measures of macroinvertebrate and fish community richness and density, but less strongly correlated to diatom acid tolerance. The model was also strongly correlated to biological communities in 18 sub-watersheds independent of the model development, with the linear correlation capturing the strongly acidic nature of small upland watersheds (< 1 km2). Overall, we demonstrated the applicability of geospatial data sets and a simple hydrogeomorphic model for estimating aquatic biological communities in areas with stream-water acidification, allowing estimates where no direct field observations are available. Similar modeling approaches have the potential to complement or refine expensive and time-consuming measurements of aquatic biota populations and to aid in regional assessments of aquatic health. PMID:23865230

  10. Hydrogeomorphology explains acidification-driven variation in aquatic biological communities in the Neversink Basin, USA

    USGS Publications Warehouse

    Harpold, Adrian A.; Burns, Douglas A.; Walter, M.T.; Steenhuis, Tammo S.

    2013-01-01

    Describing the distribution of aquatic habitats and the health of biological communities can be costly and time-consuming; therefore, simple, inexpensive methods to scale observations of aquatic biota to watersheds that lack data would be useful. In this study, we explored the potential of a simple “hydrogeomorphic” model to predict the effects of acid deposition on macroinvertebrate, fish, and diatom communities in 28 sub-watersheds of the 176-km2 Neversink River basin in the Catskill Mountains of New York State. The empirical model was originally developed to predict stream-water acid neutralizing capacity (ANC) using the watershed slope and drainage density. Because ANC is known to be strongly related to aquatic biological communities in the Neversink, we speculated that the model might correlate well with biotic indicators of ANC response. The hydrogeomorphic model was strongly correlated to several measures of macroinvertebrate and fish community richness and density, but less strongly correlated to diatom acid tolerance. The model was also strongly correlated to biological communities in 18 sub-watersheds independent of the model development, with the linear correlation capturing the strongly acidic nature of small upland watersheds (2). Overall, we demonstrated the applicability of geospatial data sets and a simple hydrogeomorphic model for estimating aquatic biological communities in areas with stream-water acidification, allowing estimates where no direct field observations are available. Similar modeling approaches have the potential to complement or refine expensive and time-consuming measurements of aquatic biota populations and to aid in regional assessments of aquatic health.

  11. Biological oxygen demand optode analysis of coral reef-associated microbial communities exposed to algal exudates.

    PubMed

    Gregg, Ak; Hatay, M; Haas, Af; Robinett, Nl; Barott, K; Vermeij, Mja; Marhaver, Kl; Meirelles, P; Thompson, F; Rohwer, F

    2013-01-01

    Algae-derived dissolved organic matter has been hypothesized to induce mortality of reef building corals. One proposed killing mechanism is a zone of hypoxia created by rapidly growing microbes. To investigate this hypothesis, biological oxygen demand (BOD) optodes were used to quantify the change in oxygen concentrations of microbial communities following exposure to exudates generated by turf algae and crustose coralline algae (CCA). BOD optodes were embedded with microbial communities cultured from Montastraea annularis and Mussismilia hispida, and respiration was measured during exposure to turf and CCA exudates. The oxygen concentrations along the optodes were visualized with a low-cost Submersible Oxygen Optode Recorder (SOOpR) system. With this system we observed that exposure to exudates derived from turf algae stimulated higher oxygen drawdown by the coral-associated bacteria than CCA exudates or seawater controls. Furthermore, in both turf and CCA exudate treatments, all microbial communities (coral-, algae-associated and pelagic) contributed significantly to the observed oxygen drawdown. This suggests that the driving factor for elevated oxygen consumption rates is the source of exudates rather than the initially introduced microbial community. Our results demonstrate that exudates from turf algae may contribute to hypoxia-induced coral stress in two different coral genera as a result of increased biological oxygen demand of the local microbial community. Additionally, the SOOpR system developed here can be applied to measure the BOD of any culturable microbe or microbial community. PMID:23882444

  12. Promoting mobility after hip fracture (ProMo): study protocol and selected baseline results of a year-long randomized controlled trial among community-dwelling older people

    PubMed Central

    2011-01-01

    Background To cope at their homes, community-dwelling older people surviving a hip fracture need a sufficient amount of functional ability and mobility. There is a lack of evidence on the best practices supporting recovery after hip fracture. The purpose of this article is to describe the design, intervention and demographic baseline results of a study investigating the effects of a rehabilitation program aiming to restore mobility and functional capacity among community-dwelling participants after hip fracture. Methods/Design Population-based sample of over 60-year-old community-dwelling men and women operated for hip fracture (n = 81, mean age 79 years, 78% were women) participated in this study and were randomly allocated into control (Standard Care) and ProMo intervention groups on average 10 weeks post fracture and 6 weeks after discharged to home. Standard Care included written home exercise program with 5-7 exercises for lower limbs. Of all participants, 12 got a referral to physiotherapy. After discharged to home, only 50% adhered to Standard Care. None of the participants were followed-up for Standard Care or mobility recovery. ProMo-intervention included Standard Care and a year-long program including evaluation/modification of environmental hazards, guidance for safe walking, pain management, progressive home exercise program and physical activity counseling. Measurements included a comprehensive battery of laboratory tests and self-report on mobility limitation, disability, physical functional capacity and health as well as assessments for the key prerequisites for mobility, disability and functional capacity. All assessments were performed blinded at the research laboratory. No significant differences were observed between intervention and control groups in any of the demographic variables. Discussion Ten weeks post hip fracture only half of the participants were compliant to Standard Care. No follow-up for Standard Care or mobility recovery occurred

  13. Impact of biological soil crusts and desert plants on soil microfaunal community composition

    USGS Publications Warehouse

    Darby, B.J.; Neher, D.A.; Belnap, J.

    2010-01-01

    Carbon and nitrogen are supplied by a variety of sources in the desert food web; both vascular and non-vascular plants and cyanobacteria supply carbon, and cyanobacteria and plant-associated rhizosphere bacteria are sources of biological nitrogen fixation. The objective of this study was to compare the relative influence of vascular plants and biological soil crusts on desert soil nematode and protozoan abundance and community composition. In the first experiment, biological soil crusts were removed by physical trampling. Treatments with crust removed had fewer nematodes and a greater relative ratio of bacterivores to microphytophages than treatments with intact crust. However, protozoa composition was similar with or without the presence of crusts. In a second experiment, nematode community composition was characterized along a spatial gradient away from stems of grasses or shrubs. Although nematodes generally occurred in increasing abundance nearer to plant stems, some genera (such as the enrichment-type Panagrolaimus) increased disproportionately more than others (such as the stress-tolerant Acromoldavicus). We propose that the impact of biological soil crusts and desert plants on soil microfauna, as reflected in the community composition of microbivorous nematodes, is a combination of carbon input, microclimate amelioration, and altered soil hydrology. ?? Springer Science + Business Media B.V. 2009.

  14. Biological Education and Community Development (Institute for Science Education (IPN), Kiel, FR Germany, 2-6 November 1979).

    ERIC Educational Resources Information Center

    Yoong, C. S.

    1980-01-01

    Presents information about the topics and discussion sessions of the Kiel Conference organized by the Commission for Biological Education (CBE) of the International Union of Biological Sciences (IUBS). Outlines the status of biological education for community development in different parts of the world and summarizes project proposals accepted by…

  15. Towards BioDBcore: a community-defined information specification for biological databases.

    PubMed

    Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K; Bateman, Alex; Blake, Judith A; Bult, Carol J; Cherry, J Michael; Chisholm, Rex L; Cochrane, Guy; Cook, Charles E; Eppig, Janan T; Galperin, Michael Y; Gentleman, Robert; Goble, Carole A; Gojobori, Takashi; Hancock, John M; Howe, Douglas G; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E; Karsch Mizrachi, Ilene; Orchard, Sandra; Ouellette, B F Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N; Smedley, Damian; Southan, Christopher; Tan, Tin W; Tatusova, Tatiana; Whetzel, Patricia L; White, Owen; Yamasaki, Chisato

    2011-01-01

    The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21205783

  16. Towards BioDBcore: a community-defined information specification for biological databases

    PubMed Central

    Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Mizrachi, Ilene Karsch; Orchard, Sandra; Ouellette, B. F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin Wee; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

    2011-01-01

    The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21097465

  17. Towards BioDBcore: a community-defined information specification for biological databases.

    PubMed

    Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K; Bateman, Alex; Blake, Judith A; Bult, Carol J; Cherry, J Michael; Chisholm, Rex L; Cochrane, Guy; Cook, Charles E; Eppig, Janan T; Galperin, Michael Y; Gentleman, Robert; Goble, Carole A; Gojobori, Takashi; Hancock, John M; Howe, Douglas G; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E; Mizrachi, Ilene Karsch; Orchard, Sandra; Ouellette, B F Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N; Smedley, Damian; Southan, Christopher; Tan, Tin Wee; Tatusova, Tatiana; Whetzel, Patricia L; White, Owen; Yamasaki, Chisato

    2011-01-01

    The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21097465

  18. Towards BioDBcore: a community-defined information specification for biological databases

    PubMed Central

    Gaudet, Pascale; Bairoch, Amos; Field, Dawn; Sansone, Susanna-Assunta; Taylor, Chris; Attwood, Teresa K.; Bateman, Alex; Blake, Judith A.; Bult, Carol J.; Cherry, J. Michael; Chisholm, Rex L.; Cochrane, Guy; Cook, Charles E.; Eppig, Janan T.; Galperin, Michael Y.; Gentleman, Robert; Goble, Carole A.; Gojobori, Takashi; Hancock, John M.; Howe, Douglas G.; Imanishi, Tadashi; Kelso, Janet; Landsman, David; Lewis, Suzanna E.; Karsch Mizrachi, Ilene; Orchard, Sandra; Ouellette, B.F. Francis; Ranganathan, Shoba; Richardson, Lorna; Rocca-Serra, Philippe; Schofield, Paul N.; Smedley, Damian; Southan, Christopher; Tan, Tin W.; Tatusova, Tatiana; Whetzel, Patricia L.; White, Owen; Yamasaki, Chisato

    2011-01-01

    The present article proposes the adoption of a community-defined, uniform, generic description of the core attributes of biological databases, BioDBCore. The goals of these attributes are to provide a general overview of the database landscape, to encourage consistency and interoperability between resources; and to promote the use of semantic and syntactic standards. BioDBCore will make it easier for users to evaluate the scope and relevance of available resources. This new resource will increase the collective impact of the information present in biological databases. PMID:21205783

  19. Science Identity's Influence on Community College Students' Engagement, Persistence, and Performance in Biology

    NASA Astrophysics Data System (ADS)

    Riccitelli, Melinda

    In the United States (U.S.), student engagement, persistence, and academic performance levels in college science, technology, engineering, and mathematics (STEM) programs have been unsatisfactory over the last decade. Low student engagement, persistence, and academic performance in STEM disciplines have been identified as major obstacles to U.S. economic goals and U.S. science education objectives. The central and salient science identity a college student claims can influence his engagement, persistence, and academic achievement in college science. While science identity studies have been conducted on four-year college populations there is a gap in the literature concerning community college students' science identity and science performance. The purpose of this quantitative correlational study was to examine the relationship between community college students claimed science identities and engagement, persistence, and academic performance. A census sample of 264 community college students enrolled in biology during the summer of 2015 was used to study this relationship. Science identity and engagement levels were calculated using the Science Identity Centrality Scale and the Biology Motivation Questionnaire II, respectively. Persistence and final grade data were collected from institutional and instructor records. Engagement significantly correlated to, r =.534, p = .01, and varied by science identity, p < .001. Percent final grade also varied by science identity (p < .005), but this relationship was weaker (r = .208, p = .01). Results for science identity and engagement and final grade were consistent with the identity literature. Persistence did not vary by science identity in this student sample (chi2 =2.815, p = .421). This result was inconsistent with the literature on science identity and persistence. Quantitative results from this study present a mixed picture of science identity status at the community college level. It is suggested, based on the findings

  20. Organizing Community-Based Data Standards: Lessons from Developing a Successful Open Standard in Systems Biology

    NASA Astrophysics Data System (ADS)

    Hucka, M.

    2015-09-01

    In common with many fields, including astronomy, a vast number of software tools for computational modeling and simulation are available today in systems biology. This wealth of resources is a boon to researchers, but it also presents interoperability problems. Despite working with different software tools, researchers want to disseminate their work widely as well as reuse and extend the models of other researchers. This situation led in the year 2000 to an effort to create a tool-independent, machine-readable file format for representing models: SBML, the Systems Biology Markup Language. SBML has since become the de facto standard for its purpose. Its success and general approach has inspired and influenced other community-oriented standardization efforts in systems biology. Open standards are essential for the progress of science in all fields, but it is often difficult for academic researchers to organize successful community-based standards. I draw on personal experiences from the development of SBML and summarize some of the lessons learned, in the hope that this may be useful to other groups seeking to develop open standards in a community-oriented fashion.

  1. Climate change and physical disturbance cause similar community shifts in biological soil crusts.

    PubMed

    Ferrenberg, Scott; Reed, Sasha C; Belnap, Jayne

    2015-09-29

    Biological soil crusts (biocrusts)—communities of mosses, lichens, cyanobacteria, and heterotrophs living at the soil surface—are fundamental components of drylands worldwide, and destruction of biocrusts dramatically alters biogeochemical processes, hydrology, surface energy balance, and vegetation cover. Although there has been long-standing concern over impacts of physical disturbances on biocrusts (e.g., trampling by livestock, damage from vehicles), there is increasing concern over the potential for climate change to alter biocrust community structure. Using long-term data from the Colorado Plateau, we examined the effects of 10 y of experimental warming and altered precipitation (in full-factorial design) on biocrust communities and compared the effects of altered climate with those of long-term physical disturbance (>10 y of replicated human trampling). Surprisingly, altered climate and physical disturbance treatments had similar effects on biocrust community structure. Warming, altered precipitation frequency [an increase of small (1.2 mm) summer rainfall events], and physical disturbance from trampling all promoted early successional community states marked by dramatic declines in moss cover and increases in cyanobacteria cover, with more variable effects on lichens. Although the pace of community change varied significantly among treatments, our results suggest that multiple aspects of climate change will affect biocrusts to the same degree as physical disturbance. This is particularly disconcerting in the context of warming, as temperatures for drylands are projected to increase beyond those imposed as treatments in our study. PMID:26371310

  2. Climate change and physical disturbance cause similar community shifts in biological soil crusts

    USGS Publications Warehouse

    Ferrenberg, Scott; Reed, Sasha C.; Belnap, Jayne

    2015-01-01

    Biological soil crusts (biocrusts)—communities of mosses, lichens, cyanobacteria, and heterotrophs living at the soil surface—are fundamental components of drylands worldwide, and destruction of biocrusts dramatically alters biogeochemical processes, hydrology, surface energy balance, and vegetation cover. While there has been long-standing concern over impacts of 5 physical disturbances on biocrusts (e.g., trampling by livestock, damage from vehicles), there is also increasing concern over the potential for climate change to alter biocrust community structure. Using long-term data from the Colorado Plateau, USA, we examined the effects of 10 years of experimental warming and altered precipitation (in full-factorial design) on biocrust communities, and compared the effects of altered climate with those of long-term physical 10 disturbance (>10 years of replicated human trampling). Surprisingly, altered climate and physical disturbance treatments had similar effects on biocrust community structure. Warming, altered precipitation frequency [an increase of small (1.2 mm) summer rainfall events], and physical disturbance from trampling all promoted early successional community states marked by dramatic declines in moss cover and increased cyanobacteria cover, with more variable effects 15 on lichens. While the pace of community change varied significantly among treatments, our results suggest that multiple aspects of climate change will affect biocrusts to the same degree as physical disturbance. This is particularly disconcerting in the context of warming, as temperatures for drylands are projected to increase beyond those imposed by the climate treatments used in our study.

  3. Climate change and physical disturbance cause similar community shifts in biological soil crusts

    PubMed Central

    Ferrenberg, Scott; Reed, Sasha C.; Belnap, Jayne

    2015-01-01

    Biological soil crusts (biocrusts)—communities of mosses, lichens, cyanobacteria, and heterotrophs living at the soil surface—are fundamental components of drylands worldwide, and destruction of biocrusts dramatically alters biogeochemical processes, hydrology, surface energy balance, and vegetation cover. Although there has been long-standing concern over impacts of physical disturbances on biocrusts (e.g., trampling by livestock, damage from vehicles), there is increasing concern over the potential for climate change to alter biocrust community structure. Using long-term data from the Colorado Plateau, we examined the effects of 10 y of experimental warming and altered precipitation (in full-factorial design) on biocrust communities and compared the effects of altered climate with those of long-term physical disturbance (>10 y of replicated human trampling). Surprisingly, altered climate and physical disturbance treatments had similar effects on biocrust community structure. Warming, altered precipitation frequency [an increase of small (1.2 mm) summer rainfall events], and physical disturbance from trampling all promoted early successional community states marked by dramatic declines in moss cover and increases in cyanobacteria cover, with more variable effects on lichens. Although the pace of community change varied significantly among treatments, our results suggest that multiple aspects of climate change will affect biocrusts to the same degree as physical disturbance. This is particularly disconcerting in the context of warming, as temperatures for drylands are projected to increase beyond those imposed as treatments in our study. PMID:26371310

  4. Integrated omics for the identification of key functionalities in biological wastewater treatment microbial communities

    PubMed Central

    Narayanasamy, Shaman; Muller, Emilie E L; Sheik, Abdul R; Wilmes, Paul

    2015-01-01

    Biological wastewater treatment plants harbour diverse and complex microbial communities which prominently serve as models for microbial ecology and mixed culture biotechnological processes. Integrated omic analyses (combined metagenomics, metatranscriptomics, metaproteomics and metabolomics) are currently gaining momentum towards providing enhanced understanding of community structure, function and dynamics in situ as well as offering the potential to discover novel biological functionalities within the framework of Eco-Systems Biology. The integration of information from genome to metabolome allows the establishment of associations between genetic potential and final phenotype, a feature not realizable by only considering single ‘omes’. Therefore, in our opinion, integrated omics will become the future standard for large-scale characterization of microbial consortia including those underpinning biological wastewater treatment processes. Systematically obtained time and space-resolved omic datasets will allow deconvolution of structure–function relationships by identifying key members and functions. Such knowledge will form the foundation for discovering novel genes on a much larger scale compared with previous efforts. In general, these insights will allow us to optimize microbial biotechnological processes either through better control of mixed culture processes or by use of more efficient enzymes in bioengineering applications. PMID:25678254

  5. Community Structure Reveals Biologically Functional Modules in MEF2C Transcriptional Regulatory Network

    PubMed Central

    Alcalá-Corona, Sergio A.; Velázquez-Caldelas, Tadeo E.; Espinal-Enríquez, Jesús; Hernández-Lemus, Enrique

    2016-01-01

    Gene regulatory networks are useful to understand the activity behind the complex mechanisms in transcriptional regulation. A main goal in contemporary biology is using such networks to understand the systemic regulation of gene expression. In this work, we carried out a systematic study of a transcriptional regulatory network derived from a comprehensive selection of all potential transcription factor interactions downstream from MEF2C, a human transcription factor master regulator. By analyzing the connectivity structure of such network, we were able to find different biologically functional processes and specific biochemical pathways statistically enriched in communities of genes into the network, such processes are related to cell signaling, cell cycle and metabolism. In this way we further support the hypothesis that structural properties of biological networks encode an important part of their functional behavior in eukaryotic cells. PMID:27252657

  6. Impact of Substratum Surface on Microbial Community Structure and Treatment Performance in Biological Aerated Filters

    PubMed Central

    Kim, Lavane; Pagaling, Eulyn; Zuo, Yi Y.

    2014-01-01

    The impact of substratum surface property change on biofilm community structure was investigated using laboratory biological aerated filter (BAF) reactors and molecular microbial community analysis. Two substratum surfaces that differed in surface properties were created via surface coating and used to develop biofilms in test (modified surface) and control (original surface) BAF reactors. Microbial community analysis by 16S rRNA gene-based PCR-denaturing gradient gel electrophoresis (DGGE) showed that the surface property change consistently resulted in distinct profiles of microbial populations during replicate reactor start-ups. Pyrosequencing of the bar-coded 16S rRNA gene amplicons surveyed more than 90% of the microbial diversity in the microbial communities and identified 72 unique bacterial species within 19 bacterial orders. Among the 19 orders of bacteria detected, Burkholderiales and Rhodocyclales of the Betaproteobacteria class were numerically dominant and accounted for 90.5 to 97.4% of the sequence reads, and their relative abundances in the test and control BAF reactors were different in consistent patterns during the two reactor start-ups. Three of the five dominant bacterial species also showed consistent relative abundance changes between the test and control BAF reactors. The different biofilm microbial communities led to different treatment efficiencies, with consistently higher total organic carbon (TOC) removal in the test reactor than in the control reactor. Further understanding of how surface properties affect biofilm microbial communities and functional performance would enable the rational design of new generations of substrata for the improvement of biofilm-based biological treatment processes. PMID:24141134

  7. The Mexican-American Trial of Community Health workers (MATCH): Design and baseline characteristics of a randomized controlled trial testing a culturally tailored community diabetes self-management intervention

    PubMed Central

    Rothschild, Steven K.; Martin, Molly A.; Swider, Susan M.; Lynas, Carmen T.; Avery, Elizabeth F.; Janssen, Imke; Powell, Lynda H.

    2012-01-01

    Objectives Community Health Workers (CHWs) have been recommended to reduce diabetes disparities, but few robust trials of this approach have been conducted. Limitations of prior studies include: unspecified a priori outcomes; lack of blinded outcome assessments; high participant attrition rates; and lack of attention to intervention fidelity. These limitations reflect challenges in balancing methodologic rigor with the needs of vulnerable populations. The Mexican-American Trial of Community Health workers (MATCH) was a blinded randomized controlled trial testing CHW efficacy in improving physiologic outcomes and self-management behaviors among Mexican-Americans with type 2 diabetes. This paper describes methods used to overcome limitations of prior studies. Research Design and Methods The primary aim was to determine if a CHW intervention would result in significant reductions in Hemoglobin A1c and rates of uncontrolled blood pressure. 144 Mexican-Americans with diabetes were randomized. The intervention consisted of self-management training delivered by CHWs over a 24-month period; the comparison population received identical information via bilingual newsletter. Blinded research assistants completed assessments at baseline, 12 months, and 24 months post-randomization. Results The MATCH cohort was characterized by low acculturation and socioeconomic status. Study participants had low rates of medication adherence and glucose monitoring. 70% had poor glycemic control with A1c levels over 7.0, and 57.3% had blood pressures worse than ADA target levels (<130/80). Conclusions MATCH preserved community sensitivity and methodologic rigor. The study’s attention to intervention fidelity, behavioral attention control, blinded outcomes assessment, and strategies to enhance participant retention can be replicated by researchers testing culturally-tailored CHW interventions. PMID:22115970

  8. An eQTL biological data visualization challenge and approaches from the visualization community

    PubMed Central

    2012-01-01

    In 2011, the IEEE VisWeek conferences inaugurated a symposium on Biological Data Visualization. Like other domain-oriented Vis symposia, this symposium's purpose was to explore the unique characteristics and requirements of visualization within the domain, and to enhance both the Visualization and Bio/Life-Sciences communities by pushing Biological data sets and domain understanding into the Visualization community, and well-informed Visualization solutions back to the Biological community. Amongst several other activities, the BioVis symposium created a data analysis and visualization contest. Unlike many contests in other venues, where the purpose is primarily to allow entrants to demonstrate tour-de-force programming skills on sample problems with known solutions, the BioVis contest was intended to whet the participants' appetites for a tremendously challenging biological domain, and simultaneously produce viable tools for a biological grand challenge domain with no extant solutions. For this purpose expression Quantitative Trait Locus (eQTL) data analysis was selected. In the BioVis 2011 contest, we provided contestants with a synthetic eQTL data set containing real biological variation, as well as a spiked-in gene expression interaction network influenced by single nucleotide polymorphism (SNP) DNA variation and a hypothetical disease model. Contestants were asked to elucidate the pattern of SNPs and interactions that predicted an individual's disease state. 9 teams competed in the contest using a mixture of methods, some analytical and others through visual exploratory methods. Independent panels of visualization and biological experts judged entries. Awards were given for each panel's favorite entry, and an overall best entry agreed upon by both panels. Three special mention awards were given for particularly innovative and useful aspects of those entries. And further recognition was given to entries that correctly answered a bonus question about how a

  9. Biological soil crusts from arctic environments: characterization of the prokaryotic community and exopolysaccharidic matrix analysis.

    NASA Astrophysics Data System (ADS)

    Mugnai, Gianmarco; Ventura, Stefano; Mascalchi, Cristina; Rossi, Federico; Adessi, Alessandra; De Philippis, Roberto

    2015-04-01

    Biological soil crusts (BSCs) are highly specialized topsoil microbial communities widespread in many ecosystems, from deserts to polar regions. BSCs play an active role in promoting soil fertility and plant growth. In Arctic environments BSCs are involved in promoting primary succession after deglaciation, increasing moisture availability and nutrient immission at the topsoil. The organisms residing on BSCs produce extracellular polymeric substances (EPS) in response to the environmental characteristics, thus contributing to the increase of constraint tolerance. The aim of this study was to investigate the taxonomic diversity of microbial communities, together with the analysis of the chemical features of EPS, from BSC samples collected in several sites near Ny-Ǻlesund, Norway. The phylogenetic composition of the prokaryotic community was assessed through a metagenomic approach. Exopolysaccharidic fractions were quantified using ion-exchange chromatography to determine the monosaccharidic composition. Size exclusion chromatography was used to determine the distribution of the EPS fractions. Abundance of phototrophic microorganisms, which are known to contribute to EPS excretion, was also evaluated. Results underlined the complexity of the microbial communities, showing a high level of diversity within the BSC sampled analyzed. The analysis of the polysaccharide composition displayed a high number of constituent sugars; the matrix was found to be constituted by two main fractions, a higher molecular weight (2 10 exp(6) Da) and a lower molecular weight fraction (< 100 10 exp(3) Da). This study presents novel data concerning EPS of BSCs matrix in relationship with the microbial communities in cold environments.

  10. Baseline Serum Osteopontin Levels Predict the Clinical Effectiveness of Tocilizumab but Not Infliximab in Biologic-Naïve Patients with Rheumatoid Arthritis: A Single-Center Prospective Study at 1 Year (the Keio First-Bio Cohort Study)

    PubMed Central

    Izumi, Keisuke; Kaneko, Yuko; Hashizume, Misato; Yoshimoto, Keiko; Takeuchi, Tsutomu

    2015-01-01

    Objective To explore the baseline predictors of clinical effectiveness after tocilizumab or infliximab treatment in biologic-naïve rheumatoid arthritis patients. Methods Consecutive biologic-naïve patients with rheumatoid arthritis initiating infliximab (n = 57) or tocilizumab (n = 70) treatment were included in our prospective cohort study. Our cohort started in February 2010, and the patients observed for at least 1 year as of April 2013 were analysed. We assessed baseline variables including patients' characteristics (age, sex, disease duration, prednisolone dose, methotrexate dose, other disease-modifying antirheumatic drug use, Clinical Disease Activity Index [CDAI]) and serum biomarker levels (C-reactive protein, immunoglobulin M-rheumatoid factor, anti-cyclic citrullinated protein/peptide antibodies, interferon-γ, interleukin (IL)-1β, IL-2, IL-6, IL-8, IL-10, IL-17, tumor necrosis factor-α, soluble intercellular adhesion molecule-1, bone alkaline phosphatase, osteonectin, osteopontin) to extract factors associated with clinical remission (CDAI≤2.8) at 1 year using univariate analyses, and the extracted factors were entered into a multivariate logistic regression model. Similar analyses were also performed for Simplified Disease Activity Index (SDAI) remission (≤3.3) and Disease Activity Score with 28 joint counts, erythrocyte sedimentation rate (DAS28-ESR) remission (<2.6). Results There were no significant differences in the baseline characteristics except for methotrexate use between the groups. In the multivariate analyses, the low baseline osteopontin levels (OR 0.9145, 95% CI 0.8399–0.9857) were identified as predictors of CDAI remission in the tocilizumab group, whereas no predictors of CDAI remission were found in the infliximab group. Similar results were obtained when using SDAI and DAS28-ESR remission criteria. Conclusion Baseline low serum osteopontin levels predict clinical remission 1 year after tocilizumab treatment and not

  11. Quantifying biological integrity of California sage scrub communities using plant life-form cover.

    SciTech Connect

    Hamada, Y.; Stow, D. A.; Franklin, J.

    2010-01-01

    The California sage scrub (CSS) community type in California's Mediterranean-type ecosystems supports a large number of rare, threatened, and endangered species, and is critically degraded and endangered. Monitoring ecological variables that provide information about community integrity is vital to conserving these biologically diverse communities. Fractional cover of true shrub, subshrub, herbaceous vegetation, and bare ground should fill information gaps between generalized vegetation type maps and detailed field-based plot measurements of species composition and provide an effective means for quantifying CSS community integrity. Remote sensing is the only tool available for estimating spatially comprehensive fractional cover over large extent, and fractional cover of plant life-form types is one of the measures of vegetation state that is most amenable to remote sensing. The use of remote sensing does not eliminate the need for either field surveying or vegetation type mapping; rather it will likely require a combination of approaches to reliably estimate life-form cover and to provide comprehensive information for communities. According to our review and synthesis, life-form fractional cover has strong potential for providing ecologically meaningful intermediate-scale information, which is unattainable from vegetation type maps and species-level field measurements. Thus, we strongly recommend incorporating fractional cover of true shrub, subshrub, herb, and bare ground in CSS community monitoring methods. Estimating life-form cover at a 25 m x 25 m spatial scale using remote sensing would be an appropriate approach for initial implementation. Investigation of remote sensing techniques and an appropriate spatial scale; collaboration of resource managers, biologists, and remote sensing specialists, and refinement of protocols are essential for integrating life-form fractional cover mapping into strategies for sustainable long-term CSS community management.

  12. Comparative metagenomics reveals microbial community differentiation in a biological heap leaching system.

    PubMed

    Hu, Qi; Guo, Xue; Liang, Yili; Hao, Xiaodong; Ma, Liyuan; Yin, Huaqun; Liu, Xueduan

    2015-01-01

    The microbial community in a biological heap leaching (BHL) system is crucial for the decomposition of ores. However, the microbial community structure and functional differentiation in different parts of a biological heap leaching system are still unknown. In this study, metagenomic sequencing was used to fully illuminate the microbial community differentiation in the pregnant leach solution (PLS) and leaching heap (LH) of a BHL system. Long-read sequences (1.3 million) were obtained for the two samples, and the MG_RAST server was used to perform further analysis. The taxa analysis results indicated that the dominant genera of PLS is autotrophic bacterium Acidithiobacillus, but heterotrophic bacterium Acidiphilium is predominant in LH. Furthermore, functional annotation and hierarchical comparison with different reference samples showed that the abundant presence of genes was involved in transposition, DNA repair and heavy metal transport. The sequences related to transposase, which is important for the survival of the organism in the hostile environment, were both mainly classified into Acidiphilium for PLS and LH. These results indicated that not only autotrophic bacteria such as Acidithiobacillus, but also heterotrophic bacteria such as Acidiphilium, were essential participants in the bioleaching process. This new meta-view research will further facilitate the effective application of bioleaching. PMID:26117598

  13. ComPratica: A Virtual Community of Practice for Promoting Biology Teachers' Professional Development in Brazil

    NASA Astrophysics Data System (ADS)

    El-Hani, Charbel N.; Greca, Ileana M.

    2013-08-01

    Teachers' professional development is a key factor in improving science education, but it shows limited impact when only a small number of teachers is reached, or when it focuses on only one aspect of teachers' development, such as learning science content, and is disconnected from teachers' practice. In order to increase the impact of our work on teachers' professional development, we implemented in 2007 ComPratica, an online network intended to establish a virtual community of practice involving biology teachers and biological education researchers. We present here the results of the first 2 years of this project, obtained through an analysis of the number and distribution of actions performed by the participants in the community, the kinds of activities in which they are engaged, and the themes addressed in their messages. From these data, we conclude that ComPratica is effectively functioning as a community of practice and is leading to changes related to both teachers' and researchers' professional development, which seem capable of reducing the research-practice gap in science education.

  14. Biological sulphide removal from anaerobically treated domestic sewage: reactor performance and microbial community dynamics.

    PubMed

    Garcia, Graziella Patrício Pereira; Diniz, Renata Côrtes Oliveira; Bicalho, Sarah Kinaip; Franco, Vitor Araujo de Souza; Gontijo, Eider Max de Oliveira; Toscano, Rodrigo Argolo; Canhestro, Kenia Oliveira; Santos, Merly Rita Dos; Carmo, Ana Luiza Rodrigues Dias; Lobato, Livia Cristina S; Brandt, Emanuel Manfred F; Chernicharo, Carlos A L; Calabria de Araujo, Juliana

    2015-01-01

    We developed a biological sulphide oxidation system and evaluated two reactors (shaped similar to the settler compartment of an up-flow anaerobic sludge blanket [UASB] reactor) with different support materials for biomass retention: polypropylene rings and polyurethane foam. The start-up reaction was achieved using microorganisms naturally occurring on the open surface of UASB reactors treating domestic wastewater. Sulphide removal efficiencies of 65% and 90% were achieved with hydraulic retention times (HRTs) of 24 and 12 h, respectively, in both reactors. However, a higher amount of elemental sulphur was formed and accumulated in the biomass from reactor 1 (20 mg S(0) g(-1) VTS) than in that from reactor 2 (2.9 mg S(0) g(-1) VTS) with an HRT of 24 h. Denaturing gradient gel electrophoresis (DGGE) results revealed that the the pink and green biomass that developed in both reactors comprised a diverse bacterial community and had sequences related to phototrophic green and purple-sulphur bacteria such as Chlorobium sp., Chloronema giganteum, and Chromatiaceae. DGGE band patterns also demonstrated that bacterial community was dynamic over time within the same reactor and that different support materials selected for distinct bacterial communities. Taken together, these results indicated that sulphide concentrations of 1-6 mg L(-1) could be efficiently removed from the effluent of a pilot-scale UASB reactor in two sulphide biological oxidation reactors at HRTs of 12 and 24 h, showing the potential for sulphur recovery from anaerobically treated domestic wastewater. PMID:25737383

  15. Breeding biology of an afrotropical forest understory bird community in northeastern Tanzania

    USGS Publications Warehouse

    Mkongewa, Victor J.; Newmark, William D.; Stanley, Thomas R.

    2013-01-01

    Many aspects of the breeding biology of Afrotropical forest birds are poorly known. Here we provide a description based on the monitoring of 1461 active nests over eight breeding seasons about one or more aspects of the breeding biology for 28 coexisting understory bird species on the Amani Plateau in the East Usambara Mountains, Tanzania. Mean nest height and mean distance of nest from forest edge varied widely among species with most species constructing nests across a broad vertical and forest edge to interior gradient. However, there were important exceptions with all sunbird species and several dove and waxbill species constructing nests in close proximity to the forest edge. For 17 common species for which we recorded two or more active nests, mean clutch size across species was 1.9 eggs per clutch, the lowest site-specific mean clutch size yet reported for a tropical forest bird community. For nine bird species, a subset of the 17 common species, length of breeding season, defined as the difference between the earliest and latest recorded incubation onset date, ranged from 88–139 days. Most of these nine species displayed a unimodal distribution in incubation onset dates across a breeding season which extended from the end of August through middle January. In summary, a wide variation exists in most aspects of the breeding biology within an understory forest bird community in the East Usambara Mountains.

  16. Including a Service Learning Educational Research Project in a Biology Course-I: Assessing Community Awareness of Childhood Lead Poisoning

    ERIC Educational Resources Information Center

    Abu-Shakra, Amal; Saliim, Eric

    2012-01-01

    A university course project was developed and implemented in a biology course, focusing on environmental problems, to assess community awareness of childhood lead poisoning. A set of 385 questionnaires was generated and distributed in an urban community in North Carolina, USA. The completed questionnaires were sorted first into yes and no sets…

  17. Climate change and physical disturbance manipulations result in distinct biological soil crust communities.

    PubMed

    Steven, Blaire; Kuske, Cheryl R; Gallegos-Graves, La Verne; Reed, Sasha C; Belnap, Jayne

    2015-11-01

    Biological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased Cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands. PMID:26276111

  18. Climate change and physical disturbance manipulations result in distinct biological soil crust communities

    USGS Publications Warehouse

    Steven, Blaire; Kuske, Cheryl R.; Gallegos-Graves, La Verne; Reed, Sasha C.; Belnap, Jayne

    2015-01-01

    Biological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remain poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2 °C soil warming, altered summer precipitation (wetting), and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional change. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities and the community functional profile can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands.

  19. Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions

    NASA Astrophysics Data System (ADS)

    Law, Yingyu; Kirkegaard, Rasmus Hansen; Cokro, Angel Anisa; Liu, Xianghui; Arumugam, Krithika; Xie, Chao; Stokholm-Bjerregaard, Mikkel; Drautz-Moses, Daniela I.; Nielsen, Per Halkjær; Wuertz, Stefan; Williams, Rohan B. H.

    2016-05-01

    Management of phosphorus discharge from human waste is essential for the control of eutrophication in surface waters. Enhanced biological phosphorus removal (EBPR) is a sustainable, efficient way of removing phosphorus from waste water without employing chemical precipitation, but is assumed unachievable in tropical temperatures due to conditions that favour glycogen accumulating organisms (GAOs) over polyphosphate accumulating organisms (PAOs). Here, we show these assumptions are unfounded by studying comparative community dynamics in a full-scale plant following systematic perturbation of operational conditions, which modified community abundance, function and physicochemical state. A statistically significant increase in the relative abundance of the PAO Accumulibacter was associated with improved EBPR activity. GAO relative abundance also increased, challenging the assumption of competition. An Accumulibacter bin-genome was identified from a whole community metagenomic survey, and comparative analysis against extant Accumulibacter genomes suggests a close relationship to Type II. Analysis of the associated metatranscriptome data revealed that genes encoding proteins involved in the tricarboxylic acid cycle and glycolysis pathways were highly expressed, consistent with metabolic modelling results. Our findings show that tropical EBPR is indeed possible, highlight the translational potential of studying competition dynamics in full-scale waste water communities and carry implications for plant design in tropical regions.

  20. Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions.

    PubMed

    Law, Yingyu; Kirkegaard, Rasmus Hansen; Cokro, Angel Anisa; Liu, Xianghui; Arumugam, Krithika; Xie, Chao; Stokholm-Bjerregaard, Mikkel; Drautz-Moses, Daniela I; Nielsen, Per Halkjær; Wuertz, Stefan; Williams, Rohan B H

    2016-01-01

    Management of phosphorus discharge from human waste is essential for the control of eutrophication in surface waters. Enhanced biological phosphorus removal (EBPR) is a sustainable, efficient way of removing phosphorus from waste water without employing chemical precipitation, but is assumed unachievable in tropical temperatures due to conditions that favour glycogen accumulating organisms (GAOs) over polyphosphate accumulating organisms (PAOs). Here, we show these assumptions are unfounded by studying comparative community dynamics in a full-scale plant following systematic perturbation of operational conditions, which modified community abundance, function and physicochemical state. A statistically significant increase in the relative abundance of the PAO Accumulibacter was associated with improved EBPR activity. GAO relative abundance also increased, challenging the assumption of competition. An Accumulibacter bin-genome was identified from a whole community metagenomic survey, and comparative analysis against extant Accumulibacter genomes suggests a close relationship to Type II. Analysis of the associated metatranscriptome data revealed that genes encoding proteins involved in the tricarboxylic acid cycle and glycolysis pathways were highly expressed, consistent with metabolic modelling results. Our findings show that tropical EBPR is indeed possible, highlight the translational potential of studying competition dynamics in full-scale waste water communities and carry implications for plant design in tropical regions. PMID:27193869

  1. Climate Change and Physical Disturbance Manipulations Result in Distinct Biological Soil Crust Communities

    PubMed Central

    Steven, Blaire; Gallegos-Graves, La Verne; Reed, Sasha C.; Belnap, Jayne

    2015-01-01

    Biological soil crusts (biocrusts) colonize plant interspaces in many drylands and are critical to soil nutrient cycling. Multiple climate change and land use factors have been shown to detrimentally impact biocrusts on a macroscopic (i.e., visual) scale. However, the impact of these perturbations on the bacterial components of the biocrusts remains poorly understood. We employed multiple long-term field experiments to assess the impacts of chronic physical (foot trampling) and climatic changes (2°C soil warming, altered summer precipitation [wetting], and combined warming and wetting) on biocrust bacterial biomass, composition, and metabolic profile. The biocrust bacterial communities adopted distinct states based on the mechanism of disturbance. Chronic trampling decreased biomass and caused small community compositional changes. Soil warming had little effect on biocrust biomass or composition, while wetting resulted in an increase in the cyanobacterial biomass and altered bacterial composition. Warming combined with wetting dramatically altered bacterial composition and decreased Cyanobacteria abundance. Shotgun metagenomic sequencing identified four functional gene categories that differed in relative abundance among the manipulations, suggesting that climate and land use changes affected soil bacterial functional potential. This study illustrates that different types of biocrust disturbance damage biocrusts in macroscopically similar ways, but they differentially impact the resident soil bacterial communities, and the communities' functional profiles can differ depending on the disturbance type. Therefore, the nature of the perturbation and the microbial response are important considerations for management and restoration of drylands. PMID:26276111

  2. Integrative microbial community analysis reveals full-scale enhanced biological phosphorus removal under tropical conditions

    PubMed Central

    Law, Yingyu; Kirkegaard, Rasmus Hansen; Cokro, Angel Anisa; Liu, Xianghui; Arumugam, Krithika; Xie, Chao; Stokholm-Bjerregaard, Mikkel; Drautz-Moses, Daniela I.; Nielsen, Per Halkjær; Wuertz, Stefan; Williams, Rohan B. H.

    2016-01-01

    Management of phosphorus discharge from human waste is essential for the control of eutrophication in surface waters. Enhanced biological phosphorus removal (EBPR) is a sustainable, efficient way of removing phosphorus from waste water without employing chemical precipitation, but is assumed unachievable in tropical temperatures due to conditions that favour glycogen accumulating organisms (GAOs) over polyphosphate accumulating organisms (PAOs). Here, we show these assumptions are unfounded by studying comparative community dynamics in a full-scale plant following systematic perturbation of operational conditions, which modified community abundance, function and physicochemical state. A statistically significant increase in the relative abundance of the PAO Accumulibacter was associated with improved EBPR activity. GAO relative abundance also increased, challenging the assumption of competition. An Accumulibacter bin-genome was identified from a whole community metagenomic survey, and comparative analysis against extant Accumulibacter genomes suggests a close relationship to Type II. Analysis of the associated metatranscriptome data revealed that genes encoding proteins involved in the tricarboxylic acid cycle and glycolysis pathways were highly expressed, consistent with metabolic modelling results. Our findings show that tropical EBPR is indeed possible, highlight the translational potential of studying competition dynamics in full-scale waste water communities and carry implications for plant design in tropical regions. PMID:27193869

  3. Biological rhythms, metabolic syndrome and current depressive episode in a community sample.

    PubMed

    Moreira, Fernanda Pedrotti; Jansen, Karen; Mondin, Thaíse Campos; Cardoso, Taiane de Azevedo; Magalhães, Pedro Vieira da Silva; Kapczinski, Flavio; Frey, Benicio N; Oses, Jean Pierre; Souza, Luciano Dias de Mattos; da Silva, Ricardo Azevedo; Wiener, Carolina David

    2016-10-01

    The purpose of this study was to assess the disruption in biological rhythms and metabolic syndrome (MetS) in individuals with depressive episode. This was a cross-sectional, population-based study with a representative sample of 905 young adults. Current depressive episode were confirmed by a psychologist using the Mini International Neuropsychiatric Interview (MINI)-Plus. Self-reported biological rhythms were assessed using the Biological Rhythms Interview of Assessment in Neuropsychiatry (BRIAN). MetS was defined using modified NCEP/ATPIII criteria. Significant main effects of current depressive episode (p<0.001, η(2)=0.163) and MetS (p=0.001, η(2)=0.011) were observed on total BRIAN score. There was a significant interaction between depression and MetS in total biological rhythm scores (p=0.002, η(2)=0.011) as well as sleep (p=0.001, η(2)=0.016) and social domains (p<0.001, η(2)=0.014). In the depressive group, subjects with MetS had a higher disruption in total BRIAN scores (p=0.010), sleep domain (p=0.004), social domain (p=0.005) and in the eating pattern domain approached the level of significance (p=0.098), when compared to subjects with no MetS. The results of the present study showed that self-reported disruptions in biological rhythms are associated with key components of the MetS in community adults with MDD. The understanding of the complex interactions between biological rhythms, MetS and depression are important in the development of preventive and therapeutic strategies. PMID:27343724

  4. Baseline assessment of instream and riparian-zone biological resources on the Rio Grande in and near Big Bend National Park, Texas

    USGS Publications Warehouse

    Moring, James Bruce

    2002-01-01

    Five study sites, and a sampling reach within each site, were established on the Rio Grande in and near Big Bend National Park in 1999 to provide the National Park Service with data and information on the status of stream habitat, fish communities, and benthic macroinvertebrates. Differences in stream-habitat conditions and riparian vegetation reflect differences in surface geology among the five sampling reaches. In the most upstream reach, Colorado Canyon, where igneous rock predominates, streambed material is larger; and riparian vegetation is less diverse and not as dense as in the four other, mostly limestone reaches. Eighteen species of fish and a total of 474 individuals were collected among the five reaches; 348 of the 474 were minnows. The most fish species (15) were collected at the Santa Elena reach and the fewest species (9) at the Colorado Canyon and Johnson Ranch reaches. The fish community at Colorado Canyon was least like the fish communities at the four other reaches. Fish trophic structure reflected fish-community structure among the five reaches. Invertivores made up at least 60 percent of the trophic structure at all reaches except Colorado Canyon. Piscivores dominated the trophic structure at Colorado Canyon. At the four other reaches, piscivores were the smallest trophic group. Eighty percent of the benthic macroinvertebrate taxa collected were aquatic insects. Two species of blackfly were the most frequently collected invertebrate taxon. Net-spinning caddisflies were common at all reaches except Santa Elena. The aquatic-insect community at the Boquillas reach was least similar to the aquatic-insect community at the other reaches.

  5. Silicon's organic pool and biological cycle in moso bamboo community of Wuyishan Biosphere Reserve.

    PubMed

    Li, Zhen-ji; Lin, Peng; He, Jian-yuan; Yang, Zhi-wei; Lin, Yi-ming

    2006-11-01

    Biomineralization of Si by plants into phytolith formation and precipitation of Si into clays during weathering are two important processes of silicon's biogeochemical cycle. As a silicon-accumulating plant, the widely distributed and woody Phyllostachys heterocycla var. pubescens (moso bamboo) contributes to storing silicon by biomineralization and, thus, prevents eutrophication of nearby waterbodies through silicon's erosion of soil particles.A study on the organic pool and biological cycle of silicon (Si) of the moso bamboo community was conducted in Wuyishan Biosphere Reserve, China. The results showed that: (1) the standing crop of the moso bamboo community was 13355.4 g/m2, of which 53.61%, 45.82% and 0.56% are represented by the aboveground and belowground parts of moso bamboos, and the understory plants, respectively; (2) the annual net primary production of the community was 2887.1 g/(m2 x a), among which the aboveground part, belowground part, litterfalls, and other fractions, accounted for 55.86%, 35.30%, 4.50% and 4.34%, respectively; (3) silicon concentration in stem, branch, leaf, base of stem, root, whip of bamboos, and other plants was 0.15%, 0.79%, 3.10%, 4.40%, 7.32%, 1.52% and 1.01%, respectively; (4) the total Si accumulated in the standing crop of moso bamboo community was 448.91 g/m2, with 99.83% of Si of the total community stored in moso bamboo populations; (5) within moso bamboo community, the annual uptake, retention, and return of Si were 95.75, 68.43, 27.32 g/(m2 x a), respectively; (6) the turnover time of Si, which is the time an average atom of Si remains in the soil before it is recycled into the trees or shrubs, was 16.4 years; (7) the enrichment ratio of Si in the moso bamboo community, which is the ratio of the mean concentration of nutrients in the net primary production to the mean concentration of nutrients in the biomass of a community, was 0.64; and lastly, (8) moso bamboo plants stored about 1.26x10(10) kg of silicon in the

  6. Silicon’s organic pool and biological cycle in moso bamboo community of Wuyishan Biosphere Reserve*

    PubMed Central

    Li, Zhen-ji; Lin, Peng; He, Jian-yuan; Yang, Zhi-wei; Lin, Yi-ming

    2006-01-01

    Biomineralization of Si by plants into phytolith formation and precipitation of Si into clays during weathering are two important processes of silicon’s biogeochemical cycle. As a silicon-accumulating plant, the widely distributed and woody Phyllostachys heterocycla var. pubescens (moso bamboo) contributes to storing silicon by biomineralization and, thus, prevents eutrophication of nearby waterbodies through silicon’s erosion of soil particles. A study on the organic pool and biological cycle of silicon (Si) of the moso bamboo community was conducted in Wuyishan Biosphere Reserve, China. The results showed that: (1) the standing crop of the moso bamboo community was 13355.4 g/m2, of which 53.61%, 45.82% and 0.56% are represented by the aboveground and belowground parts of moso bamboos, and the understory plants, respectively; (2) the annual net primary production of the community was 2887.1 g/(m2·a), among which the aboveground part, belowground part, litterfalls, and other fractions, accounted for 55.86%, 35.30%, 4.50% and 4.34%, respectively; (3) silicon concentration in stem, branch, leaf, base of stem, root, whip of bamboos, and other plants was 0.15%, 0.79%, 3.10%, 4.40%, 7.32%, 1.52% and 1.01%, respectively; (4) the total Si accumulated in the standing crop of moso bamboo community was 448.91 g/m2, with 99.83% of Si of the total community stored in moso bamboo populations; (5) within moso bamboo community, the annual uptake, retention, and return of Si were 95.75, 68.43, 27.32 g/(m2·a), respectively; (6) the turnover time of Si, which is the time an average atom of Si remains in the soil before it is recycled into the trees or shrubs, was 16.4 years; (7) the enrichment ratio of Si in the moso bamboo community, which is the ratio of the mean concentration of nutrients in the net primary production to the mean concentration of nutrients in the biomass of a community, was 0.64; and lastly, (8) moso bamboo plants stored about 1.26×1010 kg of silicon in

  7. Primary and complex stressors in polluted mediterranean rivers: Pesticide effects on biological communities

    NASA Astrophysics Data System (ADS)

    Ricart, Marta; Guasch, Helena; Barceló, Damià; Brix, Rikke; Conceição, Maria H.; Geiszinger, Anita; José López de Alda, Maria; López-Doval, Julio C.; Muñoz, Isabel; Postigo, Cristina; Romaní, Anna M.; Villagrasa, Marta; Sabater, Sergi

    2010-03-01

    SummaryWe examined the presence of pesticides in the Llobregat river basin (Barcelona, Spain) and their effects on benthic biological communities (invertebrates and diatoms). The Llobregat river is one of Barcelona's major drinking water resources. It has been highly polluted by industrial, agricultural, and urban wastewaters, and—as a typical Mediterranean river—is regularly subjected to periodic floods and droughts. Water scarcity periods result in reduced water flow and dilution capacity, increasing the potential environmental risk of pollutants. Seven sites were selected, where we analysed the occurrence of 22 pesticides (belonging to the classes of triazines, organophosphates, phenylureas, anilides, chloroacetanilides, acidic herbicides and thiocarbamates) in the water and sediment, and the benthic community structure. Biofilm samples were taken to measure several metrics related to both the algal and bacterial components of fluvial biofilms. Multivariate analyses revealed a potential relationship between triazine-type herbicides and the distribution of the diatom community, although no evidence of disruption in the invertebrate community distribution was found. Biofilm metrics were used as response variables rather than abundances of individual species to identify possible cause-effect relationships between pesticide pollution and biotic responses. Certain effects of organophosphates and phenylureas in both structural and functional aspects of the biofilm community were suggested, but the sensitivity of each metric to particular stressors must be assessed before we can confidently assign causality. Complemented with laboratory experiments, which are needed to confirm causality, this approach could be successfully incorporated into environmental risk assessments to better summarise biotic integrity and improve the ecological management.

  8. BioMart Central Portal: an open database network for the biological community.

    PubMed

    Guberman, Jonathan M; Ai, J; Arnaiz, O; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J; Di Génova, A; Forbes, Simon; Fujisawa, T; Gadaleta, E; Goodstein, D M; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D T; Wong-Erasmus, Marie; Yao, L; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

    2011-01-01

    BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities. PMID:21930507

  9. Microbial communities involved in biological ammonium removal from coal combustion wastewaters.

    PubMed

    Vishnivetskaya, Tatiana A; Fisher, L Suzanne; Brodie, Greg A; Phelps, Tommy J

    2013-07-01

    The efficiency of a novel integrated treatment system for biological removal of ammonium, nitrite, nitrate, and heavy metals from fossil power plant effluent was evaluated. Microbial communities were analyzed using bacterial and archaeal 16S rRNA gene clone libraries (Sanger sequences) and 454 pyrosequencing technology. While seasonal changes in microbial community composition were observed, the significant (P = 0.001) changes in bacterial and archaeal communities were consistent with variations in ammonium concentration. Phylogenetic analysis of 16S rRNA gene sequences revealed an increase of potential ammonium-oxidizing bacteria (AOB), Nitrosomonas, Nitrosococcus, Planctomycetes, and OD1, in samples with elevated ammonium concentration. Other bacteria, such as Nitrospira, Nitrococcus, Nitrobacter, Thiobacillus, ε-Proteobacteria, Firmicutes, and Acidobacteria, which play roles in nitrification and denitrification, were also detected. The AOB oxidized 56 % of the ammonium with the concomitant increase in nitrite and ultimately nitrate in the trickling filters at the beginning of the treatment system. Thermoprotei within the phylum Crenarchaeota thrived in the splitter box and especially in zero-valent iron extraction trenches, where an additional 25 % of the ammonium was removed. The potential ammonium-oxidizing Archaea (AOA) (Candidatus Nitrosocaldus) were detected towards the downstream end of the treatment system. The design of an integrated treatment system consisting of trickling filters, zero-valent iron reaction cells, settling pond, and anaerobic wetlands was efficient for the biological removal of ammonium and several other contaminants from wastewater generated at a coal burning power plant equipped with selective catalytic reducers for nitrogen oxide removal. PMID:23314095

  10. A comparative study of the bacterial community in denitrifying and traditional enhanced biological phosphorus removal processes.

    PubMed

    Lv, Xiao-Mei; Shao, Ming-Fei; Li, Chao-Lin; Li, Ji; Gao, Xin-Lei; Sun, Fei-Yun

    2014-09-17

    Denitrifying phosphorus removal is an attractive wastewater treatment process due to its reduced carbon source demand and sludge minimization potential. Two lab-scale sequencing batch reactors (SBRs) were operated in alternating anaerobic-anoxic (A-A) or anaerobic-oxic (A-O) conditions to achieve denitrifying enhanced biological phosphate removal (EBPR) and traditional EBPR. No significant differences were observed in phosphorus removal efficiencies between A-A SBR and A-O SBR, with phosphorus removal rates being 87.9% and 89.0% respectively. The community structures in denitrifying and traditional EBPR processes were evaluated by high-throughput sequencing of the PCR-amplified partial 16S rRNA genes from each sludge. The results obtained showed that the bacterial community was more diverse in A-O sludge than in A-A sludge. Taxonomy and β-diversity analyses indicated that a significant shift occurred in the dominant microbial community in A-A sludge compared with the seed sludge during the whole acclimation phase, while a slight fluctuation was observed in the abundance of the major taxonomies in A-O sludge. One Dechloromonas-related OTU outside the 4 known Candidatus "Accumulibacter" clades was detected as the main OTU in A-A sludge at the stationary operation, while Candidatus "Accumulibacter" dominated in A-O sludge. PMID:24964811

  11. Community college biology majors: The dynamics of the successful community college transfer program. A comparative analysis of the program determinants which lead to high transfer success in community college biology transfer programs

    NASA Astrophysics Data System (ADS)

    Harlan, Ronald Keith

    1997-09-01

    Community Colleges in California have long been asked to fulfill a number of the state's different needs in higher education including the first two years of preparation for students who plan to transfer to universities and receive their baccalaureate. Transfer rates published since the 60's suggest that community colleges in the state have largely been failures at transferring students. Current data, however, show that biology majors programs at area colleges surrounding UCLA, the primary goal of biology majors, varied widely in their transfer success. This study compared two biology majors programs with high transfer success (HTS) with two programs with low transfer success (LTS). Qualitative methods were used in the analysis to establish common themes which existed at both the HTS and LTS programs. Methodology involved: site descriptions, participant-observation, document analysis, questionnaires, and interviews of faculty, staff, and students involved with the majors program. It was concluded that the HTS institutions shared many characteristics in common. Since California abolished district boundaries, eliminated guaranteed enrollment for colleges and created a free-flow situation, colleges have competed for students. In this study, students free-flowed from colleges in higher SES communities from inner city colleges in lower SES communities. Both HTS programs were at colleges in higher SES communities. They were responsive to the articulation demands of UCLA, had firm chemistry prerequisites, and were taught as two sequential courses. Programs had one faculty member who was clearly the head of the program and had been instrumental in the evolution of the program. HTS programs had high academic rigor and included a lab portion which was instrumental in bringing the students together with each other and with the faculty. Student collaboration involved academics, transfer information, and career information and lead to transfer momentum for the class. Faculty

  12. Trait-Based Representation of Biological Nitrification: Model Development, Testing, and Predicted Community Composition

    PubMed Central

    Bouskill, Nicholas J.; Tang, Jinyun; Riley, William J.; Brodie, Eoin L.

    2012-01-01

    Trait-based microbial models show clear promise as tools to represent the diversity and activity of microorganisms across ecosystem gradients. These models parameterize specific traits that determine the relative fitness of an “organism” in a given environment, and represent the complexity of biological systems across temporal and spatial scales. In this study we introduce a microbial community trait-based modeling framework (MicroTrait) focused on nitrification (MicroTrait-N) that represents the ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) using traits related to enzyme kinetics and physiological properties. We used this model to predict nitrifier diversity, ammonia (NH3) oxidation rates, and nitrous oxide (N2O) production across pH, temperature, and substrate gradients. Predicted nitrifier diversity was predominantly determined by temperature and substrate availability, the latter was strongly influenced by pH. The model predicted that transient N2O production rates are maximized by a decoupling of the AOB and NOB communities, resulting in an accumulation and detoxification of nitrite to N2O by AOB. However, cumulative N2O production (over 6 month simulations) is maximized in a system where the relationship between AOB and NOB is maintained. When the reactions uncouple, the AOB become unstable and biomass declines rapidly, resulting in decreased NH3 oxidation and N2O production. We evaluated this model against site level chemical datasets from the interior of Alaska and accurately simulated NH3 oxidation rates and the relative ratio of AOA:AOB biomass. The predicted community structure and activity indicate (a) parameterization of a small number of traits may be sufficient to broadly characterize nitrifying community structure and (b) changing decadal trends in climate and edaphic conditions could impact nitrification rates in ways that are not captured by extant biogeochemical models. PMID

  13. The perspectives of nonscience-major students on success in community college biology

    NASA Astrophysics Data System (ADS)

    Kim-Rajab, Oriana Sharon

    With more than 36% of nonscience-major community college students unable to successfully complete their general life science courses, graduation and transfer rates to four-year universities are negatively affected. Many students also miss important opportunities to gain some level of science proficiency. In an effort to address the problem of poor science achievement, this research project determined which factors were most significantly related to student success in a community college biology course. It also aimed to understand the student perspectives on which modifications to the course would best help them in the pursuit of success. Drawing heavily on the educational psychology schools of thought on motivation and self-efficacy of science learning, this study surveyed and interviewed students on their perceptions of which factors were related to success in biology and the changes they believed were needed in the course structure to improve success. The data revealed that the primary factors related to student success are the students' study skills and their perceived levels of self-efficacy. The findings also uncovered the critical nature of the professor's role in influencing the success of the students. After assessing the needs of the community college population, meaningful and appropriate curriculum and pedagogical reforms could be created to improve student learning outcomes. This study offered recommendations for reforms that can be used by science practitioners to provide a more nurturing and inspiring environment for all students. These suggestions revolved around the role of the instructor in influencing the self-efficacy and study skills of students. Providing more opportunities for students to interact in class, testing more frequently, establishing peer assistance programs, managing better the course material, and making themselves more available to students were at the forefront of the list. Examples of the potential benefits of increasing

  14. Chemical, mineralogical and molecular biological characterization of the rocks and fluids from a natural gas storage deep reservoir as a baseline for the effects of geological hydrogen storage

    NASA Astrophysics Data System (ADS)

    Morozova, Daria; Kasina, Monika; Weigt, Jennifer; Merten, Dirk; Pudlo, Dieter; Würdemann, Hilke

    2014-05-01

    Planned transition to renewable energy production from nuclear and CO2-emitting power generation brings the necessity for large scale energy storage capacities. One possibility to store excessive energy produced is to transfer it to chemical forms like hydrogen which can be subsequently injected and stored in subsurface porous rock formations like depleted gas reservoirs and presently used gas storage sites. In order to investigate the feasibility of the hydrogen storage in the subsurface, the collaborative project H2STORE ("hydrogen to store") was initiated. In the scope of this project, potential reactions between microorganism, fluids and rocks induced by hydrogen injection are studied. For the long-term experiments, fluids of natural gas storage are incubated together with rock cores in the high pressure vessels under 40 bar pressure and 40° C temperature with an atmosphere containing 5.8% He as a tracer gas, 3.9% H2 and 90.3% N2. The reservoir is located at a depth of about 2 000 m, and is characterized by a salinity of 88.9 g l-1 NaCl and a temperature of 80° C and therefore represents an extreme environment for microbial life. First geochemical analyses showed a relatively high TOC content of the fluids (about 120 mg l-1) that were also rich in sodium, potassium, calcium, magnesium and iron. Remarkable amounts of heavy metals like zinc and strontium were also detected. XRD analyses of the reservoir sandstones revealed the major components: quartz, plagioclase, K-feldspar, anhydrite and analcime. The sandstones were intercalated by mudstones, consisting of quartz, plagioclase, K-feldspar, analcime, chlorite, mica and carbonates. Genetic profiling of amplified 16S rRNA genes was applied to characterize the microbial community composition by PCR-SSCP (PCR-Single-Strand-Conformation Polymorphism) and DGGE (Denaturing Gradient Gel Electrophoresis). First results indicate the presence of microorganisms belonging to the phylotypes alfa-, beta- and gamma

  15. Baseline levels of bioaerosols and volatile organic compounds around a municipal waste incinerator prior to the construction of a mechanical-biological treatment plant.

    PubMed

    Vilavert, Lolita; Nadal, Martí; Inza, Isabel; Figueras, María J; Domingo, José L

    2009-09-01

    New waste management programs are currently aimed at developing alternative treatment technologies such as mechanical-biological treatment (MBT) and composting plants. However, there is still a high uncertainty concerning the chemical and microbiological risks for human health, not only for workers of these facilities, but also for the population living in the neighborhood. A new MBT plant is planned to be constructed adjacently to a municipal solid waste incinerator (MSWI) in Tarragona (Catalonia, Spain). In order to evaluate its potential impact and to differentiate the impacts of MSWI from those of the MBT when the latter is operative, a pre-operational survey was initiated by determining the concentrations of 20 volatile organic compounds (VOCs) and bioaerosols (total bacteria, gram-negative bacteria, fungi and Aspergillus fumigatus) in airborne samples around the MSWI. The results indicated that the current concentrations of bioaerosols (ranges: 382-3882, 18-790, 44-926, and <1-7 CFU/m(3) for fungi at 25 degrees C, fungi at 37 degrees C, total bacteria, and gram-negative bacteria, respectively) and VOCs (ranging from 0.9 to 121.2 microg/m(3)) are very low in comparison to reported levels in indoor and outdoor air in composting and MBT plants, as well in urban and industrial zones. With the exception of total bacteria, no correlations were observed between the environmental concentrations of biological agents and the direction/distance from the facility. However, total bacteria presented significantly higher levels downwind. Moreover, a non-significant increase of VOCs was detected in sites closer to the incinerator, which means that the MSWI could have a very minor impact on the surrounding environment. PMID:19346120

  16. Baseline levels of bioaerosols and volatile organic compounds around a municipal waste incinerator prior to the construction of a mechanical-biological treatment plant

    SciTech Connect

    Vilavert, Lolita; Nadal, Marti; Inza, Isabel; Figueras, Maria J.; Domingo, Jose L.

    2009-09-15

    New waste management programs are currently aimed at developing alternative treatment technologies such as mechanical-biological treatment (MBT) and composting plants. However, there is still a high uncertainty concerning the chemical and microbiological risks for human health, not only for workers of these facilities, but also for the population living in the neighborhood. A new MBT plant is planned to be constructed adjacently to a municipal solid waste incinerator (MSWI) in Tarragona (Catalonia, Spain). In order to evaluate its potential impact and to differentiate the impacts of MSWI from those of the MBT when the latter is operative, a pre-operational survey was initiated by determining the concentrations of 20 volatile organic compounds (VOCs) and bioaerosols (total bacteria, Gram-negative bacteria, fungi and Aspergillus fumigatus) in airborne samples around the MSWI. The results indicated that the current concentrations of bioaerosols (ranges: 382-3882, 18-790, 44-926, and <1-7 CFU/m{sup 3} for fungi at 25 deg. C, fungi at 37 deg. C, total bacteria, and Gram-negative bacteria, respectively) and VOCs (ranging from 0.9 to 121.2 {mu}g/m{sup 3}) are very low in comparison to reported levels in indoor and outdoor air in composting and MBT plants, as well in urban and industrial zones. With the exception of total bacteria, no correlations were observed between the environmental concentrations of biological agents and the direction/distance from the facility. However, total bacteria presented significantly higher levels downwind. Moreover, a non-significant increase of VOCs was detected in sites closer to the incinerator, which means that the MSWI could have a very minor impact on the surrounding environment.

  17. Estimating the effects of habitat and biological interactions in an avian community

    USGS Publications Warehouse

    Dorazio, Robert M.; Connor, Edward F.; Askins, Robert A.

    2015-01-01

    We used repeated sightings of individual birds encountered in community-level surveys to investigate the relative roles of habitat and biological interactions in determining the distribution and abundance of each species. To analyze these data, we developed a multispecies N-mixture model that allowed estimation of both positive and negative correlations between abundances of different species while also estimating the effects of habitat and the effects of errors in detection of each species. Using a combination of single- and multispecies N-mixture modeling, we examined for each species whether our measures of habitat were sufficient to account for the variation in encounter histories of individual birds or whether other habitat variables or interactions with other species needed to be considered. In the community that we studied, habitat appeared to be more influential than biological interactions in determining the distribution and abundance of most avian species. Our results lend support to the hypothesis that abundances of forest specialists are negatively affected by forest fragmentation. Our results also suggest that many species were associated with particular types of vegetation as measured by structural attributes of the forests. The abundances of 6 of the 73 species observed in our study were strongly correlated. These species included large birds (American Crow and Red-winged Blackbird) that forage on the ground in open habitats and small birds (Red-eyed Vireo, House Wren, Hooded Warbler, and Prairie Warbler) that are associated with dense shrub cover. Species abundances were positively correlated within each size group and negatively correlated between groups. Except for the American Crow, which preys on eggs and nestlings of small song birds, none of the other 5 species is known to display direct interactions, so we suspect that the correlations may have been associated with species-specific responses to habitat components not adequately measured by

  18. Estimating the Effects of Habitat and Biological Interactions in an Avian Community

    PubMed Central

    Dorazio, Robert M.; Connor, Edward F.; Askins, Robert A.

    2015-01-01

    We used repeated sightings of individual birds encountered in community-level surveys to investigate the relative roles of habitat and biological interactions in determining the distribution and abundance of each species. To analyze these data, we developed a multispecies N-mixture model that allowed estimation of both positive and negative correlations between abundances of different species while also estimating the effects of habitat and the effects of errors in detection of each species. Using a combination of single- and multispecies N-mixture modeling, we examined for each species whether our measures of habitat were sufficient to account for the variation in encounter histories of individual birds or whether other habitat variables or interactions with other species needed to be considered. In the community that we studied, habitat appeared to be more influential than biological interactions in determining the distribution and abundance of most avian species. Our results lend support to the hypothesis that abundances of forest specialists are negatively affected by forest fragmentation. Our results also suggest that many species were associated with particular types of vegetation as measured by structural attributes of the forests. The abundances of 6 of the 73 species observed in our study were strongly correlated. These species included large birds (American Crow (Corvus brachyrhynchos) and Red-winged Blackbird (Agelaius phoeniceus)) that forage on the ground in open habitats and small birds (Red-eyed Vireo (Vireo olivaceus), House Wren (Troglodytes aedon), Hooded Warbler (Setophaga citrina), and Prairie Warbler (Setophaga discolor)) that are associated with dense shrub cover. Species abundances were positively correlated within each size group and negatively correlated between groups. Except for the American Crow, which preys on eggs and nestlings of small song birds, none of the other 5 species is known to display direct interactions, so we suspect that

  19. High definition for systems biology of microbial communities: metagenomics gets genome-centric and strain-resolved.

    PubMed

    Turaev, Dmitrij; Rattei, Thomas

    2016-06-01

    The systems biology of microbial communities, organismal communities inhabiting all ecological niches on earth, has in recent years been strongly facilitated by the rapid development of experimental, sequencing and data analysis methods. Novel experimental approaches and binning methods in metagenomics render the semi-automatic reconstructions of near-complete genomes of uncultivable bacteria possible, while advances in high-resolution amplicon analysis allow for efficient and less biased taxonomic community characterization. This will also facilitate predictive modeling approaches, hitherto limited by the low resolution of metagenomic data. In this review, we pinpoint the most promising current developments in metagenomics. They facilitate microbial systems biology towards a systemic understanding of mechanisms in microbial communities with scopes of application in many areas of our daily life. PMID:27115497

  20. Characterization of water quality and biological communities, Fish Creek, Teton County, Wyoming, 2007-08

    USGS Publications Warehouse

    Eddy-Miller, Cheryl A.; Peterson, David A.; Wheeler, Jerrod D.; Leemon, Daniel J.

    2010-01-01

    Fish Creek, a tributary to the Snake River, is about 25 river kilometers long and is located in Teton County in western Wyoming near the town of Wilson. Public concern about nuisance growths of aquatic plants in Fish Creek have been increasing in recent years. To address this concern, the U.S. Geological Survey conducted a study in cooperation with the Teton Conservation District to characterize the water quality and biological communities in Fish Creek. Water-quality samples were collected for analyses of physical properties and water chemistry (nutrients, nitrate isotopes, and wastewater chemicals) between March 2007 and October 2008 from seven surface-water sites and three groundwater wells. During this same period, aquatic plant and macroinvertebrate samples were collected and habitat characteristics were measured at the surface-water sites. The main objectives of this study were to (1) evaluate nutrient concentrations (that influence biological indicators of eutrophication) and potential sources of nutrients by using stable isotope analysis and other indicator chemicals (such as caffeine and disinfectants) that could provide evidence of anthropogenic sources, such as wastewater or septic tank contamination in Fish Creek and adjacent groundwater, and (2) characterize the algal, macrophyte, and macroinvertebrate communities and habitat of Fish Creek. Nitrate was the dominant species of dissolved nitrogen present in all samples and was the only bioavailable species detected at concentrations greater than the laboratory reporting level in all surface-water samples. Average concentrations of dissolved nitrate in surface water were largest in samples collected from the two sites with seasonal flow near Teton Village and decreased downstream; the smallest concentration was at downstream site A-Wck. Concentrations of dissolved nitrate in groundwater were consistently greater than concentrations in corresponding surface-water sites during the same sampling event

  1. Biological soil crusts (biocrusts) as a model system in community, landscape and ecosystem ecology

    USGS Publications Warehouse

    Bowker, Matthew A.; Maestre, Fernando T.; Eldridge, David; Belnap, Jayne; Castillo-Monroy, Andrea; Escolar, Cristina; Soliveres, Santiago

    2014-01-01

    Model systems have had a profound influence on the development of ecological theory and general principles. Compared to alternatives, the most effective models share some combination of the following characteristics: simpler, smaller, faster, general, idiosyncratic or manipulable. We argue that biological soil crusts (biocrusts) have unique combinations of these features that should be more widely exploited in community, landscape and ecosystem ecology. In community ecology, biocrusts are elucidating the importance of biodiversity and spatial pattern for maintaining ecosystem multifunctionality due to their manipulability in experiments. Due to idiosyncrasies in their modes of facilitation and competition, biocrusts have led to new models on the interplay between environmental stress and biotic interactions and on the maintenance of biodiversity by competitive processes. Biocrusts are perhaps one of the best examples of micro-landscapes—real landscapes that are small in size. Although they exhibit varying patch heterogeneity, aggregation, connectivity and fragmentation, like macro-landscapes, they are also compatible with well-replicated experiments (unlike macro-landscapes). In ecosystem ecology, a number of studies are imposing small-scale, low cost manipulations of global change or state factors in biocrust micro-landscapes. The versatility of biocrusts to inform such disparate lines of inquiry suggests that they are an especially useful model system that can enable researchers to see ecological principles more clearly and quickly.

  2. Biological soil crusts across disturbance-recovery scenarios: effect of grazing regime on community dynamics

    USGS Publications Warehouse

    Concostrina-Zubiri, L.; Huber-Sannwald, E.; Martínez, I.; Flores Flores, J. L.; Reyes-Agüero, J. A.; Escudero, A.; Belnap, Jayne

    2014-01-01

    Grazing represents one of the most common disturbances in drylands worldwide, affecting both ecosystem structure and functioning. Despite the efforts to understand the nature and magnitude of grazing effects on ecosystem components and processes, contrasting results continue to arise. This is particularly remarkable for the biological soil crust (BSC) communities (i.e., cyanobacteria, lichens, and bryophytes), which play an important role in soil dynamics. Here we evaluated simultaneously the effect of grazing impact on BSC communities (resistance) and recovery after livestock exclusion (resilience) in a semiarid grassland of Central Mexico. In particular, we examined BSC species distribution, species richness, taxonomical group cover (i.e., cyanobacteria, lichen, bryophyte), and composition along a disturbance gradient with different grazing regimes (low, medium, high impact) and along a recovery gradient with differently aged livestock exclosures (short-, medium-, long-term exclusion). Differences in grazing impact and time of recovery from grazing both resulted in slight changes in species richness; however, there were pronounced shifts in species composition and group cover. We found we could distinguish four highly diverse and dynamic BSC species groups: (1) species with high resistance and resilience to grazing, (2) species with high resistance but low resilience, (3) species with low resistance but high resilience, and (4) species with low resistance and resilience. While disturbance resulted in a novel diversity configuration, which may profoundly affect ecosystem functioning, we observed that 10 years of disturbance removal did not lead to the ecosystem structure found after 27 years of recovery. These findings are an important contribution to our understanding of BCS dynamics from a species and community perspective placed in a land use change context.

  3. Impacts of Volcanic Eruptions and Disturbances on Mid-Ocean Ridge Biological Communities

    NASA Astrophysics Data System (ADS)

    Shank, T. M.

    2009-12-01

    Understanding ecological processes in mid-ocean ridge benthic environments requires a knowledge of the temporal and spatial scales over which those processes take place. Over the past 17 years, the detection and now “direct observation” of more than nine seafloor eruptions and even more numerous and diverse geologic disturbances (e.g., dyking and cracking events) have provided a broad spectrum of perturbating seafloor phenomena that serve as key agents for creating new vent habitat, providing bursts of nutrients, supporting blooms of microbial and macrobiological communities, imparting magmatic/hydrothermal fluxes, controlling fluid geochemical composition, altering the successional stage of faunal communities, guiding the temporal and spatial scales of local extinction and recolonization, and for directing the evolution of physiological adaptations. Eruptions have now been documented on the East Pacific Rise, Southern Mid-Atlantic Ridge, Gakkel Ridge, Galapagos Rift, CoAxial, Northwest Rota, West Mata, and Loihi Seamounts, representing diverse emergent eruptive styles, from explosive pyroclastic deposits to thin lava flows, these processes are occurring in different biogeographic regions hosting different regional species pools. As such, not only do these eruptions provide a method of establishing a “time-zero” with which to construct manipulative temporal experiments, but also provide a contextual framework with which to interpret the affect eruptions and disturbance have on ecological interactions in different biogeographic regions of the world, and the timescales over which they vary. The temporal and spatial impact of these different eruptive styles in relation to the alteration of biological community structure will be discussed.

  4. A metagenome of a full-scale microbial community carrying out enhanced biological phosphorus removal

    PubMed Central

    Albertsen, Mads; Hansen, Lea Benedicte Skov; Saunders, Aaron Marc; Nielsen, Per Halkjær; Nielsen, Kåre Lehmann

    2012-01-01

    Enhanced biological phosphorus removal (EBPR) is widely used for removal of phosphorus from wastewater. In this study, a metagenome (18.2 Gb) was generated using Illumina sequencing from a full-scale EBPR plant to study the community structure and genetic potential. Quantitative fluorescence in situ hybridization (qFISH) was applied as an independent method to evaluate the community structure. The results were in qualitative agreement, but a DNA extraction bias against gram positive bacteria using standard extraction protocols was identified, which would not have been identified without the use of qFISH. The genetic potential for community function showed enrichment of genes involved in phosphate metabolism and biofilm formation, reflecting the selective pressure of the EBPR process. Most contigs in the assembled metagenome had low similarity to genes from currently sequenced genomes, underlining the need for more reference genomes of key EBPR species. Only the genome of ‘Candidatus Accumulibacter', a genus of phosphorus-removing organisms, was closely enough related to the species present in the metagenome to allow for detailed investigations. Accumulibacter accounted for only 4.8% of all bacteria by qFISH, but the depth of sequencing enabled detailed insight into their microdiversity in the full-scale plant. Only 15% of the reads matching Accumulibacter had a high similarity (>95%) to the sequenced Accumulibacter clade IIA strain UW-1 genome, indicating the presence of some microdiversity. The differences in gene complement between the Accumulibacter clades were limited to genes for extracellular polymeric substances and phage-related genes, suggesting a selective pressure from phages on the Accumulibacter diversity. PMID:22170425

  5. Learning style and concept acquisition of community college students in introductory biology

    NASA Astrophysics Data System (ADS)

    Bobick, Sandra Burin

    This study investigated the influence of learning style on concept acquisition within a sample of community college students in a general biology course. There are two subproblems within the larger problem: (1) the influence of demographic variables (age, gender, number of college credits, prior exposure to scientific information) on learning style, and (2) the correlations between prior scientific knowledge, learning style and student understanding of the concept of the gene. The sample included all students enrolled in an introductory general biology course during two consecutive semesters at an urban community college. Initial data was gathered during the first week of the semester, at which time students filled in a short questionnaire (age, gender, number of college credits, prior exposure to science information either through reading/visual sources or a prior biology course). Subjects were then given the Inventory of Learning Processes-Revised (ILP-R) which measures general preferences in five learning styles; Deep Learning; Elaborative Learning, Agentic Learning, Methodical Learning and Literal Memorization. Subjects were then given the Gene Conceptual Knowledge pretest: a 15 question objective section and an essay section. Subjects were exposed to specific concepts during lecture and laboratory exercises. At the last lab, students were given the Genetics Conceptual Knowledge Posttest. Pretest/posttest gains were correlated with demographic variables and learning styles were analyzed for significant correlations. Learning styles, as the independent variable in a simultaneous multiple regression, were significant predictors of results on the gene assessment tests, including pretest, posttest and gain. Of the learning styles, Deep Learning accounted for the greatest positive predictive value of pretest essay and pretest objective results. Literal Memorization was a significant negative predictor for posttest essay, essay gain and objective gain. Simultaneous

  6. Ground-Dwelling Arthropod Communities of a Sky Island Mountain Range in Southeastern Arizona, USA: Obtaining a Baseline for Assessing the Effects of Climate Change

    PubMed Central

    Meyer, Wallace M.; Eble, Jeffrey A.; Franklin, Kimberly; McManus, Reilly B.; Brantley, Sandra L.; Henkel, Jeff; Marek, Paul E.; Hall, W. Eugene; Olson, Carl A.; McInroy, Ryan; Bernal Loaiza, Emmanuel M.; Brusca, Richard C.; Moore, Wendy

    2015-01-01

    The few studies that have addressed past effects of climate change on species distributions have mostly focused on plants due to the rarity of historical faunal baselines. However, hyperdiverse groups like Arthropoda are vital to monitor in order to understand climate change impacts on biodiversity. This is the first investigation of ground-dwelling arthropod (GDA) assemblages along the full elevation gradient of a mountain range in the Madrean Sky Island Region, establishing a baseline for monitoring future changes in GDA biodiversity. To determine how GDA assemblages relate to elevation, season, abiotic variables, and corresponding biomes, GDA were collected for two weeks in both spring (May) and summer (September) 2011 in the Santa Catalina Mountains, Arizona, using pitfall traps at 66 sites in six distinct upland (non-riparian/non-wet canyon) biomes. Four arthropod taxa: (1) beetles (Coleoptera), (2) spiders (Araneae), (3) grasshoppers and crickets (Orthoptera), and (4) millipedes and centipedes (Myriapoda) were assessed together and separately to determine if there are similar patterns across taxonomic groups. We collected 335 species of GDA: 192/3793 (species/specimens) Coleoptera, 102/1329 Araneae, 25/523 Orthoptera, and 16/697 Myriapoda. GDA assemblages differed among all biomes and between seasons. Fifty-three percent (178 species) and 76% (254 species) of all GDA species were found in only one biome and during only one season, respectively. While composition of arthropod assemblages is tied to biome and season, individual groups do not show fully concordant patterns. Seventeen percent of the GDA species occurred only in the two highest-elevation biomes (Pine and Mixed Conifer Forests). Because these high elevation biomes are most threatened by climate change and they harbor a large percentage of unique arthropod species (11–25% depending on taxon), significant loss in arthropod diversity is likely in the Santa Catalina Mountains and other isolated

  7. Ground-Dwelling Arthropod Communities of a Sky Island Mountain Range in Southeastern Arizona, USA: Obtaining a Baseline for Assessing the Effects of Climate Change.

    PubMed

    Meyer, Wallace M; Eble, Jeffrey A; Franklin, Kimberly; McManus, Reilly B; Brantley, Sandra L; Henkel, Jeff; Marek, Paul E; Hall, W Eugene; Olson, Carl A; McInroy, Ryan; Bernal Loaiza, Emmanuel M; Brusca, Richard C; Moore, Wendy

    2015-01-01

    The few studies that have addressed past effects of climate change on species distributions have mostly focused on plants due to the rarity of historical faunal baselines. However, hyperdiverse groups like Arthropoda are vital to monitor in order to understand climate change impacts on biodiversity. This is the first investigation of ground-dwelling arthropod (GDA) assemblages along the full elevation gradient of a mountain range in the Madrean Sky Island Region, establishing a baseline for monitoring future changes in GDA biodiversity. To determine how GDA assemblages relate to elevation, season, abiotic variables, and corresponding biomes, GDA were collected for two weeks in both spring (May) and summer (September) 2011 in the Santa Catalina Mountains, Arizona, using pitfall traps at 66 sites in six distinct upland (non-riparian/non-wet canyon) biomes. Four arthropod taxa: (1) beetles (Coleoptera), (2) spiders (Araneae), (3) grasshoppers and crickets (Orthoptera), and (4) millipedes and centipedes (Myriapoda) were assessed together and separately to determine if there are similar patterns across taxonomic groups. We collected 335 species of GDA: 192/3793 (species/specimens) Coleoptera, 102/1329 Araneae, 25/523 Orthoptera, and 16/697 Myriapoda. GDA assemblages differed among all biomes and between seasons. Fifty-three percent (178 species) and 76% (254 species) of all GDA species were found in only one biome and during only one season, respectively. While composition of arthropod assemblages is tied to biome and season, individual groups do not show fully concordant patterns. Seventeen percent of the GDA species occurred only in the two highest-elevation biomes (Pine and Mixed Conifer Forests). Because these high elevation biomes are most threatened by climate change and they harbor a large percentage of unique arthropod species (11-25% depending on taxon), significant loss in arthropod diversity is likely in the Santa Catalina Mountains and other isolated

  8. Baseline surveys to detect trophic changes in shallow hard-bottom communities induced by the Dry Tortugas National Park Research Natural Area: Chapter 8

    USGS Publications Warehouse

    Kuffner, Ilsa B.; Paul, Valerie J.; Ritson-Williams, Raphael; Hickey, T. Don; Walters, Linda J.

    2012-01-01

    A study was initiated to examine the potential impacts of reduced abundance of exploited reef fish species on herbivores, macroalgae, and corals. Surveys were performed inside and outside of the RNA to characterize relationships between different trophic level organisms inhabiting the coral reef ecosystem. No significant differences in the abundance of herbivorous fish and urchins or in the abundance of exploited fish species in the shallow, lowrelief hard-bottom communities were observed inside vs. outside the RNA. Evaluating and understanding trophic changes that may occur related to the RNA will require a long-term research and monitoring effort. Future surveys will be necessary to determine if changes have occurred in the proportions of major coral reef ecosystem components and to help determine if the implementation of the RNA results in balanced benthic communities at DRTO.

  9. Biological Communities and Geomorphology of Patch Reefs in Biscayne National Park, Florida, U.S.A.

    USGS Publications Warehouse

    Kuffner, Ilsa B.; Brock, John C.; Grober-Dunsmore, Rikki; Hickey, T. Don; Bonito, Victor; Bracone, Jeremy E.; Wright, C. Wayne

    2008-01-01

    Coral reef ecosystem management benefits from continual, quantitative assessment of the resources being managed, plus assessment of factors that affect distribution patterns of organisms in the ecosystem. In this study, we investigated the relationships among physical, benthic, and fish variables in effort to help explain the distribution patterns of ecologically and economically important species on twelve patch reefs within Biscayne National Park (BNP), Florida, U.S.A. We visited 196 randomly-located sampling stations across twelve shallow (< 10m) patch reefs, using SCUBA to conduct our surveys. We measured physical variables (e.g., substratum type), estimated the percent cover of benthic community members (e.g., coral, algae), and counted and estimated mean size for each fish species observed. We also used high-density bathymetric data collected remotely via airborne laser surveying (Experimental Advanced Airborne Research Lidar (EAARL)) to calculate rugosity (bumpiness) of the reef habitat. Here we present our findings visually by graphing our quantitative community and physical structure data simultaneously in a GIS map format. You will see that biological organisms arrange themselves on each patch reef in a non-random manner. For example, many species of fish prefer to locate themselves in areas of the reef where the rugosity index is high. Rugose parts of the reef provide them with good hiding places from predators. These maps (and the data used to create them) are permanent records of the status of reef resources found on these twelve patch reefs in BNP as of September, 2003. The survey data found in the shapefile located on this CD product includes benthic percent cover data for algae, coral, encrusting invertebrates, and substratum type, in addition to gorgonian abundance and volume, total fish abundance and species richness, and specific counts for Acanthurids (surgeonfish), Scarids (parrotfish), Lutjanids (snappers), Haemulids (grunts), Serranids

  10. Expanding biological data standards development processes for US IOOS: visual line transect observing community for mammal, bird, and turtle data

    USGS Publications Warehouse

    Fornwall, M.; Gisiner, R.; Simmons, S. E.; Moustahfid, Hassan; Canonico, G.; Halpin, P.; Goldstein, P.; Fitch, R.; Weise, M.; Cyr, N.; Palka, D.; Price, J.; Collins, D.

    2012-01-01

    The US Integrated Ocean Observing System (IOOS) has recently adopted standards for biological core variables in collaboration with the US Geological Survey/Ocean Biogeographic Information System (USGS/OBIS-USA) and other federal and non-federal partners. In this Community White Paper (CWP) we provide a process to bring into IOOS a rich new source of biological observing data, visual line transect surveys, and to establish quality data standards for visual line transect observations, an important source of at-sea bird, turtle and marine mammal observation data. The processes developed through this exercise will be useful for other similar biogeographic observing efforts, such as passive acoustic point and line transect observations, tagged animal data, and mark-recapture (photo-identification) methods. Furthermore, we suggest that the processes developed through this exercise will serve as a catalyst for broadening involvement by the larger marine biological data community within the goals and processes of IOOS.

  11. Annual net community production and the biological carbon flux in the ocean

    NASA Astrophysics Data System (ADS)

    Emerson, Steven

    2014-01-01

    The flux of biologically produced organic matter from the surface ocean (the biological pump), over an annual cycle, is equal to the annual net community production (ANCP). Experimental determinations of ANCP at ocean time series sites using a variety of different metabolite mass balances have made it possible to evaluate the accuracy of sediment trap fluxes and satellite-determined ocean carbon export. ANCP values at the Hawaii Ocean Time-series (HOT), the Bermuda Atlantic Time-series Study (BATS), Ocean Station Papa (OSP) are 3 ± 1 mol C m-2 yr-1—much less variable than presently suggested by satellite remote sensing measurements and global circulation models. ANCP determined from mass balances at these locations are 3-4 times particulate organic carbon fluxes measured in sediment traps. When the roles of dissolved organic carbon (DOC) flux, zooplankton migration, and depth-dependent respiration are considered these differences are reconciled at HOT and OSP but not at BATS, where measured particulate fluxes are about 3 times lower than expected. Even in the cases where sediment trap fluxes are accurate, it is not possible to "scale up" these measurements to determine ANCP without independent determinations of geographically variable DOC flux and zooplankton migration. Estimates of ANCP from satellite remote sensing using net primary production determined by the carbon-based productivity model suggests less geographic variability than its predecessor (the vertically generalized productivity model) and brings predictions at HOT and OSP closer to measurements; however, satellite-predicted ANCP at BATS is still 3 times too low.

  12. Two-Year Community: Time for Action: Vision and Change Implementation in an Online Biology Course at a Community College

    ERIC Educational Resources Information Center

    Gonzalez, Beatriz

    2016-01-01

    The author discusses an Introduction to Biology course they created. The course was designed by following the recommendations from the Vision and Change in Undergraduate Biology Education: A Call to Action report, which stresses the need for engaging students through hands-on and student-centered activities. In the course, students perform…

  13. Development of a Model, Metal-reducing Microbial Community for a System Biology Level Assessment of Desulfovibrio vulgaris as part of a Community

    SciTech Connect

    Elias, Dwayne; Schadt, Christopher; Miller, Lance; Phelps, Tommy; Brown, S. D.; Arkin, Adam; Hazen, Terry; Drake, Megin; Yang, Z.K.; Podar, Mircea

    2010-05-17

    One of the largest experimental gaps is between the simplicity of pure cultures and the complexity of open environmental systems, particularly in metal-contaminated areas. These microbial communities form ecosystem foundations, drive biogeochemical processes, and are relevant for biotechnology and bioremediation. A model, metal-reducing microbial community was constructed as either syntrophic or competitive to study microbial cell to cell interactions, cell signaling and competition for resources. The microbial community was comprised of the metal-reducing Desulfovibrio vulgaris Hildenborough and Geobacter sulfurreducens PCA. Additionally, Methanococcus maripaludis S2 was added to study complete carbon reduction and maintain a low hydrogen partial pressure for syntrophism to occur. Further, considerable work has been published on D. vulgaris and the D. vulgaris/ Mc. maripaludis co-culture both with and without stress. We are extending this work by conducting the same stress conditions on the model community. Additionally, this comprehensive investigation includes physiological and metabolic analyses as well as specially designed mRNA microarrays with the genes for all three organisms on one slide so as to follow gene expression changes in the various cultivation conditions as well as being comparable to the co- and individual cultures. Further, state-of -the-art comprehensive AMT tag proteomics allows for these comparisons at the protein level for a systems biology assessment of a model, metal-reducing microbial community. Preliminary data revealed that lactate oxidation by D. vulgaris was sufficient to support both G. sulfurreducens and M. maripaludis via the excretion of H2 and acetate. Fumarate was utilized by G. sulfurreducens and reduced to succinate since neither of the other two organisms can reduce fumarate. Methane was quantified, suggesting acetate and H2 concentrations were sufficient for M. maripaludis. Steady state community cultivation will allow for

  14. Bacterial community dynamics over successional stages of Australian biological soil crusts

    NASA Astrophysics Data System (ADS)

    Chilton, Angela; Woodhouse, Jason; Neilan, Brett

    2015-04-01

    A key aspect for successful ecological rehabilitation is understanding the naturally occurring ecosystem and landscape function which is to be restored. This allows for recovery indicators to be identified and criteria to be developed to assess progress and outcomes. In arid rangelands, environmental stresses result in characteristically heterogeneous landscapes where biological soil crusts (BSCs) cover large expanses of inter-plant areas. Here, BSCs perform crucial roles in nutrient cycling and re-distribution, affect hydrological patterns and stabilise the soil surface. They also serve as a large reservoir of microbial and avascular plant biodiversity. The recognition of these important roles has resulted in increased global arid rehabilitation efforts employing BSCs. Within Australia, research has focused on the macro components of BSCs including lichens and mosses, however, there have been insufficient studies examining the BSC bacterial communities and their dynamics over different successional stages. This project surveyed the bacterial community of crust-free soil and three successional stages of undisturbed BSCs from New South Wales (NSW), Australia, in order to provide reference standards of naturally occurring Australian BSCs. Visual assessments were conducted and BSCs were categorised as Early, Mid or Late stage depending on colour, thickness, topography and presence of lichens and mosses. The crust-free soil and different stages were sampled within three 50 m2 plots of the same edaphic conditions near the town of Cobar, NSW. High throughput sequencing using the Illumina MiSeq platform was performed targeting the V2 region of the 16S rRNA gene. Preliminary analysis has revealed a clear distinction between the crust-free and crusted soil while Canonical Analysis of Principal Co-ordinates (CAP) suggests the presence of two distinct BSC microbial communities despite three stages being sampled. Across all sample types, the dominant phyla were Actinobacteria

  15. Community-based Inquiry Improves Critical Thinking in General Education Biology

    PubMed Central

    Faiola, Celia L.; Johnson, James E.; Kurtz, Martha J.

    2008-01-01

    National stakeholders are becoming increasingly concerned about the inability of college graduates to think critically. Research shows that, while both faculty and students deem critical thinking essential, only a small fraction of graduates can demonstrate the thinking skills necessary for academic and professional success. Many faculty are considering nontraditional teaching methods that incorporate undergraduate research because they more closely align with the process of doing investigative science. This study compared a research-focused teaching method called community-based inquiry (CBI) with traditional lecture/laboratory in general education biology to discover which method would elicit greater gains in critical thinking. Results showed significant critical-thinking gains in the CBI group but decreases in a traditional group and a mixed CBI/traditional group. Prior critical-thinking skill, instructor, and ethnicity also significantly influenced critical-thinking gains, with nearly all ethnicities in the CBI group outperforming peers in both the mixed and traditional groups. Females, who showed decreased critical thinking in traditional courses relative to males, outperformed their male counterparts in CBI courses. Through the results of this study, it is hoped that faculty who value both research and critical thinking will consider using the CBI method. PMID:18765755

  16. The Childhood Solid Tumor Network: A new resource for the developmental biology and oncology research communities.

    PubMed

    Stewart, Elizabeth; Federico, Sara; Karlstrom, Asa; Shelat, Anang; Sablauer, Andras; Pappo, Alberto; Dyer, Michael A

    2016-03-15

    Significant advances have been made over the past 25 years in our understanding of the most common adult solid tumors such as breast, colon, lung and prostate cancer. Much less is known about childhood solid tumors because they are rare and because they originate in developing organs during fetal development, childhood and adolescence. It can be very difficult to study the cellular origins of pediatric solid tumors in developing organs characterized by rapid proliferative expansion, growth factor signaling, developmental angiogenesis, programmed cell death, tissue reorganization and cell migration. Not only has the etiology of pediatric cancer remained elusive because of their developmental origins, but it also makes it more difficult to treat. Molecular targeted therapeutics that alter developmental pathway signaling may have devastating effects on normal organ development. Therefore, basic research focused on the mechanisms of development provides an essential foundation for pediatric solid tumor translational research. In this article, we describe new resources available for the developmental biology and oncology research communities. In a companion paper, we present the detailed characterization of an orthotopic xenograft of a pediatric solid tumor derived from sympathoadrenal lineage during development. PMID:26068307

  17. Evaluation of DNA extraction methods for the analysis of microbial community in biological activated carbon.

    PubMed

    Zheng, Lu; Gao, Naiyun; Deng, Yang

    2012-01-01

    It is difficult to isolate DNA from biological activated carbon (BAC) samples used in water treatment plants, owing to the scarcity of microorganisms in BAC samples. The aim of this study was to identify DNA extraction methods suitable for a long-term, comprehensive ecological analysis of BAC microbial communities. To identify a procedure that can produce high molecular weight DNA, maximizes detectable diversity and is relatively free from contaminants, the microwave extraction method, the cetyltrimethylammonium bromide (CTAB) extraction method, a commercial DNA extraction kit, and the ultrasonic extraction method were used for the extraction of DNA from BAC samples. Spectrophotometry, agarose gel electrophoresis and polymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) analysis were conducted to compare the yield and quality of DNA obtained using these methods. The results showed that the CTAB method produce the highest yield and genetic diversity of DNA from BAC samples, but DNA purity was slightly less than that obtained with the DNA extraction-kit method. This study provides a theoretical basis for establishing and selecting DNA extraction methods for BAC samples. PMID:22629615

  18. Green algae in alpine biological soil crust communities: acclimation strategies against ultraviolet radiation and dehydration.

    PubMed

    Karsten, Ulf; Holzinger, Andreas

    2014-01-01

    Green algae are major components of biological soil crusts in alpine habitats. Together with cyanobacteria, fungi and lichens, green algae form a pioneer community important for the organisms that will succeed them. In their high altitudinal habitat these algae are exposed to harsh and strongly fluctuating environmental conditions, mainly intense irradiation, including ultraviolet radiation, and lack of water leading to desiccation. Therefore, green algae surviving in these environments must have evolved with either avoidance or protective strategies, as well as repair mechanisms for damage. In this review we have highlighted these mechanisms, which include photoprotection, photochemical quenching, and high osmotic values to avoid water loss, and in some groups flexibility of secondary cell walls to maintain turgor pressure even in water-limited situations. These highly specialized green algae will serve as good model organisms to study desiccation tolerance or photoprotective mechanisms, due to their natural capacity to withstand unfavorable conditions. We point out the urgent need for modern phylogenetic approaches in characterizing these organisms, and molecular methods for analyzing the metabolic changes involved in their adaptive strategies. PMID:24954980

  19. Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal

    PubMed Central

    Mao, Yanping; Wang, Zhiping; Li, Liguan; Jiang, Xiaotao; Zhang, Xuxiang; Ren, Hongqiang; Zhang, Tong

    2016-01-01

    A sequencing batch reactor fed mainly by acetate was operated to perform enhanced biological phosphorus removal (EBPR). A short-term pH shock from 7.0 to 6.0 led to a complete loss of phosphate-removing capability and a drastic change of microbial communities. 16S rRNA gene pyrosequencing showed that large proportions of glycogen accumulating organisms (GAOs) (accounted for 16% of bacteria) bloomed, including Candidatus Competibacter phosphatis and Defluviicoccus-related tetrad-forming organism, causing deteriorated EBPR performance. The EBPR performance recovered with time and the dominant Candidatus Accumulibacter (Accumulibacter) clades shifted from Clade IIC to IIA while GAOs populations shrank significantly. The Accumulibacter population variation provided a good opportunity for genome binning using a bi-dimensional coverage method, and a genome of Accumulibacter Clade IIC was well retrieved with over 90% completeness. Comparative genomic analysis demonstrated that Accumulibacter clades had different abilities in nitrogen metabolism and carbon fixation, which shed light on enriching different Accumulibacter populations selectively. PMID:27547976

  20. Exploring the Shift in Structure and Function of Microbial Communities Performing Biological Phosphorus Removal.

    PubMed

    Mao, Yanping; Wang, Zhiping; Li, Liguan; Jiang, Xiaotao; Zhang, Xuxiang; Ren, Hongqiang; Zhang, Tong

    2016-01-01

    A sequencing batch reactor fed mainly by acetate was operated to perform enhanced biological phosphorus removal (EBPR). A short-term pH shock from 7.0 to 6.0 led to a complete loss of phosphate-removing capability and a drastic change of microbial communities. 16S rRNA gene pyrosequencing showed that large proportions of glycogen accumulating organisms (GAOs) (accounted for 16% of bacteria) bloomed, including Candidatus Competibacter phosphatis and Defluviicoccus-related tetrad-forming organism, causing deteriorated EBPR performance. The EBPR performance recovered with time and the dominant Candidatus Accumulibacter (Accumulibacter) clades shifted from Clade IIC to IIA while GAOs populations shrank significantly. The Accumulibacter population variation provided a good opportunity for genome binning using a bi-dimensional coverage method, and a genome of Accumulibacter Clade IIC was well retrieved with over 90% completeness. Comparative genomic analysis demonstrated that Accumulibacter clades had different abilities in nitrogen metabolism and carbon fixation, which shed light on enriching different Accumulibacter populations selectively. PMID:27547976

  1. A continuation of base-line studies for environmentally monitoring Space Transportation System (STS) at John F. Kennedy Space Center. Volume 1: Terrestrial community analysis

    NASA Technical Reports Server (NTRS)

    Stout, I. J.

    1979-01-01

    Vegetation and small mammal populations in or around the Merritt Island area were studied. Thirty sites were selected from plant communities which were relatively free of logging, grazing, and clearing operations. The vegetative analysis was designed to yield a quantitative description and ecological explanation of the major types of upland vegetation in order to determine the possible future effects of NASA space activities on them. Changes in the relative abundance of small mammal populations, species diversity, standing crop biomass, reproductive activity, and other demographic features were documented in order to gather sufficient information on these populations so that it would be possible to detect even the smaller nonnatural behavior changes in the mammals which might be attributable to NASA space activities.

  2. Mapping marine debris across coastal communities in Belize: developing a baseline for understanding the distribution of litter on beaches using geographic information systems.

    PubMed

    Bennett-Martin, Paulita; Visaggi, Christy C; Hawthorne, Timothy L

    2015-10-01

    Monitoring of marine debris (also known as marine litter) is an essential step in the process to eradicate ecological dangers in marine ecosystems caused by humans. This study examines marine debris in the Caribbean country of Belize using geographic information systems (GIS) to develop (1) a detailed data library for use on handheld Global Positioning System (GPS) units and tablets with mobile mapping applications for deployment in the field and (2) a freely available, online mapping portal to share data with Belizeans to encourage future citizen science efforts. Four diverse communities were targeted ranging from larger more populated towns, to smaller villages across central and southern Belize: San Pedro, Caye Caulker, Punta Gorda, and Monkey River. Fieldwork was conducted over 1 month, during which data points were collected in 50-m surveys followed by debris cleanup and removal. Features in our database included material, quantity, item, brand, and condition. Over 6000 pieces of debris were recorded in GIS for further analysis, and 299 gal of debris were removed from the shores of Belize. The most abundant form of debris observed was plastic (commonly bottles) across all locations; plastic comprised 77.6 % of all debris items observed. Through GIS, a detailed snapshot understanding of debris patterns across multiple settings in Belize was documented. Ongoing collaborations with local organizations in Belize have demonstrated significant interest and utility for such GIS approaches in analyzing and managing marine debris. The data, methodology, visual representations, and online mapping platform resulting from this research are a first step in directly supporting local Belizean community advocacy and policy, while contributing to larger institutional strategies for addressing marine debris issues in the Caribbean. PMID:27614957

  3. Soil nematode communities are ecologically more mature beneath late- than early-successional stage biological soil crusts

    USGS Publications Warehouse

    Darby, B.J.; Neher, D.A.; Belnap, J.

    2007-01-01

    Biological soil crusts are key mediators of carbon and nitrogen inputs for arid land soils and often represent a dominant portion of the soil surface cover in arid lands. Free-living soil nematode communities reflect their environment and have been used as biological indicators of soil condition. In this study, we test the hypothesis that nematode communities are successionally more mature beneath well-developed, late-successional stage crusts than immature, early-successional stage crusts. We identified and enumerated nematodes by genus from beneath early- and late-stage crusts from both the Colorado Plateau, Utah (cool, winter rain desert) and Chihuahuan Desert, New Mexico (hot, summer rain desert) at 0-10 and 10-30 cm depths. As hypothesized, nematode abundance, richness, diversity, and successional maturity were greater beneath well-developed crusts than immature crusts. The mechanism of this aboveground-belowground link between biological soil crusts and nematode community composition is likely the increased food, habitat, nutrient inputs, moisture retention, and/or environmental stability provided by late-successional crusts. Canonical correspondence analysis of nematode genera demonstrated that nematode community composition differed greatly between geographic locations that contrast in temperature, precipitation, and soil texture. We found unique assemblages of genera among combinations of location and crust type that reveal a gap in scientific knowledge regarding empirically derived characterization of dominant nematode genera in deserts soils and their functional role in a crust-associated food web. ?? 2006 Elsevier B.V. All rights reserved.

  4. A Mechanics Baseline Test.

    ERIC Educational Resources Information Center

    Hestenes, David; Wells, Malcolm

    1992-01-01

    Reports the design of the "Mechanics Baseline Test," an instrument to assess students' understandings about concepts in mechanics. Discusses how comparisons of test results with extensive baseline data can be used to evaluate instruction at all levels. Includes a copy of the instrument. (MDH)

  5. Design, methodology and baseline characteristics of Tai Chi and its protective effect against ischaemic stroke risk in an elderly community population with risk factors for ischaemic stroke: a randomised controlled trial

    PubMed Central

    Zheng, Guohua; Zheng, Xin; Li, Junzhe; Duan, Tingjin; Qi, Dalu; Ling, Kun; He, Jian; Chen, Lidian

    2015-01-01

    Introduction Controlling risk factors with regular exercise is effective and cost-effective for the primary prevention of ischaemic stroke. As a traditional Chinese form of exercise, Tai Chi might be beneficial in decreasing ischaemic stroke, but the evidence remains insufficient. We hypothesise that elderly community adults with risk factors for ischaemic stroke will decrease their ischaemic stroke risk by improving cerebral haemodynamic parameters, cardiopulmonary function, motor function, plasma risk indices, physical parameters or psychological outcomes after receiving 12 weeks of regular Tai Chi training compared with those who maintained their original physical activities. Therefore, we designed a randomised controlled trial that will systematically evaluate the protective effects of Tai Chi exercise on ischaemic stroke risk in an elderly community population with risk factors for ischaemic stroke. Methods and analysis A total of 170 eligible participants were randomly allocated into either the Tai Chi training group or the usual physical activity group. This paper reports on the design, intervention development and baseline characteristics of the participants. There were no significant differences between comparison groups in demographic characteristics or the baseline data of primary or secondary outcomes. Participants in the Tai Chi training group will receive 12 weeks of Tai Chi training with a frequency of 5 days/week and 60 min/day, while those in the usual physical activities group will maintain their original activities. Primary and secondary outcomes will be measured at the 12-week and 24-week follow-ups. Ethics and dissemination Ethical approval has been obtained from the Medical Ethics Committee of The Affiliated People's Hospital of Fujian University of Traditional Chinese Medicine (number 2013-020-02). The findings of this study will be communicated to healthcare professionals, participants and the public through peer

  6. Peer Support for Achieving Independence in Diabetes (Peer-AID): Design, methods and baseline characteristics of a randomized controlled trial of community health worker assisted diabetes self-management support

    PubMed Central

    Nelson, Karin; Drain, Nathan; Robinson, June; Kapp, Janet; Hebert, Paul; Taylor, Leslie; Silverman, Julie; Kiefer, Meghan; Lessler, Dan; Krieger, James

    2014-01-01

    Background & Objectives Community health workers (CHWs) may be an important mechanism to provide diabetes self-management to disadvantaged populations. We describe the design and baseline results of a trial evaluating a home-based CHW intervention. Methods & Research Design Peer Support for Achieving Independence in Diabetes (Peer-AID) is a randomized, controlled trial evaluating a home-based CHW-delivered diabetes self-management intervention versus usual care. The study recruited participants from 3 health systems. Change in A1c measured at 12 months is the primary outcome. Change in blood pressure, lipids, health care utilization, health-related quality of life, self-efficacy and diabetes self-management behaviors at 12 months are secondary outcomes. Results A total of 1,438 patients were identified by medical record review as potentially eligible, 445 patients were screened by telephone for eligibility and 287 were randomized. Groups were comparable at baseline on socio-demographic and clinical characteristics. All participants were low-income and were from diverse racial and ethnic backgrounds. The mean A1c was 8.9%, mean BMI was above the obese range, and non-adherence to diabetes medications was high. The cohort had high rates of co-morbid disease and low self-reported health status. Although one-third reported no health insurance, the mean number of visits to a physician in the past year was 5.7. Trial results are pending. Conclusions Peer-AID recruited and enrolled a diverse group of low income participants with poorly controlled type 2 diabetes and delivered a home-based diabetes self-management program. If effective, replication of the Peer-AID intervention in community based settings could contribute to improved control of diabetes in vulnerable populations. PMID:24956324

  7. Nontarget effects of chemical pesticides and biological pesticide on rhizospheric microbial community structure and function in Vigna radiata.

    PubMed

    Singh, Sunil; Gupta, Rashi; Kumari, Madhu; Sharma, Shilpi

    2015-08-01

    Intensive agriculture has resulted in an indiscriminate use of pesticides, which demands in-depth analysis of their impact on indigenous rhizospheric microbial community structure and function. Hence, the objective of the present work was to study the impact of two chemical pesticides (chlorpyrifos and cypermethrin) and one biological pesticide (azadirachtin) at two dosages on the microbial community structure using cultivation-dependent approach and on rhizospheric bacterial communities involved in nitrogen cycle in Vigna radiata rhizosphere through cultivation-independent technique of real-time PCR. Cultivation-dependent study highlighted the adverse effects of both chemical pesticide and biopesticide on rhizospheric bacterial and fungal communities at different plant growth stages. Also, an adverse effect on number of genes and transcripts of nifH (nitrogen fixation); amoA (nitrification); and narG, nirK, and nirS (denitrification) was observed. The results from the present study highlighted two points, firstly that nontarget effects of pesticides are significantly detrimental to soil microflora, and despite being of biological origin, azadirachtin exerted negative impact on rhizospheric microbial community of V. radiata behaving similar to chemical pesticides. Hence, such nontarget effects of chemical pesticide and biopesticide in plants' rhizosphere, which bring out the larger picture in terms of their ecotoxicological effect, demand a proper risk assessment before application of pesticides as agricultural amendments. PMID:25801369

  8. Characterization of water quality and biological communities, Fish Creek, Teton County, Wyoming, 2007-2011

    USGS Publications Warehouse

    Eddy-Miller, Cheryl A.; Peterson, David A.; Wheeler, Jerrod D.; Edmiston, C. Scott; Taylor, Michelle L.; Leemon, Daniel J.

    2013-01-01

    Fish Creek, an approximately 25-kilometer-long tributary to Snake River, is located in Teton County in western Wyoming near the town of Wilson. Fish Creek is an important water body because it is used for irrigation, fishing, and recreation and adds scenic value to the Jackson Hole properties it runs through. Public concern about nuisance growths of aquatic plants in Fish Creek has been increasing since the early 2000s. To address these concerns, the U.S. Geological Survey conducted a study in cooperation with the Teton Conservation District to characterize the hydrology, water quality, and biologic communities of Fish Creek during 2007–11. The hydrology of Fish Creek is strongly affected by groundwater contributions from the area known as the Snake River west bank, which lies east of Fish Creek and west of Snake River. Because of this continuous groundwater discharge to the creek, land-use activities in the west bank area can affect the groundwater quality. Evaluation of nitrate isotopes and dissolved-nitrate concentrations in groundwater during the study indicated that nitrate was entering Fish Creek from groundwater, and that the source of nitrate was commonly a septic/sewage effluent or manure source, or multiple sources, potentially including artificial nitrogen fertilizers, natural soil organic matter, and mixtures of sources. Concentrations of dissolved nitrate and orthophosphate, which are key nutrients for growth of aquatic plants, generally were low in Fish Creek and occasionally were less than reporting levels (not detected). One potential reason for the low nutrient concentrations is that nutrients were being consumed by aquatic plant life that increases during the summer growing season, as a result of the seasonal increase in temperature and larger number of daylight hours. Several aspects of Fish Creek’s hydrology contribute to higher productivity and biovolume of aquatic plants in Fish Creek than typically observed in streams of its size in

  9. Community-driven development for computational biology at Sprints, Hackathons and Codefests

    PubMed Central

    2014-01-01

    Background Computational biology comprises a wide range of technologies and approaches. Multiple technologies can be combined to create more powerful workflows if the individuals contributing the data or providing tools for its interpretation can find mutual understanding and consensus. Much conversation and joint investigation are required in order to identify and implement the best approaches. Traditionally, scientific conferences feature talks presenting novel technologies or insights, followed up by informal discussions during coffee breaks. In multi-institution collaborations, in order to reach agreement on implementation details or to transfer deeper insights in a technology and practical skills, a representative of one group typically visits the other. However, this does not scale well when the number of technologies or research groups is large. Conferences have responded to this issue by introducing Birds-of-a-Feather (BoF) sessions, which offer an opportunity for individuals with common interests to intensify their interaction. However, parallel BoF sessions often make it hard for participants to join multiple BoFs and find common ground between the different technologies, and BoFs are generally too short to allow time for participants to program together. Results This report summarises our experience with computational biology Codefests, Hackathons and Sprints, which are interactive developer meetings. They are structured to reduce the limitations of traditional scientific meetings described above by strengthening the interaction among peers and letting the participants determine the schedule and topics. These meetings are commonly run as loosely scheduled "unconferences" (self-organized identification of participants and topics for meetings) over at least two days, with early introductory talks to welcome and organize contributors, followed by intensive collaborative coding sessions. We summarise some prominent achievements of those meetings and describe

  10. Biologically based pesticide dose estimates for children in an agricultural community.

    PubMed Central

    Fenske, R A; Kissel, J C; Lu, C; Kalman, D A; Simcox, N J; Allen, E H; Keifer, M C

    2000-01-01

    Current pesticide health risk assessments in the United States require the characterization of aggregate exposure and cumulative risk in the setting of food tolerances. Biologic monitoring can aggregate exposures from all sources and routes, and can integrate exposures for chemicals with a common mechanism of action. Its value was demonstrated in a recent study of organophosphorus (OP) pesticide exposure among 109 children in an agricultural community in Washington State; 91 of the children had parents working in agriculture. We estimated individual OP pesticide doses from urinary metabolite concentrations with a deterministic steady state model, and compared them to toxicologic reference values. We evaluated doses by assuming that metabolites were attributable entirely to either azinphos-methyl or phosmet, the two OP pesticides used most frequently in the region. Creatinine-adjusted average dose estimates during the 6- to 8-week spraying season ranged from 0 to 36 microg/kg/day. For children whose parents worked in agriculture as either orchard applicators or as fieldworkers, 56% of the doses estimated for the spray season exceeded the U.S. Environmental Protection Agency (EPA) chronic dietary reference dose, and 19% exceeded the World Health Organization acceptable daily intake values for azinphos-methyl. The corresponding values for children whose parents did not work in agriculture were 44 and 22%, respectively. The percentage of children exceeding the relevant reference values for phosmet was substantially lower (< 10%). Single-day dose estimates ranged from 0 to 72 microg/kg/day, and 26% of these exceeded the EPA acute reference dose for azinphos-methyl. We also generated dose estimates by adjustment for total daily urine volume, and these estimates were consistently higher than the creatinine-adjusted estimates. None of the dose estimates exceeded the empirically derived no-observable-adverse-effect levels for these compounds. The study took place in an

  11. Biologically based pesticide dose estimates for children in an agricultural community.

    PubMed

    Fenske, R A; Kissel, J C; Lu, C; Kalman, D A; Simcox, N J; Allen, E H; Keifer, M C

    2000-06-01

    Current pesticide health risk assessments in the United States require the characterization of aggregate exposure and cumulative risk in the setting of food tolerances. Biologic monitoring can aggregate exposures from all sources and routes, and can integrate exposures for chemicals with a common mechanism of action. Its value was demonstrated in a recent study of organophosphorus (OP) pesticide exposure among 109 children in an agricultural community in Washington State; 91 of the children had parents working in agriculture. We estimated individual OP pesticide doses from urinary metabolite concentrations with a deterministic steady state model, and compared them to toxicologic reference values. We evaluated doses by assuming that metabolites were attributable entirely to either azinphos-methyl or phosmet, the two OP pesticides used most frequently in the region. Creatinine-adjusted average dose estimates during the 6- to 8-week spraying season ranged from 0 to 36 microg/kg/day. For children whose parents worked in agriculture as either orchard applicators or as fieldworkers, 56% of the doses estimated for the spray season exceeded the U.S. Environmental Protection Agency (EPA) chronic dietary reference dose, and 19% exceeded the World Health Organization acceptable daily intake values for azinphos-methyl. The corresponding values for children whose parents did not work in agriculture were 44 and 22%, respectively. The percentage of children exceeding the relevant reference values for phosmet was substantially lower (< 10%). Single-day dose estimates ranged from 0 to 72 microg/kg/day, and 26% of these exceeded the EPA acute reference dose for azinphos-methyl. We also generated dose estimates by adjustment for total daily urine volume, and these estimates were consistently higher than the creatinine-adjusted estimates. None of the dose estimates exceeded the empirically derived no-observable-adverse-effect levels for these compounds. The study took place in an

  12. Geotaxis baseline data for Drosophila

    NASA Technical Reports Server (NTRS)

    Schnebel, E. M.; Bhargava, R.; Grossfield, J.

    1987-01-01

    Geotaxis profiles for 20 Drosophila species and semispecies at different ages have been examined using a calibrated, adjustable slant board device. Measurements were taken at 5 deg intervals ranging from 0 deg to 85 deg. Clear strain and species differences are observed, with some groups tending to move upward (- geotaxis) with increasing angles, while others move downward (+ geotaxis). Geotactic responses change with age in some, but not all experimental groups. Sample geotaxis profiles are presented and their application to ecological and aging studies are discussed. Data provide a baseline for future evaluations of the biological effects of microgravity.

  13. State of laboratory manual instruction in California community college introductory (non-majors) biology laboratory instruction

    NASA Astrophysics Data System (ADS)

    Priest, Michelle

    College students must complete a life science course prior to graduation for a bachelor's degree. Generally, the course has lecture and laboratory components. It is in the laboratory where there are exceptional opportunities for exploration, challenge and application of the material learned. Optimally, this would utilize the best of inquiry based approaches. Most community colleges are using a home-grown or self written laboratory manual for the direction of work in the laboratory period. Little was known about the motivation, development and adaptation of use. It was also not known about the future of the laboratory manuals in light of the recent learning reform in California Community Colleges, Student Learning Outcomes. Extensive interviews were conducted with laboratory manual authors to determine the motivation, process of development, who was involved and learning framework used in the creation of the manuals. It was further asked of manual authors their ideas about the future of the manual, the development of staff and faculty and finally, the role Student Learning Outcomes would play in the manual. Science faculty currently teaching the non-majors biology laboratories for at least two semesters were surveyed on-line about actual practice of the manual, assessment, manual flexibility, faculty training and incorporation of Student Learning Outcomes. Finally, an evaluation of the laboratory manual was done using an established Laboratory Task Analysis Instrument. Laboratory manuals were evaluated on a variety of categories to determine the level of inquiry instruction done by students in the laboratory section. The results were that the development of homegrown laboratory manuals was done by community colleges in the Los Angeles and Orange Counties in an effort to minimize the cost of the manual to the students, to utilize all the exercises in a particular lab and to effectively utilize the materials already owned by the department. Further, schools wanted to

  14. Community-Based Participatory Research Integrates Behavioral and Biological Research to Achieve Health Equity for Native Hawaiians.

    PubMed

    Townsend, Claire K M; Dillard, Adrienne; Hosoda, Kelsea K; Maskarinec, Gregory G; Maunakea, Alika K; Yoshimura, Sheryl R; Hughes, Claire; Palakiko, Donna-Marie; Kehauoha, Bridget Puni; Kaholokula, Joseph Keawe'aimoku

    2016-01-01

    Native Hawaiians bear a disproportionate burden of type-2 diabetes and related complications compared to all other groups in Hawai'i (e.g., Whites, Japanese, Korean). Distrust in these communities is a significant barrier to participation in epigenetic research studies seeking to better understand disease processes. The purpose of this paper is to describe the community-based participatory research (CBPR) approach and research process we employed to integrate behavior and biological sciences with community health priorities. A CBPR approach was used to test a 3-month evidence-based, diabetes self-management intervention (N = 65). To investigate the molecular mechanisms linking inflammation with glucose homeostasis, a subset of participants (n = 16) provided peripheral blood mononuclear cells. Community and academic researchers collaborated on research design, assessment protocols, and participant recruitment, prioritizing participants' convenience and education and strictly limiting the use of the data collected. Preliminary results indicate significant changes in DNA methylation at gene regions associated with inflammation and diabetes signaling pathways and significant improvements in hemoglobin A1c, self-care activities, and diabetes distress and understanding. This study integrates community, behavioral, and epigenomic expertise to better understand the outcomes of a diabetes self-management intervention. Key lessons learned suggest the studies requiring biospecimen collection in indigenous populations require community trust of the researchers, mutual benefits for the community and researchers, and for the researchers to prioritize the community's needs. CBPR may be an important tool in providing communities the voice and protections to participate in studies requiring biospecimens. PMID:26703660

  15. Life Support Baseline Values and Assumptions Document

    NASA Technical Reports Server (NTRS)

    Anderson, Molly S.; Ewert, Michael K.; Keener, John F.; Wagner, Sandra A.

    2015-01-01

    The Baseline Values and Assumptions Document (BVAD) provides analysts, modelers, and other life support researchers with a common set of values and assumptions which can be used as a baseline in their studies. This baseline, in turn, provides a common point of origin from which many studies in the community may depart, making research results easier to compare and providing researchers with reasonable values to assume for areas outside their experience. With the ability to accurately compare different technologies' performance for the same function, managers will be able to make better decisions regarding technology development.

  16. The Southern Community Cohort Study: Investigating Health Disparities

    PubMed Central

    Signorello, Lisa B.; Hargreaves, Margaret K.; Blot, William J.

    2010-01-01

    Summary Over 73,700 adults age 40–79, nearly 70% African American, were recruited at community health centers across 12 southeastern states; individual characteristics were recorded and biologic specimens collected at baseline for later follow-up. The Southern Community Cohort Study is a unique national resource for assessing determinants of racial/ethnic differentials in diseases. PMID:20173283

  17. Supercritical fluid extraction and ultra performance liquid chromatography of respiratory quinones for microbial community analysis in environmental and biological samples.

    PubMed

    Hanif, Muhammad; Atsuta, Yoichi; Fujie, Koichi; Daimon, Hiroyuki

    2012-01-01

    Microbial community structure plays a significant role in environmental assessment and animal health management. The development of a superior analytical strategy for the characterization of microbial community structure is an ongoing challenge. In this study, we developed an effective supercritical fluid extraction (SFE) and ultra performance liquid chromatography (UPLC) method for the analysis of bacterial respiratory quinones (RQ) in environmental and biological samples. RQ profile analysis is one of the most widely used culture-independent tools for characterizing microbial community structure. A UPLC equipped with a photo diode array (PDA) detector was successfully applied to the simultaneous determination of ubiquinones (UQ) and menaquinones (MK) without tedious pretreatment. Supercritical carbon dioxide (scCO(2)) extraction with the solid-phase cartridge trap proved to be a more effective and rapid method for extracting respiratory quinones, compared to a conventional organic solvent extraction method. This methodology leads to a successful analytical procedure that involves a significant reduction in the complexity and sample preparation time. Application of the optimized methodology to characterize microbial communities based on the RQ profile was demonstrated for a variety of environmental samples (activated sludge, digested sludge, and compost) and biological samples (swine and Japanese quail feces). PMID:22391598

  18. Project FIT: Rationale, design and baseline characteristics of a school- and community-based intervention to address physical activity and healthy eating among low-income elementary school children

    PubMed Central

    2011-01-01

    Background This paper describes Project FIT, a collaboration between the public school system, local health systems, physicians, neighborhood associations, businesses, faith-based leaders, community agencies and university researchers to develop a multi-faceted approach to promote physical activity and healthy eating toward the general goal of preventing and reducing childhood obesity among children in Grand Rapids, MI, USA. Methods/design There are four overall components to Project FIT: school, community, social marketing, and school staff wellness - all that focus on: 1) increasing access to safe and affordable physical activity and nutrition education opportunities in the schools and surrounding neighborhoods; 2) improving the affordability and availability of nutritious food in the neighborhoods surrounding the schools; 3) improving the knowledge, self-efficacy, attitudes and behaviors regarding nutrition and physical activity among school staff, parents and students; 4) impacting the 'culture' of the schools and neighborhoods to incorporate healthful values; and 5) encouraging dialogue among all community partners to leverage existing programs and introduce new ones. Discussion At baseline, there was generally low physical activity (70% do not meet recommendation of 60 minutes per day), excessive screen time (75% do not meet recommendation of < 2 hours per day), and low intake of vegetables and whole grains and high intake of sugar-sweetened beverages, French fries and chips and desserts as well as a high prevalence of overweight and obesity (48.5% including 6% with severe obesity) among low income, primarily Hispanic and African American 3rd-5th grade children (n = 403). Trial registration ClinicalTrials.gov NCT01385046 PMID:21801411

  19. Identifying Reference Conditions and Quantifying Biological Variability Within Benthic Macroinvertebrate Communities in Perennial and Non-perennial Northern California Streams

    NASA Astrophysics Data System (ADS)

    Lunde, Kevin B.; Cover, Matthew R.; Mazor, Raphael D.; Sommers, Christopher A.; Resh, Vincent H.

    2013-06-01

    Identification of minimally disturbed reference sites is a critical step in developing precise and informative ecological indicators. We tested procedures to select reference sites, and quantified natural variation (inter-site and -annual variability) among reference conditions using a macroinvertebrate data set collected from 429 mediterranean-climate stream reaches in the San Francisco Bay Area, California (USA). We determined that a landscape GIS-based stressor screen followed by a local field-based stressor screen effectively identified least-disturbed reference sites that, based on NMS ordination results, supported different biological communities than sites identified with only landscape (GIS) or local (field) stressors. An examination of least-disturbed reference sites indicated that inter-site variability was strongly associated with stream hydrology (i.e., perennial vs. non-perennial flow) and annual precipitation, which highlights the need to control for such variation when developing biological indicators through natural gradient modeling or using unique biological indicators for both non-perennial and perennial streams. Metrics were more variable among non-perennial streams, indicating that additional modeling may be needed to develop precise biological indicators for non-perennial streams. Among 192 sites sampled two to six times over the 8-year study period, the biological community showed moderate inter-annual variability, with the 100 point index of biotic integrity scores varying from 0 to 51 points (mean = 11.5). Variance components analysis indicated that inter-annual variability explained only a fraction (5-18 %) of the total variation when compared against site-level variation; thus efforts to understand causes of natural variation between sites will produce more precise and accurate biological indicators.

  20. Effects of organic pollution on biological communities of marine biofilm on hard substrata.

    PubMed

    Sanz-Lázaro, C; Fodelianakis, S; Guerrero-Meseguer, L; Marín, A; Karakassis, I

    2015-06-01

    We examined the effect of organic enrichment on diatom and bacterial assemblages of marine epilithic biofilms on two locations in the Mediterranean, one situated in Spain and the other in Greece. Total organic carbon, total organic nitrogen, stable isotopes (δ(13)C and δ(15)N) and chlorophyll a indicated significant incorporation of organic wastes, increased primary production and trophic niche modifications on the biofilms close to the organic enrichment source. In Spain, where the organic load was higher than in Greece, diatom and, to some extent, bacterial assemblages varied following the organic enrichment gradient. The taxonomic richness of diatom and bacterial communities was not influenced by organic enrichment. Classical community parameters showed consistent patterns to organic pollution in both locations, whereas community assemblages were only influenced when organic pollution was greatest. The successional patterns of these communities were similar to other epilithic communities. The modification of community assemblages induced by organic pollution may affect ecological functions. PMID:25752833

  1. Community-Based Participatory Research Integrates Behavioral and Biological Research to Achieve Health Equity for Native Hawaiians

    PubMed Central

    Townsend, Claire K. M.; Dillard, Adrienne; Hosoda, Kelsea K.; Maskarinec, Gregory G.; Maunakea, Alika K.; Yoshimura, Sheryl R.; Hughes, Claire; Palakiko, Donna-Marie; Kehauoha, Bridget Puni; Kaholokula, Joseph Keawe‘aimoku

    2015-01-01

    Native Hawaiians bear a disproportionate burden of type-2 diabetes and related complications compared to all other groups in Hawai‘i (e.g., Whites, Japanese, Korean). Distrust in these communities is a significant barrier to participation in epigenetic research studies seeking to better understand disease processes. The purpose of this paper is to describe the community-based participatory research (CBPR) approach and research process we employed to integrate behavior and biological sciences with community health priorities. A CBPR approach was used to test a 3-month evidence-based, diabetes self-management intervention (N = 65). To investigate the molecular mechanisms linking inflammation with glucose homeostasis, a subset of participants (n = 16) provided peripheral blood mononuclear cells. Community and academic researchers collaborated on research design, assessment protocols, and participant recruitment, prioritizing participants’ convenience and education and strictly limiting the use of the data collected. Preliminary results indicate significant changes in DNA methylation at gene regions associated with inflammation and diabetes signaling pathways and significant improvements in hemoglobin A1c, self-care activities, and diabetes distress and understanding. This study integrates community, behavioral, and epigenomic expertise to better understand the outcomes of a diabetes self-management intervention. Key lessons learned suggest the studies requiring biospecimen collection in indigenous populations require community trust of the researchers, mutual benefits for the community and researchers, and for the researchers to prioritize the community’s needs. CBPR may be an important tool in providing communities the voice and protections to participate in studies requiring biospecimens. PMID:26703660

  2. Ecological baseline studies

    NASA Technical Reports Server (NTRS)

    Vickers, D.

    1980-01-01

    Environmental studies of Merritt Island are discussed. Five areas of the island's ecology are examined. They include: a terrestrial community analyses, a plant community study, a small mammal population study, a rainfall study, and an ichthyological analyses.

  3. Subsets of symptomatic hand osteoarthritis in community-dwelling older adults in the United Kingdom: prevalence, inter-relationships, risk factor profiles and clinical characteristics at baseline and 3-years

    PubMed Central

    Marshall, M.; Peat, G.; Nicholls, E.; van der Windt, D.; Myers, H.; Dziedzic, K.

    2013-01-01

    Summary Objective To compare the population prevalence, inter-relationships, risk factor profiles and clinical characteristics of subsets of symptomatic hand osteoarthritis (OA) with a view to understanding their relative frequency and distinctiveness. Method 1076 community-dwelling adults with hand symptoms (60% women, mean age 64.7 years) were recruited and classified into pre-defined subsets using physical examination and standardised hand radiographs, scored with the Kellgren & Lawrence (K&L) and Verbruggen–Veys grading systems. Detailed information on selected risk factors was obtained from direct measurement (Body Mass Index (BMI)), self-complete questionnaires (excessive use of hands, previous hand injury) and medical record review (hypertension, dyslipidaemia, type 2 diabetes). Hand pain and disability were self-reported at baseline and 3-year follow-up using Australian/Canadian Osteoarthritis Hand Index (AUSCAN). Results Crude population prevalence estimates for symptomatic hand OA subsets in the adult population aged 50 years and over were: thumb base OA (22.4%), nodal interphalangeal joint (IPJ) OA (15.5%), generalised hand OA (10.4%), non-nodal IPJ OA (4.9%), erosive OA (1.0%). Apart from thumb base OA, there was considerable overlap between the subsets. Erosive OA appeared the most distinctive with the highest female: male ratio, and the most disability at baseline and 3-years. A higher frequency of obesity, hypertension, dyslipidaemia, and metabolic syndrome was observed in this subset. Conclusion Overlap in the occurrence of hand OA subsets poses conceptual and practical challenges to the pursuit of distinct phenotypes. Erosive OA may nevertheless provide particular insight into the role of metabolic and cardiovascular risk factors in the pathogenesis of OA. PMID:23954700

  4. Evidence of functional declining and global comorbidity measured at baseline proved to be the strongest predictors for long-term death in elderly community residents aged 85 years: a 5-year follow-up evaluation, the OCTABAIX study

    PubMed Central

    Formiga, Francesc; Ferrer, Assumpta; Padros, Gloria; Montero, Abelardo; Gimenez-Argente, Carme; Corbella, Xavier

    2016-01-01

    Objective To investigate the predictive value of functional impairment, chronic conditions, and laboratory biomarkers of aging for predicting 5-year mortality in the elderly aged 85 years. Methods Predictive value for mortality of different geriatric assessments carried out during the OCTABAIX study was evaluated after 5 years of follow-up in 328 subjects aged 85 years. Measurements included assessment of functional status comorbidity, along with laboratory tests on vitamin D, cholesterol, CD4/CD8 ratio, hemoglobin, and serum thyrotropin. Results Overall, the mortality rate after 5 years of follow-up was 42.07%. Bivariate analysis showed that patients who survived were predominantly female (P=0.02), and they showed a significantly better baseline functional status for both basic (P<0.001) and instrumental (P<0.001) activities of daily living (Barthel and Lawton index), better cognitive performance (Spanish version of the Mini-Mental State Examination) (P<0.001), lower comorbidity conditions (Charlson) (P<0.001), lower nutritional risk (Mini Nutritional Assessment) (P<0.001), lower risk of falls (Tinetti gait scale) (P<0.001), less percentage of heart failure (P=0.03) and chronic obstructive pulmonary disease (P=0.03), and took less chronic prescription drugs (P=0.002) than nonsurvivors. Multivariate Cox regression analysis identified a decreased score in the Lawton index (hazard ratio 0.86, 95% confidence interval: 0.78–0.91) and higher comorbidity conditions (hazard ratio 1.20, 95% confidence interval: 1.08–1.33) as independent predictors of mortality at 5 years in the studied population. Conclusion The ability to perform instrumental activities of daily living and the global comorbidity assessed at baseline were the predictors of death, identified in our 85-year-old community-dwelling subjects after 5 years of follow-up. PMID:27143867

  5. Microbial communities from different subsystems in biological heap leaching system play different roles in iron and sulfur metabolisms.

    PubMed

    Xiao, Yunhua; Liu, Xueduan; Ma, Liyuan; Liang, Yili; Niu, Jiaojiao; Gu, Yabing; Zhang, Xian; Hao, Xiaodong; Dong, Weiling; She, Siyuan; Yin, Huaqun

    2016-08-01

    The microbial communities are important for minerals decomposition in biological heap leaching system. However, the differentiation and relationship of composition and function of microbial communities between leaching heap (LH) and leaching solution (LS) are still unclear. In this study, 16S rRNA gene sequencing was used to assess the microbial communities from the two subsystems in ZiJinShan copper mine (Fujian province, China). Results of PCoA and dissimilarity test showed that microbial communities in LH samples were significantly different from those in LS samples. The dominant genera of LH was Acidithiobacillus (57.2 ∼ 87.9 %), while Leptospirillum (48.6 ∼ 73.7 %) was predominant in LS. Environmental parameters (especially pH) were the major factors to influence the composition and structure of microbial community by analysis of Mantel tests. Results of functional test showed that microbial communities in LH utilized sodium thiosulfate more quickly and utilized ferrous sulfate more slowly than those in LS, which further indicated that the most sulfur-oxidizing processes of bioleaching took place in LH and the most iron-oxidizing processes were in LS. Further study found that microbial communities in LH had stronger pyrite leaching ability, and iron extraction efficiency was significantly positively correlated with Acidithiobacillus (dominated in LH), which suggested that higher abundance ratio of sulfur-oxidizing microbes might in favor of minerals decomposition. Finally, a conceptual model was designed through the above results to better exhibit the sulfur and iron metabolism in bioleaching systems. PMID:27094188

  6. Bacterial Communities in Polluted Seabed Sediments: A Molecular Biology Assay in Leghorn Harbor

    PubMed Central

    Verni, Franco; Petroni, Giulio

    2013-01-01

    Seabed sediments of commercial ports are often characterized by high pollution levels. Differences in number and distribution of bacteria in such areas can be related to distribution of pollutants in the port and to sediment conditions. In this study, the bacterial communities of five sites from Leghorn Harbor seabed were characterized, and the main bacterial groups were identified. T-RFLP was used for all samples; two 16S rRNA libraries and in silico digestion of clones were used to identify fingerprint profiles. Library data, phylogenetic analysis, and T-RFLP coupled with in silico digestion of the obtained sequences evidenced the dominance of Proteobacteria and the high percentage of Bacteroidetes in all sites. The approach highlighted similar bacterial communities between samples coming from the five sites, suggesting a modest differentiation among bacterial communities of different harbor seabed sediments and hence the capacity of bacterial communities to adapt to different levels and types of pollution. PMID:24227997

  7. Transportation Baseline Schedule

    SciTech Connect

    Fawcett, Ricky Lee; John, Mark Earl

    2000-01-01

    The “1999 National Transportation Program - Transportation Baseline Report” presents data that form a baseline to enable analysis and planning for future Department of Energy (DOE) Environmental Management (EM) waste/material transportation. The companion “1999 Transportation ‘Barriers’ Analysis” analyzes the data and identifies existing and potential problems that may prevent or delay transportation activities based on the data presented. The “1999 Transportation Baseline Schedule” (this report) uses the same data to provide an overview of the transportation activities of DOE EM waste/materials. This report can be used to identify areas where stakeholder interface is needed, and to communicate to stakeholders the quantity/schedule of shipments going through their area. Potential bottlenecks in the transportation system can be identified; the number of packages needed, and the capacity needed at receiving facilities can be planned. This report offers a visualization of baseline DOE EM transportation activities for the 11 major sites and the “Geologic Repository Disposal” site (GRD).

  8. First Grade Baseline Evaluation

    ERIC Educational Resources Information Center

    Center for Innovation in Assessment (NJ1), 2013

    2013-01-01

    The First Grade Baseline Evaluation is an optional tool that can be used at the beginning of the school year to help teachers get to know the reading and language skills of each student. The evaluation is composed of seven screenings. Teachers may use the entire evaluation or choose to use those individual screenings that they find most beneficial…

  9. Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications

    PubMed Central

    Namasivayam, Aishwarya Alex; Morales, Alejandro Ferreiro; Lacave, Ángela María Fajardo; Tallam, Aravind; Simovic, Borislav; Alfaro, David Garrido; Bobbili, Dheeraj Reddy; Martin, Florian; Androsova, Ganna; Shvydchenko, Irina; Park, Jennifer; Calvo, Jorge Val; Hoeng, Julia; Peitsch, Manuel C.; Racero, Manuel González Vélez; Biryukov, Maria; Talikka, Marja; Pérez, Modesto Berraquero; Rohatgi, Neha; Díaz-Díaz, Noberto; Mandarapu, Rajesh; Ruiz, Rubén Amián; Davidyan, Sergey; Narayanasamy, Shaman; Boué, Stéphanie; Guryanova, Svetlana; Arbas, Susana Martínez; Menon, Swapna; Xiang, Yang

    2016-01-01

    Biological network models offer a framework for understanding disease by describing the relationships between the mechanisms involved in the regulation of biological processes. Crowdsourcing can efficiently gather feedback from a wide audience with varying expertise. In the Network Verification Challenge, scientists verified and enhanced a set of 46 biological networks relevant to lung and chronic obstructive pulmonary disease. The networks were built using Biological Expression Language and contain detailed information for each node and edge, including supporting evidence from the literature. Network scoring of public transcriptomics data inferred perturbation of a subset of mechanisms and networks that matched the measured outcomes. These results, based on a computable network approach, can be used to identify novel mechanisms activated in disease, quantitatively compare different treatments and time points, and allow for assessment of data with low signal. These networks are periodically verified by the crowd to maintain an up-to-date suite of networks for toxicology and drug discovery applications. PMID:27429547

  10. BIOLOGICAL AMENDMENTS AND CROP ROTATIONS FOR MANAGING SOIL MICROBIAL COMMUNITIES AND SOILBORNE DISEASES OF POTATO

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Various biological amendments, including commercial biocontrol agents, microbial inoculants, mycorrhizae, and an aerobic compost tea (CT), were evaluated, alone and in conjunction with different crop rotations, for their efficacy in introducing beneficial microorganisms, affecting soil microbial com...

  11. Community-Issues Biology: A Different Kind of Action-Learning

    ERIC Educational Resources Information Center

    Cooley, Arthur P.

    1976-01-01

    Described is an action-learning secondary level biology course which combines science, English, and social studies. Guidelines for selecting topics to be presented and three detailed examples of topics that have been included in past courses are presented. (SL)

  12. Community-Reviewed Biological Network Models for Toxicology and Drug Discovery Applications.

    PubMed

    Namasivayam, Aishwarya Alex; Morales, Alejandro Ferreiro; Lacave, Ángela María Fajardo; Tallam, Aravind; Simovic, Borislav; Alfaro, David Garrido; Bobbili, Dheeraj Reddy; Martin, Florian; Androsova, Ganna; Shvydchenko, Irina; Park, Jennifer; Calvo, Jorge Val; Hoeng, Julia; Peitsch, Manuel C; Racero, Manuel González Vélez; Biryukov, Maria; Talikka, Marja; Pérez, Modesto Berraquero; Rohatgi, Neha; Díaz-Díaz, Noberto; Mandarapu, Rajesh; Ruiz, Rubén Amián; Davidyan, Sergey; Narayanasamy, Shaman; Boué, Stéphanie; Guryanova, Svetlana; Arbas, Susana Martínez; Menon, Swapna; Xiang, Yang

    2016-01-01

    Biological network models offer a framework for understanding disease by describing the relationships between the mechanisms involved in the regulation of biological processes. Crowdsourcing can efficiently gather feedback from a wide audience with varying expertise. In the Network Verification Challenge, scientists verified and enhanced a set of 46 biological networks relevant to lung and chronic obstructive pulmonary disease. The networks were built using Biological Expression Language and contain detailed information for each node and edge, including supporting evidence from the literature. Network scoring of public transcriptomics data inferred perturbation of a subset of mechanisms and networks that matched the measured outcomes. These results, based on a computable network approach, can be used to identify novel mechanisms activated in disease, quantitatively compare different treatments and time points, and allow for assessment of data with low signal. These networks are periodically verified by the crowd to maintain an up-to-date suite of networks for toxicology and drug discovery applications. PMID:27429547

  13. Treatment of high ethanol concentration wastewater by biological sand filters: enhanced COD removal and bacterial community dynamics.

    PubMed

    Rodriguez-Caballero, A; Ramond, J-B; Welz, P J; Cowan, D A; Odlare, M; Burton, S G

    2012-10-30

    Winery wastewater is characterized by its high chemical oxygen demand (COD), seasonal occurrence and variable composition, including periodic high ethanol concentrations. In addition, winery wastewater may contain insufficient inorganic nutrients for optimal biodegradation of organic constituents. Two pilot-scale biological sand filters (BSFs) were used to treat artificial wastewater: the first was amended with ethanol and the second with ethanol, inorganic nitrogen (N) and phosphorus (P). A number of biochemical parameters involved in the removal of pollutants through BSF systems were monitored, including effluent chemistry and bacterial community structures. The nutrient supplemented BSF showed efficient COD, N and P removal. Comparison of the COD removal efficiencies of the two BSFs showed that N and P addition enhanced COD removal efficiency by up to 16%. Molecular fingerprinting of BSF sediment samples using denaturing gradient gel electrophoresis (DGGE) showed that amendment with high concentrations of ethanol destabilized the microbial community structure, but that nutrient supplementation countered this effect. PMID:22683841

  14. The activity and community structure of total bacteria and denitrifying bacteria across soil depths and biological gradients in estuary ecosystem.

    PubMed

    Lee, Seung-Hoon; Kang, Hojeong

    2016-02-01

    The distribution of soil microorganisms often shows variations along soil depth, and even in the same soil layer, each microbial group has a specific niche. In particular, the estuary soil is intermittently flooded, and the characteristics of the surface soil layer are different from those of other terrestrial soils. We investigated the microbial community structure and activity across soil depths and biological gradients composed of invasive and native plants in the shallow surface layer of an estuary ecosystem by using molecular approaches. Our results showed that the total and denitrifying bacterial community structures of the estuarine wetland soil differed according to the short depth gradient. In growing season, gene copy number of 16S rRNA were 1.52(±0.23) × 10(11), 1.10(±0.06) × 10(11), and 4.33(±0.16) × 10(10) g(-1) soil; nirS were 5.41(±1.25) × 10(8), 4.93(±0.94) × 10(8), and 2.61(±0.28) × 10(8) g(-1) soil; and nirK were 9.67(±2.37) × 10(6), 3.42(±0.55) × 10(6), and 2.12(±0.19) × 10(6) g(-1) soil in 0 cm, 5 cm, and 10 cm depth layer, respectively. The depth-based difference was distinct in the vegetated sample and in the growing season, evidencing the important role of plants in structuring the microbial community. In comparison with other studies, we observed differences in the microbial community and functions even across very short depth gradients. In conclusion, our results suggested that (i) in the estuary ecosystem, the denitrifying bacterial community could maintain its abundance and function within shallow surface soil layers through facultative anaerobiosis, while the total bacterial community would be both quantitatively and qualitatively affected by the soil depth, (ii) the nirS gene community, rather than the nirK one, should be the first candidate used as an indicator of the microbial denitrification process in the estuary system, and (iii) as the microbial community is distributed and plays a certain

  15. The effect of the use of concept maps on community college students' conceptual understanding of biology course content

    NASA Astrophysics Data System (ADS)

    Wells, Franklin Brian

    Purpose of the study. The major purpose of this study was to measure the change, if any, in students' conceptual understanding of biology course content using concept maps (experimental) or a standard lecture format (control). In addition, the effectiveness of the use of concept maps as advance organizers was measured according to the various subgroups of cognitive development level, age, ethnicity, gender, class time, and educational background. A final concern was the relationships between conceptual understanding of biology course content and the students' cognitive development level. Procedure. A quasi-experimental design was used to conduct the study during a sixteen-week semester. The study was conducted during the fall, 1997, semester at a community college using 190 students enrolled in General Biology 1406. Major data were collected using a pretest, posttest, and the Test of Logical Thinking. Data were treated through the application of analysis of covariance, Pearson product-moment correlation, and the Fisher Z-transformation technique. Findings. The findings of this investigation were as follows: (1) Concept maps used as advance organizers had a significant effect on student conceptual understanding of biology course content. (2) The use of concept maps as advance organizers had a significant effect on student conceptual understanding of biology when students are classified according to their cognitive developmental level, age, gender, major, course time, and educational background. (3) A significant relationship between cognitive developmental level and conceptual understanding was also found. Conclusions. The use of concept maps, as advance Organizers, is an effective method for improving student learning in general biology classes. A positive relationship exists between students' cognitive developmental level and conceptual understanding.

  16. Methods for open innovation on a genome-design platform associating scientific, commercial, and educational communities in synthetic biology.

    PubMed

    Toyoda, Tetsuro

    2011-01-01

    Synthetic biology requires both engineering efficiency and compliance with safety guidelines and ethics. Focusing on the rational construction of biological systems based on engineering principles, synthetic biology depends on a genome-design platform to explore the combinations of multiple biological components or BIO bricks for quickly producing innovative devices. This chapter explains the differences among various platform models and details a methodology for promoting open innovation within the scope of the statutory exemption of patent laws. The detailed platform adopts a centralized evaluation model (CEM), computer-aided design (CAD) bricks, and a freemium model. It is also important for the platform to support the legal aspects of copyrights as well as patent and safety guidelines because intellectual work including DNA sequences designed rationally by human intelligence is basically copyrightable. An informational platform with high traceability, transparency, auditability, and security is required for copyright proof, safety compliance, and incentive management for open innovation in synthetic biology. GenoCon, which we have organized and explained here, is a competition-styled, open-innovation method involving worldwide participants from scientific, commercial, and educational communities that aims to improve the designs of genomic sequences that confer a desired function on an organism. Using only a Web browser, a participating contributor proposes a design expressed with CAD bricks that generate a relevant DNA sequence, which is then experimentally and intensively evaluated by the GenoCon organizers. The CAD bricks that comprise programs and databases as a Semantic Web are developed, executed, shared, reused, and well stocked on the secure Semantic Web platform called the Scientists' Networking System or SciNetS/SciNeS, based on which a CEM research center for synthetic biology and open innovation should be established. PMID:21601679

  17. Using Service Learning in a Course Entitled "Biology of Women" to Promote Student Engagement and Awareness of Community Needs and Resources

    ERIC Educational Resources Information Center

    Bauer-Dantoin, Angela C.

    2008-01-01

    Service learning projects were incorporated into the curriculum of an undergraduate course entitled "Biology of Women". The goals of the service learning projects were: 1) to provide students with the opportunity to consider issues pertaining to human biology in real-world settings; 2) to foster student engagement with the community; and 3) to…

  18. Pinellas Plant Environmental Baseline Report

    SciTech Connect

    Not Available

    1997-06-01

    The Pinellas Plant has been part of the Department of Energy`s (DOE) nuclear weapons complex since the plant opened in 1957. In March 1995, the DOE sold the Pinellas Plant to the Pinellas County Industry Council (PCIC). DOE has leased back a large portion of the plant site to facilitate transition to alternate use and safe shutdown. The current mission is to achieve a safe transition of the facility from defense production and prepare the site for alternative uses as a community resource for economic development. Toward that effort, the Pinellas Plant Environmental Baseline Report (EBR) discusses the current and past environmental conditions of the plant site. Information for the EBR is obtained from plant records. Historical process and chemical usage information for each area is reviewed during area characterizations.

  19. Monitoring the effect of chemicals on biological communities. The biofilm as an interface.

    PubMed

    Sabater, Sergi; Guasch, Helena; Ricart, Marta; Romaní, Anna; Vidal, Gemma; Klünder, Christina; Schmitt-Jansen, Mechthild

    2007-02-01

    Biofilms can be regarded as early warning systems for detection of the effects of toxicants on aquatic systems, because they have been successfully used for detection of other environmental stressors (e.g. pH, salinity, organic pollution). A variety of methods is used for detection of the effects of toxicants by use of biofilms. The methods range from structurally-based to functionally-based, and from in vitro-based to systemic approaches. Physiological approaches may be appropriate for detection of acute effects. Among these methods, photosynthesis is more related to the effect of toxicants affecting algal communities, directly or indirectly, and extracellular enzyme activity is less specific. Selecting one or the other may depend on the suspected direct effect of the toxicant. Integrated studies have revealed the relevance of toxicants to top-down or bottom-up regulation of the biofilm community. Persistent or chronic effects should affect other biofilm indicators, for example growth or biomass-related factors (e.g. chlorophyll), or community composition. Among these, community composition might better reflect the effects of the toxicant(s), because this may cause a shift from a sensitive to a progressively tolerant community. Community composition-based approaches do not usually adequately reflect cause-effect relationships and require complementary analysis of properties affected in the short-term, for example physiological properties. The current array of methods available must be wisely combined to disentangle the effects of chemicals on biofilms, and whether these effects are transient or persistent, to successfully translate the chemical action of toxicants into the effect they might have on the river ecosystem. PMID:17225111

  20. Transportation Baseline Report

    SciTech Connect

    Fawcett, Ricky Lee; Kramer, George Leroy Jr.

    1999-12-01

    The National Transportation Program 1999 Transportation Baseline Report presents data that form a baseline to enable analysis and planning for future Department of Energy (DOE) Environmental Management (EM) waste and materials transportation. In addition, this Report provides a summary overview of DOE’s projected quantities of waste and materials for transportation. Data presented in this report were gathered as a part of the IPABS Spring 1999 update of the EM Corporate Database and are current as of July 30, 1999. These data were input and compiled using the Analysis and Visualization System (AVS) which is used to update all stream-level components of the EM Corporate Database, as well as TSD System and programmatic risk (disposition barrier) information. Project (PBS) and site-level IPABS data are being collected through the Interim Data Management System (IDMS). The data are presented in appendices to this report.

  1. Bacterial diversity and community along the succession of biological soil crusts in the Gurbantunggut Desert, Northern China.

    PubMed

    Zhang, Bingchang; Kong, Weidong; Wu, Nan; Zhang, Yuanming

    2016-06-01

    Biological soil crusts (BSCs) are common and play critical roles in semi-arid and arid ecosystems. Bacteria, as an important community in BSCs, play critical roles in biochemical processes. However, how bacterial diversity and community change in different successional stages of BSCs is still unknown. We used 454 pyrosequencing of 16S rRNA to investigate the bacterial composition and community, and the relationships between bacterial composition and environmental factors were also explored. In different successional stages of BSCs, the number of bacteria operational taxonomic units (OTUs) detected in each sample ranged from 2572 to 3157. Proteobacteria, Cyanobacteria, Bacteroidetes were dominant in BSCs, followed by Firmicutes, Acidobacteria, and Actinobacteria. At the successional stages of BSCs, bacterial communities, OTU composition and their relative abundance notably differentiated, and Cyanobacteria, especially Microcoleus vaginatus, dominated algal crust and lichen crust, and were the main C-fixing bacteria in BSCs. Proteobacteria and Bacteroidetes increased with the development of BSCs. OTUs related to Planomicrobium Chinese, Desulfobulbus sp., Desulfomicrobium sp., Arthrobacter sp., and Ahhaerbacter sp. showed higher relative abundance in bare sand than other successional stages of BSCs, while relative abundance of Sphingomonas sp. Niastella sp., Pedobacter, Candidatus solobacter, and Streptophyta increased with the development of BSCs. In successional stages of BSCs, bacterial OTUs composition demonstrated strong correlations with soil nutrients, soil salts, and soil enzymes. Additionally, variation of bacterial composition led to different ecological function. In bare sand, some species were related with mineral metabolism or promoting plant growth, and in algal crust and lichen crust, C-fixing bacteria increased and accumulated C to the desert soil. In later developed stage of BSCs, bacteria related with decomposition of organic matter, such as

  2. Groundwater's significance to changing hydrology, water chemistry, and biological communities of a floodplain ecosystem, Everglades, South Florida, USA

    USGS Publications Warehouse

    Harvey, J.W.; McCormick, P.V.

    2009-01-01

    The Everglades (Florida, USA) is one of the world's larger subtropical peatlands with biological communities adapted to waters low in total dissolved solids and nutrients. Detecting how the pre-drainage hydrological system has been altered is crucial to preserving its functional attributes. However, reliable tools for hindcasting historic conditions in the Everglades are limited. A recent synthesis demonstrates that the proportion of surface-water inflows has increased relative to precipitation, accounting for 33% of total inputs compared with 18% historically. The largest new source of water is canal drainage from areas of former wetlands converted to agriculture. Interactions between groundwater and surface water have also increased, due to increasing vertical hydraulic gradients resulting from topographic and water-level alterations on the otherwise extremely flat landscape. Environmental solute tracer data were used to determine groundwater's changing role, from a freshwater storage reservoir that sustained the Everglades ecosystem during dry periods to a reservoir of increasingly degraded water quality. Although some of this degradation is attributable to increased discharge of deep saline groundwater, other mineral sources such as fertilizer additives and peat oxidation have made a greater contribution to water-quality changes that are altering mineral-sensitive biological communities. ?? Springer-Verlag 2008.

  3. Biological Mass Spectrometry and Shotgun Proteomics of Microbial Systems: Methods for studying microbial physiology from isolates to environmental communities

    SciTech Connect

    Dill, Brian; Young, Jacque C; Carey, Patricia A; Verberkmoes, Nathan C

    2010-01-01

    Microbial ecology is currently experiencing a renaissance spurred by the rapid development of molecular techniques and omics technologies in particular. As never before, these tools have allowed researchers in the field to produce a massive amount of information through in situ measurements and analysis of natural microbial communities, both vital approaches to the goal of unraveling the interactions of microbes with their environment and with one another. While genomics can provide information regarding the genetic potential of microbes, proteomics characterizes the primary end-stage product, proteins, thus conveying functional information concerning microbial activity. Advances in mass spectrometry instrumentation and methodologies, along with bioinformatic approaches, have brought this analytic chemistry technique to relevance in the biological realm due to its powerful applications in proteomics. Mass spectrometry-enabled proteomics, including bottom-up and top-down approaches, is capable of supplying a wealth of biologically-relevant information, from simple protein cataloging of the proteome of a microbial community to identifying post-translational modifications of individual proteins.

  4. Lagrangian evolution of DMS during the Southern Ocean gas exchange experiment: The effects of vertical mixing and biological community shift

    NASA Astrophysics Data System (ADS)

    Yang, M.; Archer, S. D.; Blomquist, B. W.; Ho, D. T.; Lance, V. P.; Torres, R. J.

    2013-12-01

    Concentrations of dimethylsulfide (DMS) and its precursor dimethylsulfoniopropionate (DMSP) are highly variable in time and space. What is driving the variability in DMS(P), and can those variability be explained by physical processes and changes in the biological community? During the Southern Ocean Gas Exchange Experiment (SO GasEx) in the austral fall of 2008, two 3He/SF6 labeled patches were created in the surface water. SF6 and DMS were surveyed continuously in a Lagrangian framework, while direct measurements of air-sea exchange further constrained the gas budgets. Turbulent diffusivity at the base of the mixed layer was estimated from SF6 profiles and used to calculate the vertical fluxes of DMS and nutrients. Increasing mixed layer nutrient concentrations due to mixing were associated with a shift in the phytoplankton community structure, which in turned likely affected the sulfur dynamics on timescales of days. DMS concentration as well as air-sea DMS flux appeared to be decoupled from the DMSP concentration, possibly due to grazing and bacterial DMS production. Contrary to expectations, in an environment with high winds and modest productivity, physical processes (air-sea exchange, photochemistry, vertical mixing) only accounted for a small fraction of DMS loss from the surface water. Among the DMS sinks, inferred biological consumption most likely dominated during SO GasEx.

  5. Configuration of biological wastewater treatment line and influent composition as the main factors driving bacterial community structure of activated sludge.

    PubMed

    Jaranowska, Paulina; Cydzik-Kwiatkowska, Agnieszka; Zielińska, Magdalena

    2013-07-01

    The structure of microbial consortia in wastewater treatment facilities is a resultant of environmental conditions created by the operational parameters of the purification process. In the research, activated sludge from nine Polish wastewater treatment plants (WWTPs) was investigated at a molecular level to determine the impact of the complexity of biological treatment line and the influent composition on the species structure and the diversity of bacterial consortia. The community fingerprints and technological data were subjected to the canonical correspondence and correlation analyses. The number of separated biological processes realized in the treatment line and the presence of industrial wastewater in the influent were the key factors determining the species structure of total and ammonia-oxidizing bacteria in biomass. The N2O-reducers community composition depended significantly on the design of the facility; the highest species richness of denitrifiers was noted in the WWTPs with separated denitrification tanks. The contribution of industrial streams to the inflow affected the diversity of total and denitrifying bacterial consortia and diminished the diversity of ammonia oxidizers. The obtained data are valuable for engineers since they revealed the main factors, including the design of wastewater treatment plant, influencing the microbial groups critical for the stability of purification processes. PMID:23397107

  6. Using Open-Book Tests to Strengthen the Study Skills of Community-College Biology Students

    ERIC Educational Resources Information Center

    Phillips, Gregory

    2006-01-01

    The author observed that students enrolled in first-year college biology courses often had weak study skills. This longitudinal study examined the use of open-book tests to encourage reading and to assess the improvement of college students' study skills. There was a statistically significant improvement from the initial test to the final test…

  7. Transforming Biology Curriculum at Navajo Community College to Include Navajo and Western Cultural Knowledge.

    ERIC Educational Resources Information Center

    Garrison, Edward R.

    1994-01-01

    Describes how a college teacher used Navajo traditional knowledge to rethink the teaching of college biology. Suggests that teachers intimidated by the intricate Dine Philosophy of Education may integrate Navajo knowledge into their courses through focused research guided by Navajo consultants. Includes five examples of redesigned curricula for…

  8. QUANTIFYING THE RELATIONSHIPS BETWEEN LANDSCAPE IMPERVIOUSNESS AND AQUATIC BIOLOGICAL COMMUNITY RESPONSE

    EPA Science Inventory

    The relationship between landscape impervious surface area and instream biological integrity was investigated for watersheds in the Eastern CornBelt Plains ecoregion (ECBP) in western Ohio. Landsat TM imagery was classified to create an impervious surface map for the ECBP. The ac...

  9. Compost and Biological Amendment Effects on Soilborne Disease and Soil Microbial Communities

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Effects of compost and biological amendments on soilborne diseases and microorganisms were assessed in field trials in northern Maine under both conventional and organic potato production practices. Three different biocontrol amendments, hypovirulent Rhizoctonia solani Rhs 1A1 (HvRs), Bacillus subti...

  10. Integrated Temporal and Spatial Studies of Biological Community Structure, Fluid Geochemistry, and Geological Perturbations on the East Pacific Rise

    NASA Astrophysics Data System (ADS)

    Shank, T. M.; Govenar, B.; Luther, G.; Lutz, R.; Vetriani, C.; Tolstoy, M.; Moore, T.; Nuzzio, D.

    2008-12-01

    Over the past 19 years, temporal and spatial changes in vent faunal community structure, fluid chemistry, and geological features have been tracked on the East Pacific Rise. Specifically, co-located studies of temporal and spatial changes within the Integrated Study Site region of the EPR have included the: 1) photographic documentation of more than 30 diffuse-flow habitats; 2) characterization of in situ fluid chemistry, temperature, and pH in these habitats; 3) characterization of basalts influenced by venting to enumerate microbial, meiofaunal, and metazoan colonists; 4) characterization of low-temperature hydrothermal fluids for microbial and chemical analyses; and 5) characterization of colonization substrates along with time-lapse camera systems and autonomous chemical and temperature sensors; and 6) characterization of seismic activity spatially targeted at these experimental locations. The goal of this work has been to address first order questions and the existence of correlative patterns among microbial communities, metazoan colonization, and fluid chemical composition- an essential prerequisite for further detailed studies of biological interactions and community dynamics at hydrothermal vents. These co-located activities, which now span a volcanic eruption, have yielded individual and interdependent datasets, which are currently at different stages of analyses and synthesis toward the examination of the interactions of subseafloor perturbations, fluid chemistry and microbes on faunal colonization. Ongoing analytical activities for integration and modeling include: 1) characterizing the composition of microbial colonizers; 2) assigning physiological and functional attributes of microbial colonizers; 3) comparing microbial community composition and physiology with patterns of metazoan colonization; 4) correlating relationships between microbial and metazoan colonization to relationships between fluid chemistry, pH, temperature; 5) relating results of

  11. Bridging levels of pharmaceuticals in river water with biological community structure in the Llobregat River basin (northeast Spain).

    PubMed

    Muñoz, Isabel; López-Doval, Julio C; Ricart, Marta; Villagrasa, Marta; Brix, Rikke; Geiszinger, Anita; Ginebreda, Antoni; Guasch, Helena; de Alda, M José López; Romaní, Anna M; Sabater, Sergi; Barceló, Damià

    2009-12-01

    A wide range of human pharmaceuticals are present at low concentrations in freshwater systems, particularly in sections of polluted river. These compounds show high biological activity, often associated with a high stability. These characteristics imply a potential impact of these substances on aquatic biota even when present at low environmental concentrations. Low flow conditions in Mediterranean rivers, most of which flow through densely populated areas and are subjected to intensive water use, increase the environmental risk of these emergent compounds. Here, we studied whether pharmaceuticals in river water affect the local benthic community structure (diatoms and invertebrates). For this purpose, we analyzed the occurrence of pharmaceuticals along the Llobregat River and examined the benthic community structure (diatoms and invertebrates) of this system. Some pharmaceutical products in the Llobregat River registered concentrations greater than those cited in the literature. Multivariate analyses revealed a potential causal association between the concentrations of some anti-inflammatories and beta-blockers and the abundance and biomass of several benthic invertebrates (Chironomus spp. and Tubifex tubifex). Further interpretation in terms of cause-and-effect relationships is discussed; however, it must be always taken with caution because other pollutants also may have significant contributions. Combined with further community experiments in the laboratory, our approach could be a desirable way to proceed in future risk management decisions. PMID:19908929

  12. Diazotrophic Community Structure and Function in Two Successional Stages of Biological Soil Crusts from the Colorado Plateau and Chihuahuan Desert

    USGS Publications Warehouse

    Yeager, C.M.; Kornosky, J.L.; Housman, D.C.; Grote, E.E.; Belnap, J.; Kuske, C.R.

    2004-01-01

    The objective of this study was to characterize the community structure and activity of N2-fixing microorganisms in mature and poorly developed biological soil crusts from both the Colorado Plateau and Chihuahuan Desert. Nitrogenase activity was approximately 10 and 2.5 times higher in mature crusts than in poorly developed crusts at the Colorado Plateau site and Chihuahuan Desert site, respectively. Analysis of nifH sequences by clone sequencing and the terminal restriction fragment length polymorphism technique indicated that the crust diazotrophic community was 80 to 90% heterocystous cyanobacteria most closely related to Nostoc spp. and that the composition of N2-fixing species did not vary significantly between the poorly developed and mature crusts at either site. In contrast, the abundance of nifH sequences was approximately 7.5 times greater (per microgram of total DNA) in mature crusts than in poorly developed crusts at a given site as measured by quantitative PCR. 16S rRNA gene clone sequencing and microscopic analysis of the cyanobacterial community within both crust types demonstrated a transition from a Microcoleus vaginatus-dominated, poorly developed crust to mature crusts harboring a greater percentage of Nostoc and Scytonema spp. We hypothesize that ecological factors, such as soil instability and water stress, may constrain the growth of N2-fixing microorganisms at our study sites and that the transition to a mature, nitrogen-producing crust initially requires bioengineering of the surface microenvironment by Microcoleus vaginatus.

  13. Common and distinguishing features of the bacterial and fungal communities in biological soil crusts and shrub root zone soils

    USGS Publications Warehouse

    Steven, Blaire; Gallegos-Graves, La Verne; Yeager, Chris; Belnap, Jayne; Kuske, Cheryl R.

    2013-01-01

    Soil microbial communities in dryland ecosystems play important roles as root associates of the widely spaced plants and as the dominant members of biological soil crusts (biocrusts) colonizing the plant interspaces. We employed rRNA gene sequencing (bacterial 16S/fungal large subunit) and shotgun metagenomic sequencing to compare the microbial communities inhabiting the root zones of the dominant shrub, Larrea tridentata (creosote bush), and the interspace biocrusts in a Mojave desert shrubland within the Nevada Free Air CO2 Enrichment (FACE) experiment. Most of the numerically abundant bacteria and fungi were present in both the biocrusts and root zones, although the proportional abundance of those members differed significantly between habitats. Biocrust bacteria were predominantly Cyanobacteria while root zones harbored significantly more Actinobacteria and Proteobacteria. Pezizomycetes fungi dominated the biocrusts while Dothideomycetes were highest in root zones. Functional gene abundances in metagenome sequence datasets reflected the taxonomic differences noted in the 16S rRNA datasets. For example, functional categories related to photosynthesis, circadian clock proteins, and heterocyst-associated genes were enriched in the biocrusts, where populations of Cyanobacteria were larger. Genes related to potassium metabolism were also more abundant in the biocrusts, suggesting differences in nutrient cycling between biocrusts and root zones. Finally, ten years of elevated atmospheric CO2 did not result in large shifts in taxonomic composition of the bacterial or fungal communities or the functional gene inventories in the shotgun metagenomes.

  14. Metagenomic characterization of viral communities in corals: mining biological signal from methodological noise.

    PubMed

    Wood-Charlson, Elisha M; Weynberg, Karen D; Suttle, Curtis A; Roux, Simon; van Oppen, Madeleine J H

    2015-10-01

    Reef-building corals form close associations with organisms from all three domains of life and therefore have many potential viral hosts. Yet knowledge of viral communities associated with corals is barely explored. This complexity presents a number of challenges in terms of the metagenomic assessments of coral viral communities and requires specialized methods for purification and amplification of viral nucleic acids, as well as virome annotation. In this minireview, we conduct a meta-analysis of the limited number of existing coral virome studies, as well as available coral transcriptome and metagenome data, to identify trends and potential complications inherent in different methods. The analysis shows that the method used for viral nucleic acid isolation drastically affects the observed viral assemblage and interpretation of the results. Further, the small number of viral reference genomes available, coupled with short sequence read lengths might cause errors in virus identification. Despite these limitations and potential biases, the data show that viral communities associated with corals are diverse, with double- and single-stranded DNA and RNA viruses. The identified viruses are dominated by double-stranded DNA-tailed bacteriophages, but there are also viruses that infect eukaryote hosts, likely the endosymbiotic dinoflagellates, Symbiodinium spp., host coral and other eukaryotes in close association. PMID:25708646

  15. Physical-chemical determinant properties of biological communities in continental semi-arid waters.

    PubMed

    da Rocha, Francisco Cleiton; de Andrade, Eunice Maia; Lopes, Fernando Bezerra; de Paula Filho, Francisco José; Filho, José Hamilton Costa; da Silva, Merivalda Doroteu

    2016-08-01

    Throughout human history, water has undergone changes in quality. This problem is more serious in dry areas, where there is a natural water deficit due to climatic factors. The aims of this study, therefore, were (i) to verify correlations between physical attributes, chemical attributes and biological metrics and (ii) from the biological attributes, to verify the similarity between different points of a body of water in a tropical semi-arid region. Samples were collected every 2 months, from July 2009 to July 2011, at seven points. Four physical attributes, five chemical attributes and four biological metrics were investigated. To identify the correlations between the physicochemical properties and the biological metrics, hierarchical cluster analysis (HCA) and canonical correlation analysis (CCA) were applied. Nine classes of phytoplankton were identified, with the predominance of species of cyanobacteria, and ten families of macroinvertebrates. The use of HCA resulted in the formation of three similar groups, showing that it was possible to reduce the number of sampling points when monitoring water quality with a consequent reduction in cost. Group I was formed from the waters at the high end of the reservoir (points P1, P2 and P3), group II by the waters from the middle third (points P4 and P5), and group III by the waters from the lower part of the reservoir (points P6 and P7). Richness of the phytoplanktons Cyanophyceae, Chorophyceae and Bacillariophyceae was the attribute which determined dissimilarity in water quality. Using CCA, it was possible to identify the spatial variability of the physicochemical attributes (TSS, TKN, nitrate and total phosphorus) that most influence the metrics of the macroinvertebrates and phytoplankton present in the water. Low macroinvertebrate diversity, with a predominance of indicator families for deterioration in water quality, and the composition of phytoplankton showing a predominance of cyanobacteria, suggests greater

  16. RIA use in a community orthopedic trauma practice: applying technology, respecting biology.

    PubMed

    Cobbs, Kenneth F

    2010-11-01

    The RIA (Reamer Irrigator Aspirator) device is an incredibly powerful tool. It can be used to obtain biologically active tissue for healing at local or distant sites. Additionally, it can be used to lower the negative bioburden of disease and even to assist in diagnosis. As with any powerful tool, it should be used with detailed pre-planning and great respect. Once properly understood and implemented, the device can be used in many ways: PMID:21144934

  17. Learning-style preferences of Latino/Hispanic community college students enrolled in an introductory biology course

    NASA Astrophysics Data System (ADS)

    Sarantopoulos, Helen D.

    Purpose. The purpose of this study was to identify, according to the Productivity Environment Preference Survey (PEPS) instrument, which learning-style domains (environmental, emotional, sociological, and physiological) were favored among Latino/Hispanic community college students enrolled in introductory biology classes in a large, urban community college. An additional purpose of this study was to determine whether statistically significant differences existed between the learning-style preferences and the demographic variables of age, gender, number of prior science courses, second language learner status, and earlier exposure to scientific information. Methodology. The study design was descriptive and ex post facto. The sample consisted of a total of 332 Latino/Hispanic students enrolled in General Biology 3. Major findings. The study revealed that Latino/Hispanic students enrolled in introductory biology at a large urban community college scored higher for the learning preference element of structure. Students twenty-five years and older scored higher for the learning preference elements of light, design, persistence, responsibility, and morning time (p <= 0.05). Females scored higher in the preference elements of (a) light, (b) temperature (warmth), (c) authority and (d) auditory (p <= 0.05). Significant differences were found for the elements of sound, warmth, motivation, several ways, and intake between the students with no prior science coursework and those who completed more than one (p <= 0.05). No significant learning-style preferences were found between second English language learners and those who learned English as their primary language (p <= 0.05). Students who frequently read science articles scored higher for the elements of motivation, persistence, responsibility, and tactile (p <= 0.05). Conclusions and recommendations. The conclusions were that Latino/Hispanic students need detailed guidance and clearly stated course objectives. The

  18. Modern and fossilized biological communities from sediments of Bolshoy Harbei lake (Bolshezemelskaya tundra, Russia) and their response to climate change

    NASA Astrophysics Data System (ADS)

    Tumanov, Oleg; Nazarova, Larisa; Fefilova, Elena; Baturina, Maria; Loskutova, Olga; Frolova, Larisa; Palagushkina, Olga

    2013-04-01

    High-altitude regions are subjected to the threats of global warming. During the last decade the depth of seasonal melting of permafrost in Northern Russia, significantly increased. Investigation of lake sediments from polar regions has an extreme importance for understanding of the modern environmental processes and their influence on northern ecosystems and biological diversity of these regions. Invertebrate communities are used for diagnostic of lake ecosystems because they have a great sensitivity to climatic changes (Andronnikova, 1996; Lazareva, 2008; O'Brien et al., 2005). The data can be used as well as a basis for inference models for reconstruction of the paleoclimatic conditions. Chironomid-based, Cladocera-based and diatom models have successfully been developed (Nazarova et al., 2008, 2011; Self et al., 2011) and can be used for precise paleotemperature reconstructions (Kienast et al., 2011). In summer 2012, we investigated complex of Kharbei lakes, located in the interfluve of Korotaiha and Bolshaya Rogovaya rivers in the east side of Bolshezemelskaya tundra, Russia (67°33'22″ N, 62°53'23″ E). Six different lakes were investigated using modern hydrobiological and palaeoecological methods. In total 9 cores were obtained, cut, dated and further investigated using sedimenthological, geochemical, and paleobiological methods. The standard hydrobiological methods have shown that the modern zooplankton communities did not change significantly during the last 40 years. Taxonomic composition and structure of planktonic communities didn't change, except for appearance of crustaceans Polyarthra euryptera and Daphnia cucullata. In planktonic communities of Bolshoy Harbei lake we revealed 39 species and forms of Rotifera, 19 - Cladocera and 11 - Copepoda. In zoobenthic communities we registered 24 taxonomical groups characteristic for large tundra lakes of the North East of Russia. Chironomids and Oligochaeta are dominant groups of invertebrates. 103 taxa of

  19. Mass wasting, methane venting, and biological communities on the Mendocino transform fault

    NASA Astrophysics Data System (ADS)

    Stakes, Debra S.; Trehu, Anne M.; Goffredi, Shana K.; Naehr, Thomas H.; Duncan, Robert A.

    2002-05-01

    Chemosynthetic cold-seep vestimentiferan tubeworms and vesicomyid clams inhabiting oceanic basaltic rock have been discovered on the Gorda Escarpment sector of the Mendocino transform fault 73 km west of Cape Mendocino, northern California. The sparse cold-seep animals are “biomarkers” that identify zones of focused fluid venting from a methane gas horizon seismically imaged as a bottom-simulating reflector (BSR) within sediments on the southern flank of the escarpment. This is the first example of a methane-based cold-seep community on exposed oceanic basement rock within an area dominated by transform tectonics. This discovery extends the range of known environments in which the subsurface flow and venting of methane-rich fluids are linked both with geological activity and chemosynthetic communities. Observations by remotely operated vehicle of the distribution of the animals, sediment, basaltic talus, and basement outcrop delineate a large slump headscarp that channels subsurface fluid. Seismic surveys of the southern flank of the Mendocino transform fault (the Vizcaino block) define a BSR hosted in the thick sedimentary sequence that projects to the wall of the Gorda Escarpment at the same depth as the chemosynthetic community. The well-defined BSR in the marine sediment of the Vizcaino block results from an accumulation of methane gas possibly capped by methane hydrate. The isotopic composition of Mg-calcite found along the headscarp (δ13C = -65‰; δ18O = 4.8‰) is consistent with fluids derived from dissociated methane hydrate. We propose that the tectonic uplift along this transform margin has resulted in the lateral, northward movement of methane from the Vizcaino sedimentary sequence to the east-trending wall of the north-facing Gorda Escarpment.

  20. Climate-driven regime shifts in the biological communities of arctic lakes

    PubMed Central

    Smol, John P.; Wolfe, Alexander P.; Birks, H. John B.; Douglas, Marianne S. V.; Jones, Vivienne J.; Korhola, Atte; Pienitz, Reinhard; Rühland, Kathleen; Sorvari, Sanna; Antoniades, Dermot; Brooks, Stephen J.; Fallu, Marie-Andrée; Hughes, Mike; Keatley, Bronwyn E.; Laing, Tamsin E.; Michelutti, Neal; Nazarova, Larisa; Nyman, Marjut; Paterson, Andrew M.; Perren, Bianca; Quinlan, Roberto; Rautio, Milla; Saulnier-Talbot, Émilie; Siitonen, Susanna; Solovieva, Nadia; Weckström, Jan

    2005-01-01

    Fifty-five paleolimnological records from lakes in the circumpolar Arctic reveal widespread species changes and ecological reorganizations in algae and invertebrate communities since approximately anno Domini 1850. The remoteness of these sites, coupled with the ecological characteristics of taxa involved, indicate that changes are primarily driven by climate warming through lengthening of the summer growing season and related limnological changes. The widespread distribution and similar character of these changes indicate that the opportunity to study arctic ecosystems unaffected by human influences may have disappeared. PMID:15738395

  1. Nitric oxide and nitrous oxide turnover in natural and engineered microbial communities: biological pathways, chemical reactions, and novel technologies

    PubMed Central

    Schreiber, Frank; Wunderlin, Pascal; Udert, Kai M.; Wells, George F.

    2012-01-01

    Nitrous oxide (N2O) is an environmentally important atmospheric trace gas because it is an effective greenhouse gas and it leads to ozone depletion through photo-chemical nitric oxide (NO) production in the stratosphere. Mitigating its steady increase in atmospheric concentration requires an understanding of the mechanisms that lead to its formation in natural and engineered microbial communities. N2O is formed biologically from the oxidation of hydroxylamine (NH2OH) or the reduction of nitrite (NO−2) to NO and further to N2O. Our review of the biological pathways for N2O production shows that apparently all organisms and pathways known to be involved in the catabolic branch of microbial N-cycle have the potential to catalyze the reduction of NO−2 to NO and the further reduction of NO to N2O, while N2O formation from NH2OH is only performed by ammonia oxidizing bacteria (AOB). In addition to biological pathways, we review important chemical reactions that can lead to NO and N2O formation due to the reactivity of NO−2, NH2OH, and nitroxyl (HNO). Moreover, biological N2O formation is highly dynamic in response to N-imbalance imposed on a system. Thus, understanding NO formation and capturing the dynamics of NO and N2O build-up are key to understand mechanisms of N2O release. Here, we discuss novel technologies that allow experiments on NO and N2O formation at high temporal resolution, namely NO and N2O microelectrodes and the dynamic analysis of the isotopic signature of N2O with quantum cascade laser absorption spectroscopy (QCLAS). In addition, we introduce other techniques that use the isotopic composition of N2O to distinguish production pathways and findings that were made with emerging molecular techniques in complex environments. Finally, we discuss how a combination of the presented tools might help to address important open questions on pathways and controls of nitrogen flow through complex microbial communities that eventually lead to N2O build

  2. Spatial variation in the littoral vertebrate community of a reservoir relative to physical and biological gradients

    PubMed Central

    Soski, Jessica J.; Roosenburg, Willem M.

    2014-01-01

    Reservoirs possess gradients in conditions and resources along their long (deep-shallow) axis, but the response of littoral vertebrates (fish and turtles) to these gradients is poorly understood. We have quantified the littoral vertebrate communities throughout a small reservoir in Southeastern Ohio during July and August using traps, and related community composition to environmental variables using NMDS ordination. Ordination revealed that fish and turtles were broadly separated in ordination space, and three distinctly different environmental gradients were significantly associated with the underlying observed species abundances. Observed turtle abundance was explained by measurements of bathymetry, turbidity, and benthic resources, but none of these environmental variables were a reliable predictor of observed fish abundance. Temperature was a poor predictor of observed abundance for both fish and turtles independently, but when fish and turtles were considered together, it became apparent that there were cold areas of the reservoir where observed fish and turtle abundances were different than in other areas of the reservoir. These results suggest that the predictor (environmental) variables we used were appropriate for investigating turtle ecology in reservoirs, but that observed fish abundance is mediated by factors that were not modeled. The efficacy of using traps, the ecological implications of considering fish and turtles together as sympatric and potentially competing species, and directions for future study are discussed. PMID:25538870

  3. Biologic interactions determining geographic range size: a one species response to phylogenetic community structure

    PubMed Central

    Herrera-Alsina, Leonel; Villegas-Patraca, Rafael

    2014-01-01

    Range size variation in closely related species suggests different responses to biotic and abiotic heterogeneity across large geographic regions. Species turnover generates a wide spectrum of species assemblages, resulting in different competition intensities among taxa, creating restrictions as important as environmental constraints. We chose to adopt the widely used phylogenetic relatedness (NRI) measurement to define a metric that depicts competition strength (via phylogenetic similarity), which one focal species confronts in its environment. This new approach (NRIfocal) measures the potential of the community structure effect over performance of a single species. We chose two ecologically similar Peucaea sparrows, which co-occur and have highly dissimilar range size to test whether the population response to competition intensity is different between species. We analyzed the correlation between both Peucaea species population sizes and NRIfocal using data from point counts. Results indicated that the widespread species population size was not associated with NRIfocal, whereas the population of restricted-sized species exhibited a negative relationship with competition intensity. Consequently, a species' sensitivity to competition might be a limiting factor to range expansion, which provides new insights into geographic range analysis and community ecology. PMID:24772275

  4. Parasitoid nutritional ecology in a community context: the importance of honeydew and implications for biological control.

    PubMed

    Tena, Alejandro; Wäckers, Felix L; Heimpel, George E; Urbaneja, Alberto; Pekas, Apostolos

    2016-04-01

    One focus of conservation biological control studies has been to improve the nutritional state and fitness of parasitoids by adding nectar and artificial sugars to agroecosystems. This approach has largely overlooked the presence of honeydew, which is likely the primary carbohydrate source available to parasitoids in many agroecosystems. Over the last decade, it has been demonstrated that parasitoids often utilize this sugar source and there is evidence that honeydew can indirectly impact the population dynamics of herbivores through its nutritional value for parasitoids. The consumption of honeydew by parasitoids can shape direct and indirect interactions with other arthropods. The strength of these effects will depend on: first, parasitoid biology, second, the presence of other sugar sources (mainly nectar), third, the quality and quantity of the honeydew, and fourth, the presence and competitive strength of other honeydew consumers such as ants. The combination of these four factors is expected to result in distinct scenarios that should be analyzed for each agroecosystem. This analysis can reveal opportunities to increase the biocontrol services provided by parasitoids. Moreover, honeydew can be a resource-rich habitat for insect pathogens; or contain plant secondary chemicals sequestered by hemipterans or systemic insecticides toxic for the parasitoid. Their presence and effect on parasitoid fitness will need to be addressed in future research. PMID:27436654

  5. Development of a Knowledgebase to Integrate, Analyze, Distribute, and Visualize Microbial Community Systems Biology Data

    SciTech Connect

    Banfield, Jillian; Thomas, Brian

    2015-01-15

    We have developed a flexible knowledgebase system, ggKbase, (http://gg.berkeley.edu), to enable effective data analysis and knowledge generation from samples from which metagenomic and other ‘omics’ data are obtained. Within ggKbase, data can be interpreted, integrated and linked to other databases and services. Sequence information from complex metagenomic samples can be quickly and effectively resolved into genomes and biologically meaningful investigations of an organism’s metabolic potential can then be conducted. Critical features make analyses efficient, allowing analysis of hundreds of genomes at a time. The system is being used to support research in multiple DOE-relevant systems, including the LBNL SFA subsurface science biogeochemical cycling research at Rifle, Colorado. ggKbase is supporting the research of a rapidly growing group of users. It has enabled studies of carbon cycling in acid mine drainage ecosystems, biologically-mediated transformations in deep subsurface biomes sampled from mines and the north slope of Alaska, to study the human microbiome and for laboratory bioreactor-based remediation investigations.

  6. Biological affinities and regional microevolution among pre-Hispanic communities of Colombia's Northern Andes.

    PubMed

    Rodríguez Flórez, C D; Colantonio, S E

    2015-01-01

    Dental non-metric data were used to examine the biological continuity of pre-Hispanic peoples of Colombia's Northern Andes, including highland, lowland and coastal peoples. This report contributes to studies regarding the peopling of South America by establishing a benchmark comparison that includes pre-Hispanic populations of the Northern Andes. The sample consisted of a total of 583 individuals from 56 cemeteries ranging in time from the Early Holocene (10,000 BP) to the Final Late Holocene (500 BP). Permanent dentitions from individuals between 5 and 40 years of age were scored for 87 dental traits based on the ASUDAS. A divergence matrix was programmed using the Smith's Mean Measure of Divergence equation (MMD). Bartlett's adjustment and Ascombe transformation were considered into MMD calculations. Principal Coordenate analysis was applied based on MMD matrix scores. A clear group was found that associated Initial Late Holocene samples with Final Late Holocene samples. Early Holocene samples are very different to that, and Middle Holocene samples show as morphologically intermediate series. A comparison of the frequencies by time and period showed that a limited biological continuity existed. Interbreeding among initial populations of the same regions is expressed in similar frequencies of dental traits within Early Holocene and Middle Holocene samples. Early Holocene samples did not match with Sinodont pattern according to discriminant function analysis. These findings help us to better understand the settlement process of human groups in the Northern Andes and its relationship with migratory movements in South America. PMID:25807169

  7. Association of a complement receptor 1 gene variant with baseline erythrocyte sedimentation rate levels in patients starting anti-TNF therapy in a UK rheumatoid arthritis cohort: results from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate cohort

    PubMed Central

    Bluett, J; Ibrahim, I; Plant, D; Hyrich, K L; Morgan, A W; Wilson, A G; Isaacs, J D; Gaston, H; Mulherin, D; Price, T; Sheeran, T; Chalam, V; Baskar, S; Emery, P; Morgan, A; Buch, M; Bingham, S; O'Reilly, S; Badcock, L; Regan, M; Ding, T; Deighton, C; Summers, G; Raj, N; Stevens, R; Williams, N; Isaacs, J; Platt, P; Walker, D; Kay, L; Griffiths, B; Ng, W-F; Peterson, P; Lorenzi, A; Foster, H; Friswell, M; Thompson, B; Lee, M; Griffiths, I; Hassell, A; Dawes, P; Dowson, C; Kamath, S; Packham, J; Shadforth, M; Brownfield, Ann; Williams, R; Mukhtyar, C; Harrison, B; Snowden, N; Naz, S; Ledingham, J; Hull, R; McCrae, F; Thomas, A; Min, S Young; Shaban, R; Wong, E; Kelly, C; Heycock, C; Hamilton, J; Saravanan, V; Wilson, G; Bax, D; Dunkley, L; Akil, M; Tattersall, R; Kilding, R; Till, S; Boulton, J; Tait, T; Bukhari, M; Halsey, J; Ottewell, L; Buckley, C; Situnayake, D; Carruthers, D; Grindulis, K; Khatack, F; Elamanchi, S; Raza, K; Filer, A; Jubb, R; Abernathy, R; Plant, M; Pathare, S; Clarke, F; Tuck, S; Fordham, J; Paul, A; Bridges, M; Hakim, A; O'Reilly, D; Rajagopal, V; Bhagat, S; Edwards, C; Prouse, P; Moitra, R; Shawe, D; Bamji, A; Klimiuk, P; Bowden, A; Mitchell, W; Bruce, I; Barton, A; Gorodkin, R; Ho, P; Hyrich, K; Dixon, W; Rai, A; Kitas, G; Erb, N; Klocke, R; Douglas, K; Pace, A; Sandhu, R; Whallett, A; Birrell, F; Allen, M; Chaudhuri, K; Chattopadhyay, C; McHale, J; Jones, A; Gupta, A; Pande, I; Gaywood, I; Lanyon, P; Courtney, P; Doherty, M; Chinoy, H; O'Neill, T; Herrick, A; Jones, A; Cooper, R; Bucknall, R; Marguerie, C; Rigby, S; Dunn, N; Green, S; Al-Ansari, A; Webber, S; Hopkinson, N; Dunne, C; Quilty, B; Szebenyi, B; Green, M; Quinn, M; Isdale, A; Brown, A; Saleem, B; Samanta, A; Sheldon, P; Hassan, W; Francis, J; Kinder, A; Neame, R; Moorthy, A; Al-Allaf, W; Taggart, A; Fairburn, K; McKenna, F; Green, M; Gough, A; Lawson, C; Piper, M; Korendowych, E; Jenkinson, T; Sengupta, R; Bhalla, A; McHugh, N; Bond, Debbie; Luqmani, R; Bowness, B; Wordsworth, P; David, J; Smith, W; Mewar, D; Tunn, E; Nelson, K; Kennedy, T; Nixon, J; Woolf, A; Davis, M; Hutchinson, D; Endean, A; Coady, D; Wright, D; Morley, C; Raftery, G; Bracewell, C; Kidd, L; Abbas, I; Filer, C; Kallarackal, G; Barton, A

    2014-01-01

    Eligibility for anti-tumour necrosis factor (TNF) therapy in most European countries is restricted to severe, active rheumatoid arthritis (RA). The DAS28 score is a marker of disease severity and incorporates one of two inflammatory markers, erythrocyte sedimentation rate (ESR) or C-reactive protein. We aimed to determine the relation between genetic variants known to affect ESR and levels of ESR in patients with active RA. DNA samples were genotyped for four single-nucleotide polymorphisms (SNPs) rs7527798 (CR1L), rs6691117 (CR1), rs10903129 (TMEM57) and rs1043879 (C1orf63). The association between SNPs and baseline ESR, baseline DAS28-ESR, and change in DAS28-ESR was evaluated. Baseline ESR was significantly associated with CR1 rs6691117 genotype (P=0.01). No correlation was identified between baseline DAS28-ESR or change in DAS28-ESR. In conclusion, genetic variation in the gene encoding CR1 may alter ESR levels but not DAS28-ESR, indicating no adjustment for CR1 genotype is required in the assessment of patients with severe active RA. PMID:23856853

  8. Association of a complement receptor 1 gene variant with baseline erythrocyte sedimentation rate levels in patients starting anti-TNF therapy in a UK rheumatoid arthritis cohort: results from the Biologics in Rheumatoid Arthritis Genetics and Genomics Study Syndicate cohort.

    PubMed

    Bluett, J; Ibrahim, I; Plant, D; Hyrich, K L; Morgan, A W; Wilson, A G; Isaacs, J D; Barton, A

    2014-04-01

    Eligibility for anti-tumour necrosis factor (TNF) therapy in most European countries is restricted to severe, active rheumatoid arthritis (RA). The DAS28 score is a marker of disease severity and incorporates one of two inflammatory markers, erythrocyte sedimentation rate (ESR) or C-reactive protein. We aimed to determine the relation between genetic variants known to affect ESR and levels of ESR in patients with active RA. DNA samples were genotyped for four single-nucleotide polymorphisms (SNPs) rs7527798 (CR1L), rs6691117 (CR1), rs10903129 (TMEM57) and rs1043879 (C1orf63). The association between SNPs and baseline ESR, baseline DAS28-ESR, and change in DAS28-ESR was evaluated. Baseline ESR was significantly associated with CR1 rs6691117 genotype (P=0.01). No correlation was identified between baseline DAS28-ESR or change in DAS28-ESR. In conclusion, genetic variation in the gene encoding CR1 may alter ESR levels but not DAS28-ESR, indicating no adjustment for CR1 genotype is required in the assessment of patients with severe active RA. PMID:23856853

  9. Hydro-acoustic remote sensing of benthic biological communities on the shallow South East Australian continental shelf

    NASA Astrophysics Data System (ADS)

    Rattray, Alex; Ierodiaconou, Daniel; Laurenson, Laurie; Burq, Shoaib; Reston, Marcus

    2009-09-01

    Information regarding the composition and extent of benthic habitats on the South East Australian continental shelf is limited. In this habitat mapping study, multibeam echosounder (MBES) data are integrated with precisely geo-referenced video ground-truth data to quantify benthic biotic communities at Cape Nelson, Victoria, Australia. Using an automated decision tree classification approach, 5 representative biotic groups defined from video analysis were related to hydro-acoustically derived variables in the Cape Nelson survey area. Using a combination of multibeam bathymetry, backscatter and derivative products produced highest overall accuracy (87%) and kappa statistic (0.83). This study demonstrates that decision tree classifiers are capable of integrating variable data types for mapping distributions of benthic biological assemblages, which are important in maintaining biodiversity and other system services in the marine environment.

  10. Community proteogenomics highlights microbial strain-variant protein expression within activated sludge performing enhanced biological phosphorus removal.

    SciTech Connect

    Wilmes, P; Andersson, Anders F.; Lefsrud, Mark G; Wexler, Margaret; Shah, Manesh B; Zhang, B; Hettich, Robert {Bob} L; Bond, P. L.; Verberkmoes, Nathan C; Banfield, Jillian F.

    2008-01-01

    Enhanced biological phosphorus removal (EBPR) selects for polyphosphate accumulating organisms to achieve phosphate removal from wastewater. We used highresolution community proteomics to identify key metabolic pathways in "Candidatus Accumulibacter phosphatis"-mediated EBPR and to evaluate the contributions of co- 5 existing strains within the dominant population. Results highlight the importance of denitrification, fatty acid cycling and the glyoxylate bypass in EBPR. Despite overall strong similarity in protein profiles under anaerobic and aerobic conditions, fatty acid degradation proteins were more abundant during the anaerobic phase. By comprehensive genome-wide alignment of orthologous proteins, we uncovered strong 10 functional partitioning for enzyme variants involved in both core-metabolism and EBPR-specific pathways among the dominant strains. These findings emphasize the importance of genetic diversity in maintaining the stable performance of EBPR systems and demonstrate the power of integrated cultivation-independent genomics and proteomics for analysis of complex biotechnological systems.

  11. Icecolors`93: Biological weighting function for the ultraviolet inhibition of carbon fixation in a natural antarctic phytoplankton community

    SciTech Connect

    Boucher, N.; Prezelin, B.B.; Evens, T.

    1994-12-31

    The goals of the Icecolors 1993 expedition were (1) to develop a space/time climatology of incident and penetrating spectral irradiance for the southern oceans, (2) to quantify the ultraviolet (UV) dependency of primary production for pelagic and substrate-associated antarctic phytoplankton communities, and (3) to determine the UV inhibition effects on key target sites. The study was conducted at Palmer Station, Antarctica, prior to the opening of the ozone `hole` and during the onset of depletion of ozone, the most severe ever recorded over the Antarctic Peninsula. This paper discusses results from an experiment designed to estimate a biological weight function for primary production inhibition in Antarctic phytoplankton under natural irradiance. The newly derived function is presented and it is shown that the sensitivity of in situ phytoplankton to ambient UV-B at the end of winter was greater than that measured under artificial light conditions for temperate marine phytoplankton and terrestrial plants. 18 refs., 3 figs.

  12. Some Like it High! Phylogenetic Diversity of High-Elevation Cyanobacterial Community from Biological Soil Crusts of Western Himalaya.

    PubMed

    Čapková, Kateřina; Hauer, Tomáš; Řeháková, Klára; Doležal, Jiří

    2016-01-01

    The environment of high-altitudinal cold deserts of Western Himalaya is characterized by extensive development of biological soil crusts, with cyanobacteria as dominant component. The knowledge of their taxonomic composition and dependency on soil chemistry and elevation is still fragmentary. We studied the abundance and the phylogenetic diversity of the culturable cyanobacteria and eukaryotic microalgae in soil crusts along altitudinal gradients (4600-5900 m) at two sites in the dry mountains of Ladakh (SW Tibetan Plateau and Eastern Karakoram), using both microscopic and molecular approaches. The effects of environmental factors (altitude, mountain range, and soil physico-chemical parameters) on the composition and biovolume of phototrophs were tested by multivariate redundancy analysis and variance partitioning. Both phylogenetic diversity and composition of morphotypes were similar between Karakorum and Tibetan Plateau. Phylogenetic analysis of 16S rRNA gene revealed strains belonging to at least five genera. Besides clusters of common soil genera, e.g., Microcoleus, Nodosilinea, or Nostoc, two distinct clades of simple trichal taxa were newly discovered. The most abundant cyanobacterial orders were Oscillatoriales and Nostacales, whose biovolume increased with increasing elevation, while that of Chroococales decreased. Cyanobacterial species richness was low in that only 15 morphotypes were detected. The environmental factors accounted for 52 % of the total variability in microbial data, 38.7 % of which was explained solely by soil chemical properties, 14.5 % by altitude, and 8.4 % by mountain range. The elevation, soil phosphate, and magnesium were the most important predictors of soil phototrophic communities in both mountain ranges despite their different bedrocks and origin. The present investigation represents a first record on phylogenetic diversity of the cyanobacterial community of biological soil crusts from Western Himalayas and first record

  13. Effects of Altered Temperature & Precipitation on Soil Bacterial & Microfaunal Communities as Mediated by Biological Soil Crusts

    SciTech Connect

    Neher, Deborah A.

    2004-08-31

    With increased temperatures in our original pot study we observed a decline in lichen/moss crust cover and with that a decline in carbon and nitrogen fixation, and thus a probable decline of C and N input into crusts and soils. Soil bacteria and fauna were affected negatively by increased temperature in both light and dark crusts, and with movement from cool to hot and hot to hotter desert climates. Crust microbial biomass and relative abundance of diazotrophs was reduced greatly after one year, even in pots that were not moved from their original location, although no change in diazotroph community structure was observed. Populations of soil fauna moved from cool to hot deserts were affected more negatively than those moved from hot to hotter deserts.

  14. Biological community structure on patch reefs in Biscayne National Park, FL, USA.

    PubMed

    Kuffner, Ilsa B; Grober-Dunsmore, Rikki; Brock, John C; Hickey, T Don

    2010-05-01

    Coral reef ecosystem management benefits from continual quantitative assessment of the resources being managed, plus assessment of factors that affect distribution patterns of organisms in the ecosystem. In this study, we investigate the relationships among physical, benthic, and fish variables in an effort to help explain the distribution patterns of organisms on patch reefs within Biscayne National Park, FL, USA. We visited a total of 196 randomly selected sampling stations on 12 shallow (<10 m) patch reefs and measured physical variables (e.g., substratum rugosity, substratum type) and benthic and fish community variables. We also incorporated data on substratum rugosity collected remotely via airborne laser surveying (Experimental Advanced Airborne Research Lidar-EAARL). Across all stations, only weak relationships were found between physical, benthic cover, and fish assemblage variables. Much of the variance was attributable to a "reef effect," meaning that community structure and organism abundances were more variable at stations among reefs than within reefs. However, when the reef effect was accounted for and removed statistically, patterns were detected. Within reefs, juvenile scarids were most abundant at stations with high coverage of the fleshy macroalgae Dictyota spp., and the calcified alga Halimeda tuna was most abundant at stations with low EAARL rugosity. Explanations for the overwhelming importance of "reef" in explaining variance in our dataset could include the stochastic arrangement of organisms on patch reefs related to variable larval recruitment in space and time and/or strong historical effects due to patchy disturbances (e.g., hurricanes, fishing), as well as legacy effects of prior residents ("priority" effects). PMID:19399634

  15. Biological Filtration Limits Carbon Availability and Affects Downstream Biofilm Formation and Community Structure†

    PubMed Central

    Pang, Chee Meng; Liu, Wen-Tso

    2006-01-01

    Carbon removal strategies have gained popularity in the mitigation of biofouling in water reuse processes, but current biofilm-monitoring practices based on organic-carbon concentrations may not provide an accurate representation of the in situ biofilm problem. This study evaluated a submerged microtiter plate assay for direct and rapid monitoring of biofilm formation by subjecting the plates to a continuous flow of either secondary effluent (SE) or biofilter-treated secondary effluent (BF). This method was very robust, based on a high correlation (R2 = 0.92) between the biomass (given by the A600 in the microtiter plate assay) and the biovolume (determined from independent biofilms developed on glass slides under identical conditions) measurements, and revealed that the biomasses in BF biofilms were consistently lower than those in SE biofilms. The influence of the organic-carbon content on the biofilm community composition and succession was further evaluated using molecular tools. Terminal restriction fragment length polymorphism analysis of 16S rRNA genes revealed a group of pioneer colonizers, possibly represented by Sphingomonadaceae and Caulobacter organisms, to be common in both SE and BF biofilms. However, differences in organic-carbon availabilities in the two water samples eventually led to the selection of distinct biofilm communities. Alphaproteobacterial populations were confirmed by fluorescence in situ hybridization to be enriched in SE biofilms, while Betaproteobacteria were dominant in BF biofilms. Cloning analyses further demonstrated that microorganisms adapted for survival under low-substrate conditions (e.g., Aquabacterium, Caulobacter, and Legionella) were preferentially selected in the BF biofilm, suggesting that carbon limitation strategies may not achieve adequate biofouling control in the long run. PMID:16957184

  16. Biological community structure on patch reefs in Biscayne National Park, FL, USA

    USGS Publications Warehouse

    Kuffner, Ilsa B.; Grober-Dunsmore, Rikki; Brock, John C.; Hickey, T. Don

    2010-01-01

    Coral reef ecosystem management benefits from continual quantitative assessment of the resources being managed, plus assessment of factors that affect distribution patterns of organisms in the ecosystem. In this study, we investigate the relationships among physical, benthic, and fish variables in an effort to help explain the distribution patterns of organisms on patch reefs within Biscayne National Park, FL, USA. We visited a total of 196 randomly selected sampling stations on 12 shallow (<10 m) patch reefs and measured physical variables (e.g., substratum rugosity, substratum type) and benthic and fish community variables. We also incorporated data on substratum rugosity collected remotely via airborne laser surveying (Experimental Advanced Airborne Research Lidar—EAARL). Across all stations, only weak relationships were found between physical, benthic cover, and fish assemblage variables. Much of the variance was attributable to a “reef effect,” meaning that community structure and organism abundances were more variable at stations among reefs than within reefs. However, when the reef effect was accounted for and removed statistically, patterns were detected. Within reefs, juvenile scarids were most abundant at stations with high coverage of the fleshy macroalgae Dictyota spp., and the calcified alga Halimeda tuna was most abundant at stations with low EAARL rugosity. Explanations for the overwhelming importance of “reef” in explaining variance in our dataset could include the stochastic arrangement of organisms on patch reefs related to variable larval recruitment in space and time and/or strong historical effects due to patchy disturbances (e.g., hurricanes, fishing), as well as legacy effects of prior residents (“priority” effects).

  17. The effect of the chemical, biological, and physical environment on quorum sensing in structured microbial communities

    PubMed Central

    Horswill, Alexander R.; Stoodley, Paul; Stewart, Philip S.

    2006-01-01

    As researchers attempt to study quorum sensing in relevant clinical or environmental settings, it is apparent that many factors have the potential to affect signaling. These factors span a range of physical, chemical, and biological variables that can impact signal production, stability and distribution. Optimizing experimental systems to natural or clinical environments may be crucial for defining when and where quorum sensing occurs. These points are illustrated in our case study of S. aureus signaling in biofilms, where signal stability may be affected by the host environment. The basic signaling schemes have been worked out at the molecular level for a few of the major quorum-sensing systems. As these studies continue to refine our understanding of these mechanisms, an emerging challenge is to identify if and when the local environment can affect signaling. PMID:17047948

  18. Effect of substrate characteristics on microbial community structure, function, resistance, and resilience; application to coupled photocatalytic-biological treatment.

    PubMed

    Marsolek, Michael D; Rittmann, Bruce E

    2016-03-01

    Advanced oxidation (AO) coupled with biodegradation is an emerging treatment technology for wastewaters containing biologically recalcitrant and inhibitory organics, including those containing chlorinated aromatic compounds. The composition of the AO effluent organics can vary significantly with reaction conditions, and this composition can affect the performance of subsequent biodegradation. Three synthetic effluents were used to mimic varying degrees of AO of 2,4,5-trichlorophenol: 4-chlorocatechol to mimic light transformation, 2-chloromuconic acid to mimic moderate transformation, and acetate to mimic extensive transformation. The substrates were fed to identical chemostats and analyzed at steady state for removal of chemical oxygen demand (COD) and dissolved organic carbon (DOC), biomass concentration, and bacterial diversity. The chemostat fed acetate performed best at steady state. The 2-chloromuconic acid chemostat was next in terms of steady-state performance, and the 4-chlorocatechol reactor performed worst, correlating with degree of AO transformation. A spike of 100 μM 2,4,5-trichlorophenol was then applied to each chemostat. The chemostat fed 4-chlorocatechol exhibited the best resistance to the perturbation in terms of maintaining consistent community structure and biomass concentration, whereas the performance of the acetate-fed chemostat was severely impaired in these categories, although it quickly regained capacity to remove organics near pre-perturbation levels demonstrating good resilience. The opposing trends for steady-state versus perturbed performance highlight tradeoffs inherent in coupled chemical-biological systems. PMID:26722990

  19. Effects of shallow-water hydrothermal venting on biological communities of coastal marine ecosystems of the western Pacific.

    PubMed

    Tarasov, V G

    2006-01-01

    This review is based on integrated studies of the composition, structure and function of shallow-water ecosystems in the western Pacific that are influenced by underwater gas-hydrothermal activity. Most of the data were collected from 1985 to 1997 by the Institute of Marine Biology of the Far East Branch of the Russian Academy of Science during expeditions to zones of modern volcanism. Gas-hydrothermal activity of volcanoes has a great influence on the physicochemical characteristics of the water column and plankton, and of bottom sediment and benthic communities. The abundance of nutrients (SiO(3)(2-), PO(4)(3-), NO(3)(-)), gases (CO(2), CH(4), H(2), H(2)S) and other reduced compounds (C(n)H(n), S(0), S(2)O(3)(2-), NH(4)(+)) in zones of shallow-water hydrothermal vents provides conditions for the use of two energy sources for primary production: sunlight (photosynthesis) and the oxidation of reduced compounds (bacterial chemosynthesis). In areas of shallow-water volcanic activity, chemosynthesis occurs not only in the immediate vicinity of venting fluid release but also in the surface layer of the water column, where it occurs together with intense photosynthesis. This surface photosynthesis is found below the layer of chemosynthesis, which is related to the distribution of hydrothermal fluids at the water surface. The contribution of each of these processes to total primary production depends on the physical and chemical conditions created by the vents and on the range and adaptation potential of the organisms. On the seabed in zones of shallow-water venting, microorganisms form mats that consist of bacteria of various physiological groups, microalgae, the products of their metabolism and sedimentary particles. Oxygenic photosynthesis of benthic diatoms, bacterial photosynthesis (anoxygenic photosynthesis) and autotrophic chemosynthesis in algobacterial and bacterial mats generate organic matter additional to that produced in the water column. The high rates of

  20. Changes and recovery of soil bacterial communities influenced by biological soil disinfestation as compared with chloropicrin-treatment

    PubMed Central

    2013-01-01

    Soil bacterial composition, as influenced by biological soil disinfestation (BSD) associated with biomass incorporation was investigated to observe the effects of the treatment on the changes and recovery of the microbial community in a commercial greenhouse setting. Chloropicrin (CP) was also used for soil disinfestation to compare with the effects of BSD. The fusarium wilt disease incidence of spinach cultivated in the BSD- and CP-treated plots was reduced as compared with that in the untreated control plots, showing effectiveness of both methods to suppress the disease. The clone library analyses based on 16S rRNA gene sequences showed that members of the Firmicutes became dominant in the soil bacterial community after the BSD-treatment. Clone groups related to the species in the class Clostridia, such as Clostridium saccharobutylicum, Clostridium tetanomorphum, Clostridium cylindrosporum, Oxobacter pfennigii, etc., as well as Bacillus niacini in the class Bacilli were recognized as the most dominant members in the community. For the CP-treated soil, clones affiliated with the Bacilli related to acid-tolerant or thermophilic bacteria such as Tuberibacillus calidus, Sporolactobacillus laevolacticus, Pullulanibacillus naganoensis, Alicyclobacillus pomorum, etc. were detected as the major groups. The clone library analysis for the soil samples collected after spinach cultivation revealed that most of bacterial groups present in the original soil belonging to the phyla Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, TM7, etc. were recovered in the BSD-treated soil. For the CP-treated soil, the recovery of the bacterial groups belonging to the above phyla was also noted, but some major clone groups recognized in the original soil did not recover fully. PMID:23958081

  1. Changes and recovery of soil bacterial communities influenced by biological soil disinfestation as compared with chloropicrin-treatment.

    PubMed

    Mowlick, Subrata; Inoue, Takashi; Takehara, Toshiaki; Kaku, Nobuo; Ueki, Katsuji; Ueki, Atsuko

    2013-01-01

    Soil bacterial composition, as influenced by biological soil disinfestation (BSD) associated with biomass incorporation was investigated to observe the effects of the treatment on the changes and recovery of the microbial community in a commercial greenhouse setting. Chloropicrin (CP) was also used for soil disinfestation to compare with the effects of BSD. The fusarium wilt disease incidence of spinach cultivated in the BSD- and CP-treated plots was reduced as compared with that in the untreated control plots, showing effectiveness of both methods to suppress the disease. The clone library analyses based on 16S rRNA gene sequences showed that members of the Firmicutes became dominant in the soil bacterial community after the BSD-treatment. Clone groups related to the species in the class Clostridia, such as Clostridium saccharobutylicum, Clostridium tetanomorphum, Clostridium cylindrosporum, Oxobacter pfennigii, etc., as well as Bacillus niacini in the class Bacilli were recognized as the most dominant members in the community. For the CP-treated soil, clones affiliated with the Bacilli related to acid-tolerant or thermophilic bacteria such as Tuberibacillus calidus, Sporolactobacillus laevolacticus, Pullulanibacillus naganoensis, Alicyclobacillus pomorum, etc. were detected as the major groups. The clone library analysis for the soil samples collected after spinach cultivation revealed that most of bacterial groups present in the original soil belonging to the phyla Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes, Planctomycetes, TM7, etc. were recovered in the BSD-treated soil. For the CP-treated soil, the recovery of the bacterial groups belonging to the above phyla was also noted, but some major clone groups recognized in the original soil did not recover fully. PMID:23958081

  2. Impact of titanium dioxide nanoparticles on the bacterial communities of biological activated carbon filter intended for drinking water treatment.

    PubMed

    Zhiyuan, Liu; Shuili, Yu; Heedeung, Park; Qingbin, Yuan; Guicai, Liu; Qi, Li

    2016-08-01

    Titanium dioxide nanoparticles (TiO2 NPs) are inevitably present in the aquatic environment owing to their increasing production and use. However, knowledge of the potential effects of TiO2 NPs on the treatment of drinking water is scarce. Herein, the effects of two types of anatase TiO2 NPs (TP1, 25 nm; TP2, 100 nm) on the bacterial community in a biological activated carbon (BAC) filter were investigated via quantitative polymerase chain reaction (Q-PCR) analysis, ATP quantification, and 454 pyrosequencing analysis. Both TP1 and TP2 significantly inhibited the bacterial ATP level (p < 0.01) and induced a decrease in the abundance of bacterial 16S rDNA gene copies at doses of 0.1 and 100 mg L(-1). Simultaneously, the diversity and evenness of the bacterial communities were considerably reduced. The relative abundances of bacteria annotated to OTUs from Nitrospira class and Betaproteobacteria class decreased upon TiO2 NP treatment, whereas those of Bacilli class and Gammaproteobacteria class increased. TiO2 NP size showed a greater effect on the bacterial composition than did the dose based on Bray-Curtis distances. These findings identified negative effects of TiO2 NPs on the bacterial community in the BAC filter. Given the fact that BAC filters are used widely in drinking water treatment plants, these results suggested a potential threat by TiO2 NP to drinking water treatment system. PMID:27126871

  3. Auditory learning through active engagement with sound: biological impact of community music lessons in at-risk children.

    PubMed

    Kraus, Nina; Slater, Jessica; Thompson, Elaine C; Hornickel, Jane; Strait, Dana L; Nicol, Trent; White-Schwoch, Travis

    2014-01-01

    The young nervous system is primed for sensory learning, facilitating the acquisition of language and communication skills. Social and linguistic impoverishment can limit these learning opportunities, eventually leading to language-related challenges such as poor reading. Music training offers a promising auditory learning strategy by directing attention to meaningful acoustic elements of the soundscape. In light of evidence that music training improves auditory skills and their neural substrates, there are increasing efforts to enact community-based programs to provide music instruction to at-risk children. Harmony Project is a community foundation that has provided free music instruction to over 1000 children from Los Angeles gang-reduction zones over the past decade. We conducted an independent evaluation of biological effects of participating in Harmony Project by following a cohort of children for 1 year. Here we focus on a comparison between students who actively engaged with sound through instrumental music training vs. students who took music appreciation classes. All children began with an introductory music appreciation class, but midway through the year half of the children transitioned to the instrumental training. After the year of training, the children who actively engaged with sound through instrumental music training had faster and more robust neural processing of speech than the children who stayed in the music appreciation class, observed in neural responses to a speech sound /d/. The neurophysiological measures found to be enhanced in the instrumentally-trained children have been previously linked to reading ability, suggesting a gain in neural processes important for literacy stemming from active auditory learning. Despite intrinsic constraints on our study imposed by a community setting, these findings speak to the potential of active engagement with sound (i.e., music-making) to engender experience-dependent neuroplasticity and may inform the

  4. Auditory learning through active engagement with sound: biological impact of community music lessons in at-risk children

    PubMed Central

    Kraus, Nina; Slater, Jessica; Thompson, Elaine C.; Hornickel, Jane; Strait, Dana L.; Nicol, Trent; White-Schwoch, Travis

    2014-01-01

    The young nervous system is primed for sensory learning, facilitating the acquisition of language and communication skills. Social and linguistic impoverishment can limit these learning opportunities, eventually leading to language-related challenges such as poor reading. Music training offers a promising auditory learning strategy by directing attention to meaningful acoustic elements of the soundscape. In light of evidence that music training improves auditory skills and their neural substrates, there are increasing efforts to enact community-based programs to provide music instruction to at-risk children. Harmony Project is a community foundation that has provided free music instruction to over 1000 children from Los Angeles gang-reduction zones over the past decade. We conducted an independent evaluation of biological effects of participating in Harmony Project by following a cohort of children for 1 year. Here we focus on a comparison between students who actively engaged with sound through instrumental music training vs. students who took music appreciation classes. All children began with an introductory music appreciation class, but midway through the year half of the children transitioned to the instrumental training. After the year of training, the children who actively engaged with sound through instrumental music training had faster and more robust neural processing of speech than the children who stayed in the music appreciation class, observed in neural responses to a speech sound /d/. The neurophysiological measures found to be enhanced in the instrumentally-trained children have been previously linked to reading ability, suggesting a gain in neural processes important for literacy stemming from active auditory learning. Despite intrinsic constraints on our study imposed by a community setting, these findings speak to the potential of active engagement with sound (i.e., music-making) to engender experience-dependent neuroplasticity and may inform the

  5. Identification of migratory bird flyways in North America using community detection on biological networks.

    PubMed

    Buhnerkempe, Michael G; Webb, Colleen T; Merton, Andrew A; Buhnerkempe, John E; Givens, Geof H; Miller, Ryan S; Hoeting, Jennifer A

    2016-04-01

    Migratory behavior of waterfowl populations in North America has traditionally been broadly characterized by four north-south flyways, and these flyways have been central to the management of waterfowl populations for more than 80 yr. However, previous flyway characterizations are not easily updated with current bird movement data and fail to provide assessments of the importance of specific geographical regions to the identification of flyways. Here, we developed a network model of migratory movement for four waterfowl species, Mallard (Anas platyrhnchos), Northern Pintail (A. acuta), American Green-winged Teal (A. carolinensis), and Canada Goose (Branta canadensis), in North America, using bird band and recovery data. We then identified migratory flyways using a community detection algorithm and characterized the importance of smaller geographic regions in identifying flyways using a novel metric, the consolidation factor. We identified four main flyways for Mallards, Northern Pintails, and American Green-winged Teal, with the flyway identification in Canada Geese exhibiting higher complexity. For Mallards, flyways were relatively consistent through time. However, consolidation factors revealed that for Mallards and Green-winged Teal, the presumptive Mississippi flyway was potentially a zone of high mixing between other flyways. Our results demonstrate that the network approach provides a robust method for flyway identification that is widely applicable given the relatively minimal data requirements and is easily updated with future movement data to reflect changes in flyway definitions and management goals. PMID:27411247

  6. 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

  7. Accessing Novel Conoidean Venoms: Biodiverse Lumun-lumun Marine Communities, An Untapped Biological and Toxinological Resource

    PubMed Central

    Seronay, Romell A.; Fedosov, Alexander E.; Astilla, Mary Anne; Watkins, Maren; Saguil, Noel; Heralde, Francisco M.; Tagaro, Sheila; Poppe, Guido T.; Aliño, Porfirio M.; Oliverio, Marco; Kantor, Yuri I.; Concepcion, Gisela P.; Olivera, Baldomero M.

    2010-01-01

    Cone snail venoms have yielded pharmacologically-active natural products of exceptional scientific interest. However, cone snails are a small minority of venomous molluscan biodiversity, the vast majority being tiny venomous morphospecies in the family Turridae. A novel method called lumun-lumun opens access to these micromolluscs and their venoms. Old fishing nets are anchored to the sea bottom for a period of 1–6 months and marine biotas rich in small molluscs are established. In a single lumun-lumun community, we found a remarkable gastropod biodiversity (155 morphospecies). Venomous predators belonging to the superfamily Conoidea (36 morphospecies) were the largest group, the majority being micromolluscs in the family Turridae. We carried out an initial analysis of the most abundant of the turrid morphospecies recovered, Clathurella (Lienardia) cincta (Dunker, 1871). In contrast to all cDNA clones characterized from cone snail venom ducts, one of the C. cincta clones identified encoded two different peptide precursors presumably translated from a single mRNA. The prospect of easily accessing so many different morphospecies of venomous marine snails raises intriguing toxinological possibilities: the 36 conoidean morphospecies in this one net alone have the potential to yield thousands of novel pharmacologically-active compounds. PMID:20005243

  8. Long Baseline Neutrino Experiments

    NASA Astrophysics Data System (ADS)

    Mezzetto, Mauro

    2016-05-01

    Following the discovery of neutrino oscillations by the Super-Kamiokande collaboration, recently awarded with the Nobel Prize, two generations of long baseline experiments had been setup to further study neutrino oscillations. The first generation experiments, K2K in Japan, Minos in the States and Opera in Europe, focused in confirming the Super-Kamiokande result, improving the precision with which oscillation parameters had been measured and demonstrating the ντ appearance process. Second generation experiments, T2K in Japan and very recently NOνA in the States, went further, being optimized to look for genuine three neutrino phenomena like non-zero values of θ13 and first glimpses to leptonic CP violation (LCPV) and neutrino mass ordering (NMO). The discovery of leptonic CP violation will require third generation setups, at the moment two strong proposals are ongoing, Dune in the States and Hyper-Kamiokande in Japan. This review will focus a little more in these future initiatives.

  9. A baseline lunar mine

    NASA Technical Reports Server (NTRS)

    Gertsch, Richard E.

    1992-01-01

    A models lunar mining method is proposed that illustrates the problems to be expected in lunar mining and how they might be solved. While the method is quite feasible, it is, more importantly, a useful baseline system against which to test other, possible better, methods. Our study group proposed the slusher to stimulate discussion of how a lunar mining operation might be successfully accomplished. Critics of the slusher system were invited to propose better methods. The group noted that while nonterrestrial mining has been a vital part of past space manufacturing proposals, no one has proposed a lunar mining system in any real detail. The group considered it essential that the design of actual, workable, and specific lunar mining methods begin immediately. Based on an earlier proposal, the method is a three-drum slusher, also known as a cable-operated drag scraper. Its terrestrial application is quite limited, as it is relatively inefficient and inflexible. The method usually finds use in underwater mining from the shore and in moving small amounts of ore underground. When lunar mining scales up, the lunarized slusher will be replaced by more efficient, high-volume methods. Other aspects of lunar mining are discussed.

  10. Geochemistry of pore-fluids related to the distribution of the biological communities on the giant Regab pockmark, off Gabon

    NASA Astrophysics Data System (ADS)

    de Prunelé, A.; Caprais, J.; Ruffine, L.; Cassarino, L.; Guyader, V.; Bollinger, C.; Ondréas, H.; Donval, J.; Olu, K.; Geli, L. B.; Cunningham, K. L.; Cauquil, E.

    2013-12-01

    The Regab pockmark is a giant structure located at 3200 m water depth offshore Gabon and ~ 10 km north to the deep Congo channel (Zaïre canyon) (Gay et al. 2006; Ondréas et al. 2005). It has been visited for the first time in 2000 during the Zairov cruise. Since that time, several scientific cruises have allowed further investigations of this pockmark. The last cruise, WACS, for West Africa Cold Seeps, in January- February 2010, was undertaken on board the R/V ';Pourquoi Pas?' with the aim of identifying changes which can occur over time on this pockmark. Besides intensive ROV dives, three calypso cores and several push cores have been collected to better understand the relationships between the distribution of the living communities and the pore-fluids chemistry. In two calypso cores one collected within the pockmark and one outside, and both in areas without visible biological communities, pore-fluids profiles of dissolved elements (Alk, SO42-, Mn2+, Fe2+) show that degradation of organic matter is occurring and likely plays an important role in the sulfate reduction (Froelich et al. 1979). Methane was not detected. The Analysis of the pore-fluids by Thermal Desorption-Gas Chromatography-Mass Spectrometry (TD-GC-MS) has shown the presence of alcohols, acid and phenol. These molecules are likely related to the degradation of organic matter and/or the production of the biological communities. Further investigations are ongoing to provide us with a clearer picture regarding the source of these molecules. The third calypso core collected in the northeast part of the pockmark containing gas hydrates. Sulfate profiles from the push cores show significant difference from one community to another. The analyses of both major and minor dissolved elements, along with molecular and isotopic methane concentration measurements are in progress for the push cores. The latter was done using a new analyzer G2201-i from Picarro for which new methods applied to pore-fluids has

  11. Regional constraints to biological nitrogen fixation in post-fire forest communities

    USGS Publications Warehouse

    Yelenik, Stephanie; Perakis, Steven S.; Hibbs, David

    2013-01-01

    Biological nitrogen fixation (BNF) is a key ecological process that can restore nitrogen (N) lost in wildfire and shape the pace and pattern of post-fire forest recovery. To date, there is limited information on how climate and soil fertility interact to influence different pathways of BNF in early forest succession. We studied asymbiotic (forest floor and soil) and symbiotic (the shrub Ceanothus integerrimus) BNF rates across six sites in the Klamath National Forest, California, USA. We used combined gradient and experimental phosphorus (P) fertilization studies to explore cross-site variation in BNF rates and then related these rates to abiotic and biotic variables. We estimate that our measured BNF rates 22 years after wildfire (6.1–12.1 kg N·ha-1·yr-1) are unlikely to fully replace wildfire N losses. We found that asymbiotic BNF is P limited, although this is not the case for symbiotic BNF in Ceanothus. In contrast, Ceanothus BNF is largely driven by competition from other vegetation: in high-productivity sites with high potential evapotranspiration (Et), shrub biomass is suppressed as tree biomass increases. Because shrub biomass governed cross-site variation in Ceanothus BNF, this competitive interaction led to lower BNF in sites with high productivity and Et. Overall, these results suggest that the effects of nutrients play a larger role in driving asymbiotic than symbiotic fixation across our post-fire sites. However, because symbiotic BNF is 8–90x greater than asymbiotic BNF, it is interspecific plant competition that governs overall BNF inputs in these forests.

  12. Life, Learning, and Community: Concepts and Models for Service-Learning in Biology. AAHE's Series on Service-Learning in the Disciplines.

    ERIC Educational Resources Information Center

    Brubaker, David C., Ed.; Ostroff, Joel H., Ed.

    This volume is the 18th in a series of monographs on service learning and the academic disciplines. The articles in this volume provide an array of service learning courses in biology that demonstrate active student participation in thoughtfully organized service experiences that meet real community needs and are integrated with the students'…

  13. Long-term temperature monitoring at the biological community site on the Nankai accretionary prism off Kii Peninsula

    NASA Astrophysics Data System (ADS)

    Goto, S.; Hamamoto, H.; Yamano, M.; Kinoshita, M.; Ashi, J.

    2008-12-01

    Nankai subduction zone off Kii Peninsula is one of the most intensively surveyed areas for studies on the seismogenic zone. Multichannel seismic reflection surveys carried out in this area revealed the existence of splay faults that branched from the subduction zone plate boundary [Park et al., 2002]. Along the splay faults, reversal of reflection polarity was observed, indicating elevated pore fluid pressure along the faults. Cold seepages with biological communities were discovered along a seafloor outcrop of one of the splay faults through submersible observations. Long-term temperature monitoring at a biological community site along the outcrop revealed high heat flow carried by upward fluid flow (>180 mW/m2) [Goto et al., 2003]. Toki et al. [2004] estimated upward fluid flow rates of 40-200 cm/yr from chloride distribution of interstitial water extracted from sediments in and around biological community sites along the outcrop. These observation results suggest upward fluid flow along the splay fault. In order to investigate hydrological nature of the splay fault, we conducted long-term temperature monitoring again in the same cold seepage site where Goto et al. [2003] carried out long-term temperature monitoring. In this presentation, we present results of the temperature monitoring and estimate heat flow carried by upward fluid flow from the temperature records. In this long-term temperature monitoring, we used stand-alone heat flow meter (SAHF), a probe-type sediment temperature recorder. Two SAHFs (SAHF-3 and SAHF-4) were used in this study. SAHF-4 was inserted into a bacterial mat, within several meters of which the previous long-term temperature monitoring was conducted. SAHF-3 was penetrated into ordinary sediment near the bacterial mat. The sub-bottom temperature records were obtained for 8 months. The subsurface temperatures oscillated reflecting bottom- water temperature variation (BTV). For sub-bottom temperatures measured with SAHF-3 (outside of

  14. Biological interactions and their role in community structure in the rocky intertidal of Helgoland (German Bight, North Sea)

    NASA Astrophysics Data System (ADS)

    Janke, Klaus

    1990-06-01

    of F. serratus, herbivores such as L. littorea and L. mariae, and increasing number of predators such as Carcinus), the feeding activity of herbivores can neither prevent the settlement of the fucoid sporelings nor reduce the growth of macroalgae. F. serratus achieved a total canopy on the rock within one year. Doubled density of herbivores prevented the settlement of Fucus and most of the undercover algae. Predation by Carcinus on Littorina spp. had little influence on the herbivore community patterns. However, the crabs supported the establishment of macroalgae by excluding the mussels from the lower intertidal. In summary, the community organization and maintenance in the mid and lower intertidal is influenced to a high degree by biological interactions. Whereas both the relatively important herbivory by L. littorea and competition for space between mussels and macroalgae dominate in the mid intertidal, predation reaches its highest relative degree of importance for community structure in the lower intertidal.

  15. Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

    PubMed Central

    Cormier, Catherine Y.; Mohr, Stephanie E.; Zuo, Dongmei; Hu, Yanhui; Rolfs, Andreas; Kramer, Jason; Taycher, Elena; Kelley, Fontina; Fiacco, Michael; Turnbull, Greggory; LaBaer, Joshua

    2010-01-01

    The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery. PMID:19906724

  16. Baseline Familiarity in Lie Detection.

    ERIC Educational Resources Information Center

    Feeley, Thomas H.; And Others

    1995-01-01

    Reports on a study in which subjects judged the veracity of truthful and deceptive communicators after viewing no, one, two, or four case-relevant baseline exposures (familiarity) of truthful communication. Finds a positive linear relationship between detection accuracy and amount of baseline familiarity. (SR)

  17. Assessment of Meeting Employer Needs and the Labor Market Experience of Job Upgrading and Retraining Students in Washington Community Colleges. A Baseline Report. Operations Report No. 91-3.

    ERIC Educational Resources Information Center

    Seppanen, Loretta

    In 1991, the Washington State Board for Community College Education conducted a study to determine the strengths and shortcomings of Washington community colleges' efforts to provide upgrading and retraining for employed workers. Data were derived from four separate studies conducted in 1990, including a survey of 1,151 employed students at eight…

  18. Plutonium Immobilization Project Baseline Formulation

    SciTech Connect

    Ebbinghaus, B.

    1999-02-01

    A key milestone for the Immobilization Project (AOP Milestone 3.2a) in Fiscal Year 1998 (FY98) is the definition of the baseline composition or formulation for the plutonium ceramic form. The baseline formulation for the plutonium ceramic product must be finalized before the repository- and plant-related process specifications can be determined. The baseline formulation that is currently specified is given in Table 1.1. In addition to the baseline formulation specification, this report provides specifications for two alternative formulations, related compositional specifications (e.g., precursor compositions and mixing recipes), and other preliminary form and process specifications that are linked to the baseline formulation. The preliminary specifications, when finalized, are not expected to vary tremendously from the preliminary values given.

  19. Parasites as Biological Tags for Stock Discrimination of Beaked Redfish (Sebastes mentella): Parasite Infra-Communities vs. Limited Resolution of Cytochrome Markers

    PubMed Central

    Klapper, Regina; Kochmann, Judith; O’Hara, Robert B.; Karl, Horst; Kuhn, Thomas

    2016-01-01

    The use of parasites as biological tags for discrimination of fish stocks has become a commonly used approach in fisheries management. Metazoan parasite community analysis and anisakid nematode population genetics based on a mitochondrial cytochrome marker were applied in order to assess the usefulness of the two parasitological methods for stock discrimination of beaked redfish Sebastes mentella of three fishing grounds in the North East Atlantic. Multivariate, model-based approaches demonstrated that the metazoan parasite fauna of beaked redfish from East Greenland differed from Tampen, northern North Sea, and Bear Island, Barents Sea. A joint model (latent variable model) was used to estimate the effects of covariates on parasite species and identified four parasite species as main source of differences among fishing grounds; namely Chondracanthus nodosus, Anisakis simplex s.s., Hysterothylacium aduncum, and Bothriocephalus scorpii. Due to its high abundance and differences between fishing grounds, Anisakis simplex s.s. was considered as a major biological tag for host stock differentiation. Whilst the sole examination of Anisakis simplex s.s. on a population genetic level is only of limited use, anisakid nematodes (in particular, A. simplex s.s.) can serve as biological tags on a parasite community level. This study confirmed the use of multivariate analyses as a tool to evaluate parasite infra-communities and to identify parasite species that might serve as biological tags. The present study suggests that S. mentella in the northern North Sea and Barents Sea is not sub-structured. PMID:27104735

  20. Parasites as Biological Tags for Stock Discrimination of Beaked Redfish (Sebastes mentella): Parasite Infra-Communities vs. Limited Resolution of Cytochrome Markers.

    PubMed

    Klapper, Regina; Kochmann, Judith; O'Hara, Robert B; Karl, Horst; Kuhn, Thomas

    2016-01-01

    The use of parasites as biological tags for discrimination of fish stocks has become a commonly used approach in fisheries management. Metazoan parasite community analysis and anisakid nematode population genetics based on a mitochondrial cytochrome marker were applied in order to assess the usefulness of the two parasitological methods for stock discrimination of beaked redfish Sebastes mentella of three fishing grounds in the North East Atlantic. Multivariate, model-based approaches demonstrated that the metazoan parasite fauna of beaked redfish from East Greenland differed from Tampen, northern North Sea, and Bear Island, Barents Sea. A joint model (latent variable model) was used to estimate the effects of covariates on parasite species and identified four parasite species as main source of differences among fishing grounds; namely Chondracanthus nodosus, Anisakis simplex s.s., Hysterothylacium aduncum, and Bothriocephalus scorpii. Due to its high abundance and differences between fishing grounds, Anisakis simplex s.s. was considered as a major biological tag for host stock differentiation. Whilst the sole examination of Anisakis simplex s.s. on a population genetic level is only of limited use, anisakid nematodes (in particular, A. simplex s.s.) can serve as biological tags on a parasite community level. This study confirmed the use of multivariate analyses as a tool to evaluate parasite infra-communities and to identify parasite species that might serve as biological tags. The present study suggests that S. mentella in the northern North Sea and Barents Sea is not sub-structured. PMID:27104735

  1. Case studies of community college non-science majors: Effects of self-regulatory interventions on biology self-efficacy and biological literacy

    NASA Astrophysics Data System (ADS)

    Maurer, Matthew J.

    Science literacy has been at the heart of current reform efforts in science education. The focus on developing essential skills needed for individual ability to be literate in science has been at the forefront of most K--12 science curricula. Reform efforts have begun to stretch into the postsecondary arena as well, with an ever increasing dialogue regarding the need for attention to science literacy by college students, especially non-science majors. This study set out to investigate how the use of self-regulatory interventions (specifically, goal setting, concept mapping, and reflective writing) affected student biology self-efficacy and biological literacy. This study employed a qualitative research design, analyzing three case studies. Participants in the study received ten self-regulatory interventions as a set of portfolio assignments. Portfolio work was qualitatively analyzed and coded for self-efficacy, as well as evidence of biological literacy. A biology self-efficacy survey was administered pre- and post- to provide a means of self-efficacy data triangulation. Literacy data was supported via a biological literacy rubric, constructed specifically for this study. Results indicated that mastery experiences were the source of biology self-efficacy. Self-efficacy for specific tasks increased over time, and changes in self-efficacy were corroborated by the self-efficacy survey. Students were found to express biological literacy at nominal, functional, or conceptual levels depending on the specific task. This was supported by data from the biological literacy rubric scores. Final conclusions and implications for the study indicated the need for further research with more samples of students in similar and different contexts. Given the fact that the literature in this area is sparse, the results obtained here have only begun to delve into this area of research. Generalization to other biology courses or contexts outside of the one presented in this study was

  2. Baseline gamut mapping method for the perceptual reference medium gamut

    NASA Astrophysics Data System (ADS)

    Green, Phil

    2015-01-01

    A need for a baseline algorithm for mapping from the Perceptual Reference Medium Gamut to destination media in ICC output profiles has been identified. Before such a baseline algorithm can be recommended, it requires careful evaluation by the user community. A framework for encoding the gamut boundary and computing intersections with the PRMG and output gamuts respectively is described. This framework provides a basis for comparing different gamut mapping algorithms, and a candidate algorithm is also described.

  3. Changes in lake levels, salinity and the biological community of Great Salt Lake (Utah, USA), 1847-1987

    USGS Publications Warehouse

    Stephens, D.W.

    1990-01-01

    Great Salt Lake is the fourth largest terminal lake in the world, with an area of about 6000 square kilometers at its historic high elevation. Since its historic low elevation of 1277.52 meters in 1963, the lake has risen to a new historic high elevation of 1283.77 meters in 1986-1987, a net increase of about 6.25 meters. About 60 percent of this increase, 3.72 meters, has occurred since 1982 in response to greater than average precipitation and less than average evaporation. Variations in salinity have resulted in changes in the composition of the aquatic biological community which consists of bacteria, protozoa, brine shrimp and brine flies. These changes were particularly evident following the completion of a causeway in 1959 which divided the lake. Subsequent salinities in the north part of the lake have ranged from 16 to 29 percent and in the south part from 6 to 28 percent. Accompanying the rise in lake elevation from 1982 to 1987 have been large decreases in salinity of both parts of the lake. This has resulted in changes in the biota from obligate halophiles, such as Dunaliella salina and D. viridis, to opportunistic forms such as a blue-green alga (Nodularia spumigena). The distribution and abundance of brine shrimp (Artemia salina) in the lake also have followed closely the salinity. In 1986, when the salinity of the south part of the lake was about 6 percent, a population of brackish-water killifish (Lucania parva) was observed along the shore near inflow from a spring. ?? 1990 Kluwer Academic Publishers.

  4. 324 Building Baseline Radiological Characterization

    SciTech Connect

    R.J. Reeder, J.C. Cooper

    2010-06-24

    This report documents the analysis of radiological data collected as part of the characterization study performed in 1998. The study was performed to create a baseline of the radiological conditions in the 324 Building.

  5. Comparing Biology Grades Based on Instructional Delivery and Instructor at a Community College: Face-to-Face Course Versus Online Course

    NASA Astrophysics Data System (ADS)

    Rosenzweig, Amanda H.

    Through distance learning, the community college system has been able to serve more students by providing educational opportunities to students who would otherwise be unable to attend college. The community college of focus in the study increased its online enrollments and online course offerings due to the growth of overall enrollment. The need and purpose of the study is to address if there is a difference in students' grades between face-to-face and online biology related courses and if there are differences in grades between face-to-face and online biology courses taught by different instructors and the same instructor. The study also addresses if online course delivery is a viable method to educate students in biology-related fields. The study spanned 14 semesters between spring 2006 and summer 2011. Data were collected for 6,619 students. For each student, demographic information, cumulative grade point average, ACT, and data on course performance were gathered. Student data were gathered from General Biology I, Microbiology of Human Pathogens, Human Anatomy and Physiology I, and Human Anatomy and Physiology II courses. Univariate analysis of variance, linear regression, and descriptive analysis were used to analyze the data and determine which variables significantly impacted grade achievement for face-to-face and online students in biology classes. The findings from the study showed that course type, face-to-face or online, was significant for Microbiology of Human Pathogens and Human Anatomy and Physiology I, both upper level courses. Teachers were significant for General Biology I, a lower level course, Human Anatomy and Physiology I, and Human Anatomy and Physiology II. However, in every class, there were teachers who had significant differences within their courses between their face-to-face and online courses. This study will allow information to be concluded about the relationship between the students' final grades and class type, face-to-face or

  6. Sources of Low-Chloride Fluids in Sediments beneath Biological Communities on the Nankai Accretionary Wedge off Kumano

    NASA Astrophysics Data System (ADS)

    Toki, T.; Tsunogai, U.; Gamo, T.; Kuramoto, S.; Ashi, J.

    2003-12-01

    We report chemical and isotopic compositions of interstitial waters extracted from surface sediments inside and outside of dense biological communities on the seafloor of the Nankai accretionary prism off Kumano. Particularly those taken within bacterial mat at the Oomine Ridge site show the following characteristics: (1) CH4 enrichment (more than 600 μ mol/kg), (2) chloride depletion (up to 10% depletion from bottom seawater), and (3) δ DH2O and δ 18OH2O depletion (more than 4‰ and 0.7‰ depletion, respectively), compared with bottom seawater. The highest CH4 value observed at the Oomine Ridge samples is compatible with that previously reported at one of the most active seep areas within Nankai Trough, suggesting that also this site should be one of the most active seep sites in Nankai Trough. The fluid chemistries of these samples show that the fluids of CH4 enrichment, chloride depletion, and low δ DH2O and δ 18OH2O value relative to bottom seawater are ascending from deeper zone to sediments beneath the Oomine Ridge site. Assuming simple two-component mixing of ambient seawater with fresh water of Cl- = 0 mmol/kg, the estimated end-member δ DH2O and δ 18OH2O values were -46+/-7‰ SMOW and -6.3+/-0.7‰ SMOW, respectively. The δ DH2O and δ 18OH2O values coincide with those of groundwater at nearby land area. Land-derived groundwater could be one of the possible sources for the low chloride fluids, while we donOt have any idea for such underground lateral flow system of groundwater to the depth of ca. 2,500 m and ca. 100 km off the Japan Islands. Alternative possible source to produce the fluid of low Cl-, δ DH2O and δ 18OH2O is phase separation of seawater. Phase separation would lower Cl-, δ DH2O and δ 18OH2O of vapor phase by a fractionation process during boiling, while we have no idea for a heat source to induce phase separation at the area. Fault slips during large earthquake could possibly be result in such source of heat.

  7. Changing tides for Lake Erie: the biogeochemical evolution of a Laurentian Great Lake and implications for biological communities of the future (Invited)

    NASA Astrophysics Data System (ADS)

    Wilhelm, S.; Steffen, M.; Belisle, B. S.; Dearth, S.; Campbell, M.; Boyer, G. L.; Watson, S.; Bourbonniere, R. A.; DeBruyn, J.; Campagna, S.

    2013-12-01

    Lake Erie is perhaps the most anthropogenically influenced of all the Laurentian Great Lakes. The history of the lake clearly demonstrates one where external loads of phosphorous drove primary production to a point where the lake was declared dead in the 1970's. The lake however, is also one of the greatest environmental success stories, as abatement programs had seen this system begin to return to health until the mid-1990's. In recent years, however, new cyanobacterial blooms of the potentially toxic cyanobacterium Microcystis have dominated the water column in late-summer months. Driven by a combination of changes in water column chemistry and regional climate, Lake Erie is no longer predictably P-limited through summer months and in some cases experiments have clearly shown that within the lake primary productivity is now N-limited. Experimentally, our goal has been to couple water column geochemistry with biomolecular pathways in cells to have the biology tell us which elements are driving community structure and function. Using community level transcriptomics and metabolomics, our observations suggest that changes in the chemical species of nitrogen, and especially the presence of urea, may be controlling the biological community structure of microbial communities in Lake Erie and may in part shape the extent of toxic cyanobacterial blooms. Moreover, data from multiple sampling surveys now demonstrates that additives designed to shape nutrient use in terrestrial environments may be influencing nitrogen cycles within the lake. Coupled to historical data sets dating back decades, we will discuss how seemingly minor alterations in system geochemistry over time have major biological implications for regional stakeholders. MODIS image of Lake Erie algal bloom in 2012

  8. Including a Service Learning Educational Research Project in a Biology Course-II: Assessing Community Awareness of Legionnaires' Disease?

    ERIC Educational Resources Information Center

    Abu-Shakra, Amal

    2012-01-01

    For a university service learning educational research project addressing Legionnaires' disease (LD), a Yes/No questionnaire on community awareness of LD was developed and distributed in an urban community in North Carolina, USA. The 456 questionnaires completed by the participants were sorted into yes and no sets based on responses obtained to…

  9. A Comparison of Traditional and Television Lectures as a Means of Instruction in Biology at a Community College.

    ERIC Educational Resources Information Center

    Firstman, Aranga

    A study was conducted to compare the effectiveness of using the television lecture series "Introducing Biology" to traditional lecture techniques in a college-level Animal Biology course. The interest levels and subject course mastery of three groups of students were compared: (1) a control group who attended two 50-minute lectures per week; (2)…

  10. Integrated Baseline Review (IBR) Handbook

    NASA Technical Reports Server (NTRS)

    2013-01-01

    An Integrated Baseline Review (IBR) is a review of a supplier?s Performance Measurement Baseline (PMB). It is conducted by Program/Project Managers and their technical staffs on contracts and in-house work requiring compliance with NASA Earned Value Management System (EVMS) policy as defined in program/project policy, NPR 7120.5, or in NASA Federal Acquisition Regulations. The IBR Handbook may also be of use to those responsible for preparing the Terms of Reference for internal project reviews. While risks may be identified and actions tracked as a result of the IBR, it is important to note that an IBR cannot be failed.