WorldWideScience

Sample records for biological function environmental

  1. From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis

    Directory of Open Access Journals (Sweden)

    Ward Alister C

    2007-10-01

    Full Text Available Abstract Background Our understanding of the importance of transcriptional regulation for biological function is continuously improving. We still know, however, comparatively little about how environmentally induced stress affects gene expression in vertebrates, and the consistency of transcriptional stress responses to different types of environmental stress. In this study, we used a multi-stressor approach to identify components of a common stress response as well as components unique to different types of environmental stress. We exposed individuals of the coral reef fish Pomacentrus moluccensis to hypoxic, hyposmotic, cold and heat shock and measured the responses of approximately 16,000 genes in liver. We also compared winter and summer responses to heat shock to examine the capacity for such responses to vary with acclimation to different ambient temperatures. Results We identified a series of gene functions that were involved in all stress responses examined here, suggesting some common effects of stress on biological function. These common responses were achieved by the regulation of largely independent sets of genes; the responses of individual genes varied greatly across different stress types. In response to heat exposure over five days, a total of 324 gene loci were differentially expressed. Many heat-responsive genes had functions associated with protein turnover, metabolism, and the response to oxidative stress. We were also able to identify groups of co-regulated genes, the genes within which shared similar functions. Conclusion This is the first environmental genomic study to measure gene regulation in response to different environmental stressors in a natural population of a warm-adapted ectothermic vertebrate. We have shown that different types of environmental stress induce expression changes in genes with similar gene functions, but that the responses of individual genes vary between stress types. The functions of heat

  2. Functional traits of selected mangrove species in Brazil as biological indicators of different environmental conditions.

    Science.gov (United States)

    Arrivabene, Hiulana Pereira; Souza, Iara; Có, Walter Luiz Oliveira; Rodella, Roberto Antônio; Wunderlin, Daniel Alberto; Milanez, Camilla Rozindo

    2014-04-01

    Ecological studies on phenotypic plasticity illustrate the relevance of this phenomenon in nature. Conditions of biota reflect environmental changes, highlighting the adaptability of resident species that can be used as bioindicators of such changes. We report the morpho-anatomical plasticity of leaves of Avicennia schaueriana Stapf & Leechm. ex Moldenke, Laguncularia racemosa (L.) C.F.Gaertn. and Rhizophora mangle L., evaluated in three estuaries (Vitória bay, Santa Cruz and Itaúnas River; state of Espírito Santo, Brazil), considering five areas of mangrove ecosystems with diverse environmental issues. Two sampling sites are part of the Ecological Station Lameirão Island in Vitória bay, close to a harbor. A third sampling site in Cariacica (Vitória bay) is inside the Vitória harbor and also is influenced by domestic sewage. The fourth studied area (Santa Cruz) is part of Piraquê Mangrove Ecological Reservation, while the fifth (Itaúnas River) is a small mangrove, with sandy sediment and greater photosynthetically active radiation, also not strongly influenced by anthropic activity. Results pointed out the morpho-anatomical plasticity in studied species, showing that A. schaueriana and L. racemosa might be considered the most appropriate bioindicators to indicate different settings and environmental conditions. Particularly, the dry mass per leaf area (LMA) of A. schaueriana was the main biomarker measured. In our study, LMA of A. schaueriana was positively correlated with salinity (Spearman 0.71), Mn content (0.81) and pH (0.82) but negatively correlated with phosphorus content (-0.63). Thus, the evaluation of modification in LMA of A. schaueriana pointed out changes among five studied sites, suggesting its use to reflect changes in the environment, which could be also useful in the future to evaluate the climate change. PMID:24496023

  3. Functional traits of selected mangrove species in Brazil as biological indicators of different environmental conditions

    Energy Technology Data Exchange (ETDEWEB)

    Arrivabene, Hiulana Pereira [Universidade Federal do Espírito Santo, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, 29075-910 Vitória, Espírito Santo (Brazil); Souza, Iara [Universidade Federal de São Carlos, Centro de Ciências Biológicas e da Saúde, Departamento de Ciências Fisiológicas, 13565-905 São Carlos (Brazil); Có, Walter Luiz Oliveira [Associação Educational de Vitória, Departamento de Biologia, 29053-360 Vitória (Brazil); Rodella, Roberto Antônio [Universidade Estadual Paulista Júlio de Mesquita Filho, Campus de Botucatu, Instituto de Biociências, Departamento de Botânica, C. Postal 510, 18618-000 Botucatu, São Paulo (Brazil); Wunderlin, Daniel Alberto, E-mail: dwunder@fcq.unc.edu.ar [Instituto de Ciencia y Tecnología de Alimentos Córdoba (ICYTAC), CONICET, Dpto. Qca. Orgánica, Fac. Cs. Químicas, Universidad Nacional de Córdoba, Ciudad Universitaria, 5000, Córdoba (Argentina); and others

    2014-04-01

    Ecological studies on phenotypic plasticity illustrate the relevance of this phenomenon in nature. Conditions of biota reflect environmental changes, highlighting the adaptability of resident species that can be used as bioindicators of such changes. We report the morpho-anatomical plasticity of leaves of Avicennia schaueriana Stapf and Leechm. ex Moldenke, Laguncularia racemosa (L.) C.F.Gaertn. and Rhizophora mangle L., evaluated in three estuaries (Vitória bay, Santa Cruz and Itaúnas River; state of Espírito Santo, Brazil), considering five areas of mangrove ecosystems with diverse environmental issues. Two sampling sites are part of the Ecological Station Lameirão Island in Vitória bay, close to a harbor. A third sampling site in Cariacica (Vitória bay) is inside the Vitória harbor and also is influenced by domestic sewage. The fourth studied area (Santa Cruz) is part of Piraquê Mangrove Ecological Reservation, while the fifth (Itaúnas River) is a small mangrove, with sandy sediment and greater photosynthetically active radiation, also not strongly influenced by anthropic activity. Results pointed out the morpho-anatomical plasticity in studied species, showing that A. schaueriana and L. racemosa might be considered the most appropriate bioindicators to indicate different settings and environmental conditions. Particularly, the dry mass per leaf area (LMA) of A. schaueriana was the main biomarker measured. In our study, LMA of A. schaueriana was positively correlated with salinity (Spearman 0.71), Mn content (0.81) and pH (0.82) but negatively correlated with phosphorus content (− 0.63). Thus, the evaluation of modification in LMA of A. schaueriana pointed out changes among five studied sites, suggesting its use to reflect changes in the environment, which could be also useful in the future to evaluate the climate change. - Highlights: • We investigated adaptive modifications in plants in response to differences among three estuaries. • We used

  4. The Role of Biology in Environmental Education

    Science.gov (United States)

    Xingcun, Lu

    2004-01-01

    The principal mode of environmental education is to integrate environmental education into science classes. Biology is a life science. To study biology it is necessary to talk about the living environment and the relationship between biological organisms and their environment. Studying biology not only enables students to learn a great deal of…

  5. Functions in Biological Kind Classification

    Science.gov (United States)

    Lombrozo, Tania; Rehder, Bob

    2012-01-01

    Biological traits that serve functions, such as a zebra's coloration (for camouflage) or a kangaroo's tail (for balance), seem to have a special role in conceptual representations for biological kinds. In five experiments, we investigate whether and why functional features are privileged in biological kind classification. Experiment 1…

  6. Translational environmental biology: cell biology informing conservation.

    Science.gov (United States)

    Traylor-Knowles, Nikki; Palumbi, Stephen R

    2014-05-01

    Typically, findings from cell biology have been beneficial for preventing human disease. However, translational applications from cell biology can also be applied to conservation efforts, such as protecting coral reefs. Recent efforts to understand the cell biological mechanisms maintaining coral health such as innate immunity and acclimatization have prompted new developments in conservation. Similar to biomedicine, we urge that future efforts should focus on better frameworks for biomarker development to protect coral reefs.

  7. The relativity of biological function.

    Science.gov (United States)

    Laubichler, Manfred D; Stadler, Peter F; Prohaska, Sonja J; Nowick, Katja

    2015-12-01

    Function is a central concept in biological theories and explanations. Yet discussions about function are often based on a narrow understanding of biological systems and processes, such as idealized molecular systems or simple evolutionary, i.e., selective, dynamics. Conflicting conceptions of function continue to be used in the scientific literature to support certain claims, for instance about the fraction of "functional DNA" in the human genome. Here we argue that all biologically meaningful interpretations of function are necessarily context dependent. This implies that they derive their meaning as well as their range of applicability only within a specific theoretical and measurement context. We use this framework to shed light on the current debate about functional DNA and argue that without considering explicitly the theoretical and measurement contexts all attempts to integrate biological theories are prone to fail. PMID:26449352

  8. The relativity of biological function.

    Science.gov (United States)

    Laubichler, Manfred D; Stadler, Peter F; Prohaska, Sonja J; Nowick, Katja

    2015-12-01

    Function is a central concept in biological theories and explanations. Yet discussions about function are often based on a narrow understanding of biological systems and processes, such as idealized molecular systems or simple evolutionary, i.e., selective, dynamics. Conflicting conceptions of function continue to be used in the scientific literature to support certain claims, for instance about the fraction of "functional DNA" in the human genome. Here we argue that all biologically meaningful interpretations of function are necessarily context dependent. This implies that they derive their meaning as well as their range of applicability only within a specific theoretical and measurement context. We use this framework to shed light on the current debate about functional DNA and argue that without considering explicitly the theoretical and measurement contexts all attempts to integrate biological theories are prone to fail.

  9. Molecular Biological Methods in Environmental Engineering.

    Science.gov (United States)

    Zhang, Guocai; Wei, Li; Chang, Chein-Chi; Zhang, Yuhua; Wei, Dong

    2016-10-01

    Bacteria, acting as catalysts, perform the function of degrading pollutants. Molecular biological techniques play an important role in research on the community analysis, the composition and the functions of complex microbial communities. The development of secondary high-throughput pyrosequencing techiniques enhances the understanding of the composition of the microbial community. The literatures of 2015 indicated that 16S rDNA gene as genetic tag is still the important method for bacteria identification and classification. 454 high throughput sequencing and Illumina MiSeq sequencing have been the primary and widely recognized methods to analyze the microbial. This review will provide environmental engineers and microbiologists an overview of important advancements in molecular techniques and highlight the application of these methods in diverse environments. PMID:27620079

  10. Practical Statistics for Environmental and Biological Scientists

    CERN Document Server

    Townend, John

    2012-01-01

    All students and researchers in environmental and biological sciences require statistical methods at some stage of their work. Many have a preconception that statistics are difficult and unpleasant and find that the textbooks available are difficult to understand. Practical Statistics for Environmental and Biological Scientists provides a concise, user-friendly, non-technical introduction to statistics. The book covers planning and designing an experiment, how to analyse and present data, and the limitations and assumptions of each statistical method. The text does not refer to a specific comp

  11. The biological function of consciousness

    Science.gov (United States)

    Earl, Brian

    2014-01-01

    This research is an investigation of whether consciousness—one's ongoing experience—influences one's behavior and, if so, how. Analysis of the components, structure, properties, and temporal sequences of consciousness has established that, (1) contrary to one's intuitive understanding, consciousness does not have an active, executive role in determining behavior; (2) consciousness does have a biological function; and (3) consciousness is solely information in various forms. Consciousness is associated with a flexible response mechanism (FRM) for decision-making, planning, and generally responding in nonautomatic ways. The FRM generates responses by manipulating information and, to function effectively, its data input must be restricted to task-relevant information. The properties of consciousness correspond to the various input requirements of the FRM; and when important information is missing from consciousness, functions of the FRM are adversely affected; both of which indicate that consciousness is the input data to the FRM. Qualitative and quantitative information (shape, size, location, etc.) are incorporated into the input data by a qualia array of colors, sounds, and so on, which makes the input conscious. This view of the biological function of consciousness provides an explanation why we have experiences; why we have emotional and other feelings, and why their loss is associated with poor decision-making; why blindsight patients do not spontaneously initiate responses to events in their blind field; why counter-habitual actions are only possible when the intended action is in mind; and the reason for inattentional blindness. PMID:25140159

  12. Graphene for Environmental and Biological Applications

    Science.gov (United States)

    Sreeprasad, T. S.; Pradeep, T.

    2012-08-01

    The latest addition to the nanocarbon family, graphene, has been proclaimed to be the material of the century. Its peculiar band structure, extraordinary thermal and electronic conductance and room temperature quantum Hall effect have all been used for various applications in diverse fields ranging from catalysis to electronics. The difficulty to synthesize graphene in bulk quantities was a limiting factor of it being utilized in several fields. Advent of chemical processes and self-assembly approaches for the synthesis of graphene analogues have opened-up new avenues for graphene based materials. The high surface area and rich abundance of functional groups present make chemically synthesized graphene (generally known as graphene oxide (GO) and reduced graphene oxide (RGO) or chemically converted graphene) an attracting candidate in biotechnology and environmental remediation. By functionalizing graphene with specific molecules, the properties of graphene can be tuned to suite applications such as sensing, drug delivery or cellular imaging. Graphene with its high surface area can act as a good adsorbent for pollutant removal. Graphene either alone or in combination with other materials can be used for the degradation or removal of a large variety of contaminants through several methods. In this review some of the relevant efforts undertaken to utilize graphene in biology, sensing and water purification are described. Most recent efforts have been given precedence over older works, although certain specific important examples of the past are also mentioned.

  13. Functional Aspects of Biological Networks

    Science.gov (United States)

    Sneppen, Kim

    2007-03-01

    We discuss biological networks with respect to 1) relative positioning and importance of high degree nodes, 2) function and signaling, 3) logic and dynamics of regulation. Visually the soft modularity of many real world networks can be characterized in terms of number of high and low degrees nodes positioned relative to each other in a landscape analogue with mountains (high-degree nodes) and valleys (low-degree nodes). In these terms biological networks looks like rugged landscapes with separated peaks, hub proteins, which each are roughly as essential as any of the individual proteins on the periphery of the hub. Within each sup-domain of a molecular network one can often identify dynamical feedback mechanisms that falls into combinations of positive and negative feedback circuits. We will illustrate this with examples taken from phage regulation and bacterial uptake and regulation of small molecules. In particular we find that a double negative regulation often are replaced by a single positive link in unrelated organisms with same functional requirements. Overall we argue that network topology primarily reflects functional constraints. References: S. Maslov and K. Sneppen. ``Computational architecture of the yeast regulatory network." Phys. Biol. 2:94 (2005) A. Trusina et al. ``Functional alignment of regulatory networks: A study of temerate phages". Plos Computational Biology 1:7 (2005). J.B. Axelsen et al. ``Degree Landscapes in Scale-Free Networks" physics/0512075 (2005). A. Trusina et al. ``Hierarchy and Anti-Hierarchy in Real and Scale Free networks." PRL 92:178702 (2004) S. Semsey et al. ``Genetic Regulation of Fluxes: Iron Homeostasis of Escherichia coli". (2006) q-bio.MN/0609042

  14. Nuclear energy: biological effects and environmental impact

    International Nuclear Information System (INIS)

    This thesis is concerned with the large development of nuclear power plants and the recent nuclear catastrophe which has made clear how the hazards resulting from radioactivity affect public health and the environment. Environmental effects of nuclear power plants operating in normal conditions are small, but to obtain nuclear power plants of reduced radioactivity, optimization of their design, construction, operation and waste processing plays a decisive role. Biological effects of ionizing radiations and environmental impacts of Nuclear Power plants are developed

  15. Biological couplings: Function, characteristics and implementation mode

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    Through rigorous natural selection, biological organisms have evolved exceptional functions highly adaptable to their living environments. Biological organisms can achieve a variety of biological functions efficiently by using the synergic actions of two or more different parts of the body, or the coupling effects of multiple factors, and demonstrate optimal adaptations to the living environment. In this paper, the function, characteristics and types of biological couplings are analyzed, the implementation mechanism and mode of biological coupling functions are revealed from the bionic viewpoint. Finally, the technological prospects of the bionic implementation of biological coupling function are predicted.

  16. Seasonality of suicides: environmental, sociological and biological covariations.

    Science.gov (United States)

    Souêtre, E; Salvati, E; Belugou, J L; Douillet, P; Braccini, T; Darcourt, G

    1987-01-01

    The monthly rates of completed suicides in France from 1978 until 1982 were analyzed. The seasonal variations of environmental (daylight and sunlight durations, mean temperature, geomagnetism), sociological (unemployment, deaths of all causes, birth and conception rates), and biological (melatonin, cortisol and serotonin circannual rhythms) factors were compared to the seasonal patterns of suicides. A clear seasonal variation (with peaks in May and September) in suicidal behavior was detected. These patterns tended to differ as a function of age (bimodal in young, unimodal in old people). The component analysis clearly pointed out that seasonal patterns of suicides may be considered as the sum of two components, unimodal and bimodal. Almost similar covariations were found between the main seasonal (unimodal) component of suicides and environmental (daylight duration and mean monthly temperature) or sociological factors whereas the secondary component was more correlated to variations in environmental factors and, to some extent, to biological parameters. PMID:2960714

  17. Functional quantum biology in photosynthesis and magnetoreception

    CERN Document Server

    Lambert, Neill; Cheng, Yuan-Chung; Li, Che-Ming; Chen, Guang-Yin; Nori, Franco

    2012-01-01

    Is there a functional role for quantum mechanics or coherent quantum effects in biological processes? While this question is as old as quantum theory, only recently have measurements on biological systems on ultra-fast time-scales shed light on a possible answer. In this review we give an overview of the two main candidates for biological systems which may harness such functional quantum effects: photosynthesis and magnetoreception. We discuss some of the latest evidence both for and against room temperature quantum coherence, and consider whether there is truly a functional role for coherence in these biological mechanisms. Finally, we give a brief overview of some more speculative examples of functional quantum biology including the sense of smell, long-range quantum tunneling in proteins, biological photoreceptors, and the flow of ions across a cell membrane.

  18. Integrating Functional, Developmental and Evolutionary Biology into Biology Curricula

    Science.gov (United States)

    Haave, Neil

    2012-01-01

    A complete understanding of life involves how organisms are able to function in their environment and how they arise. Understanding how organisms arise involves both their evolution and development. Thus to completely comprehend living things, biology must study their function, development and evolution. Previous proposals for standardized…

  19. Department of Radiation and Environmental Biology - Overview

    International Nuclear Information System (INIS)

    Full text: In the year 2000 we completed our study of the genotoxic influence of occupational exposure to pesticides on human cells, and their susceptibility to radiation in particular. Examining blood samples from four countries: Greece, Hungary, Poland and Spain we found that exposure to pesticides usually resulted in an increased susceptibility to the UV-C radiation, although statistical significance could only be concluded for inhabitants of Poland. In Spain, exposure to pesticides was proved to impair the lymphocyte DNA repair capability, while for the Polish group this repair capability appeared enhanced in people exposed to pesticides (see the research reports below). The possible influence of lifestyle or particular diet on the observed national differences would probably be worth analyzing. We also investigate the biological effectiveness of therapeutic beams (neutrons and X-rays). Experimental part of such study, concerning neutrons of different mean energies, is over and the results are now being processed. Our work covers hot issues of environmental and radiation biology making us research partners to many domestic and foreign scientific institutions. Our proficiency in the field is also reflected by membership in various expert boards (e.g. evaluating research applications for the Fifth EU Framework Programme for RTD and Demonstration Activities in the field 'Environment and Health', lecturing in the 2000 NATO IOS Life Science Books). We have entered the 5th EU Programme Scheme within the EXPAH project starting January 1, 2001. (author)

  20. Biological and Environmental Research Network Requirements

    Energy Technology Data Exchange (ETDEWEB)

    Balaji, V. [Princeton Univ., NJ (United States). Earth Science Grid Federation (ESGF); Boden, Tom [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Cowley, Dave [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Dart, Eli [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Dattoria, Vince [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Desai, Narayan [Argonne National Lab. (ANL), Argonne, IL (United States); Egan, Rob [Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Foster, Ian [Argonne National Lab. (ANL), Argonne, IL (United States); Goldstone, Robin [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Gregurick, Susan [U.S. Dept. of Energy, Washington, DC (United States). Biological Systems Science Division; Houghton, John [U.S. Dept. of Energy, Washington, DC (United States). Biological and Environmental Research (BER) Program; Izaurralde, Cesar [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Johnston, Bill [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Joseph, Renu [U.S. Dept. of Energy, Washington, DC (United States). Climate and Environmental Sciences Division; Kleese-van Dam, Kerstin [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Lipton, Mary [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Monga, Inder [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Pritchard, Matt [British Atmospheric Data Centre (BADC), Oxon (United Kingdom); Rotman, Lauren [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Strand, Gary [National Center for Atmospheric Research (NCAR), Boulder, CO (United States); Stuart, Cory [Argonne National Lab. (ANL), Argonne, IL (United States); Tatusova, Tatiana [National Inst. of Health (NIH), Bethesda, MD (United States); Tierney, Brian [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). ESNet; Thomas, Brian [Univ. of California, Berkeley, CA (United States); Williams, Dean N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Zurawski, Jason [Internet2, Washington, DC (United States)

    2013-09-01

    The Energy Sciences Network (ESnet) is the primary provider of network connectivity for the U.S. Department of Energy (DOE) Office of Science (SC), the single largest supporter of basic research in the physical sciences in the United States. In support of SC programs, ESnet regularly updates and refreshes its understanding of the networking requirements of the instruments, facilities, scientists, and science programs that it serves. This focus has helped ESnet be a highly successful enabler of scientific discovery for over 25 years. In November 2012, ESnet and the Office of Biological and Environmental Research (BER) of the DOE SC organized a review to characterize the networking requirements of the programs funded by the BER program office. Several key findings resulted from the review. Among them: 1) The scale of data sets available to science collaborations continues to increase exponentially. This has broad impact, both on the network and on the computational and storage systems connected to the network. 2) Many science collaborations require assistance to cope with the systems and network engineering challenges inherent in managing the rapid growth in data scale. 3) Several science domains operate distributed facilities that rely on high-performance networking for success. Key examples illustrated in this report include the Earth System Grid Federation (ESGF) and the Systems Biology Knowledgebase (KBase). This report expands on these points, and addresses others as well. The report contains a findings section as well as the text of the case studies discussed at the review.

  1. Matching biological traits to environmental conditions in marine benthic ecosystems

    Science.gov (United States)

    Bremner, J.; Rogers, S. I.; Frid, C. L. J.

    2006-05-01

    The effects of variability in environmental conditions on species composition in benthic ecosystems are well established, but relatively little is known about how environmental variability relates to ecosystem functioning. Benthic invertebrate assemblages are heavily involved in the maintenance of ecological processes and investigation of the biological characteristics (traits) expressed in these assemblages can provide information about some aspects of functioning. The aim of this study was to establish and explore relationships between environmental variability and biological traits expressed in megafauna assemblages in two UK regions. Patterns of trait composition were matched to environmental conditions and subsets of variables best describing these patterns determined. The nature of the relationships were subsequently examined at two separate scales, both between and within the regions studied. Over the whole area, some traits related to size, longevity, reproduction, mobility, flexibility, feeding method, sociability and living habit were negatively correlated with salinity, sea surface temperature, annual temperature range and the level of fishing effort, and positively associated with fish taxon richness and shell content of the substratum. Between the two regions, reductions in temperature range and shell content were associated with infrequent relative occurrences of short-lived, moderately mobile, flexible, solitary, opportunistic, permanent-burrow dwelling fauna and those exhibiting reproductive strategies based on benthic development. Relationships between some traits and environmental conditions diverged within the two regions, with increases in fishing effort and shell content of the substratum being associated with low frequencies of occurrence of moderately mobile and moderately to highly flexible fauna within one region, but high frequencies in the other. These changes in trait composition have implications for ecosystem processes, with, for

  2. Photosynthetic system as a biological functional element

    International Nuclear Information System (INIS)

    Photosynthetic apparatus of high plants and photosynthetic bacteria is essentially autonomic system in terms of genetics and structural -functional properties located in specific medium, a bio-membrane. Processes of light absorption and exciton migration in light harvesting antenna, separation and further transfer of charges in reaction centers have specific features, which may be used for application of these objects as key elements in construction of future biological functional elements. Progress in study and genetic modification of photosynthetic membranes achieved during the last decade opens great prospects in development biological functional elements and systems. The main characteristics of photosynthetic system for these purposes are: (i) energy conversion processes in the first light phase of the photosynthesis have very short periods, up to picoseconds, which indicates possibility of creation of ultrafast functional elements on their basis; (ii) characteristics sizes of photosynthetic units, 10-100 nm, and possibility to arrange regularly disposed elements in relevant membranes could be prospective point for creation of nano structures and on their basis relevant biologic functional elements; (iii) elements based on modified photosynthetic apparatus and bio-membranes might be efficiently created by methods of gene engineering and manipulation, that open huge opportunities for development of read biological functional systems. In the paper structural-functional properties and characteristics of high plants and purple photosynthetic bacteria, which may be useful for creation of future biological functional elements are considered. (author)

  3. Metacognition: computation, biology and function.

    Science.gov (United States)

    Fleming, Stephen M; Dolan, Raymond J; Frith, Christopher D

    2012-05-19

    Many complex systems maintain a self-referential check and balance. In animals, such reflective monitoring and control processes have been grouped under the rubric of metacognition. In this introductory article to a Theme Issue on metacognition, we review recent and rapidly progressing developments from neuroscience, cognitive psychology, computer science and philosophy of mind. While each of these areas is represented in detail by individual contributions to the volume, we take this opportunity to draw links between disciplines, and highlight areas where further integration is needed. Specifically, we cover the definition, measurement, neurobiology and possible functions of metacognition, and assess the relationship between metacognition and consciousness. We propose a framework in which level of representation, order of behaviour and access consciousness are orthogonal dimensions of the conceptual landscape. PMID:22492746

  4. Functional biology of sympatric krill species

    DEFF Research Database (Denmark)

    Agersted, Mette Dalgaard; Nielsen, Torkel Gissel

    2016-01-01

    Here we compare the functional biology of the sympatric krill species, Meganyctiphanes norvegica and Thysanoessa inermis. For M. norvegica, we investigated functional responses on diatoms and copepods, together with prey size spectra on plankton ,400 mm and copepods in the size range 500–3220 mm...

  5. Marine Carotenoids: Biological Functions and Commercial Applications

    OpenAIRE

    Vega, José M.; Inés Garbayo; Francisco Bédmar; María Cuaresma; Carlos Vílchez; Eduardo Forján

    2011-01-01

    Carotenoids are the most common pigments in nature and are synthesised by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functions of carotenoids relevant for life on earth. Biological properties of carotenoids allow for wide range of commercial applications. Indeed, recent interest in the carotenoids has be...

  6. Biologic markers in risk assessment for environmental carcinogens

    OpenAIRE

    Perera, F.; Mayer, J.; Santella, R. M.; Brenner, D; Jeffrey, A.; Latriano, L; Smith, S.; Warburton, D; Young, T. L.; Tsai, W. Y.; Hemminki, K; Brandt-Rauf, P

    1991-01-01

    The potential of biologic markers to provide more timely and precise risk assessments for environmental carcinogens is viewed against the current state-of-the-art in biological monitoring/molecular epidemiology. Biologic markers such as carcinogen-DNA adducts and oncogene activation are currently considered valid qualitative indicators of potential risk, but for most chemical exposures research is needed to establish their validity as quantitative predictors of cancer risk. Biologic markers h...

  7. Understanding biological functions through molecular networks

    Institute of Scientific and Technical Information of China (English)

    Jing-Dong Jackie Han

    2008-01-01

    The completion of genome sequences and subsequent high-throughput mapping of molecular networks have allowed us to study biology from the network perspective. Experimental, statistical and mathematical modeling approaches have been employed to study the structure, function and dynamics of molecular networks, and begin to reveal important links of various network properties to the functions of the biological systems. In agreement with these functional links, evolutionary selection of a network is apparently based on the function, rather than directly on the structure of the network. Dynamic modularity is one of the prominent features of molecular networks. Taking advantage of such a feature may simplify network-based biological studies through construction of process-specific modular networks and provide functional and mechanistic insights linking genotypic variations to complex traits or diseases, which is likely to be a key approach in the next wave of understanding complex human diseases. With the development of ready-to-use network analysis and modeling tools the networks approaches will be infused into everyday biological research in the near future.

  8. Inferring Biologically Relevant Models: Nested Canalyzing Functions

    CERN Document Server

    Hinkelmann, Franziska

    2010-01-01

    Inferring dynamic biochemical networks is one of the main challenges in systems biology. Given experimental data, the objective is to identify the rules of interaction among the different entities of the network. However, the number of possible models fitting the available data is huge and identifying a biologically relevant model is of great interest. Nested canalyzing functions, where variables in a given order dominate the function, have recently been proposed as a framework for modeling gene regulatory networks. Previously we described this class of functions as an algebraic toric variety. In this paper, we present an algorithm that identifies all nested canalyzing models that fit the given data. We demonstrate our methods using a well-known Boolean model of the cell cycle in budding yeast.

  9. PIXE - Analysis for environmental and biological samples

    International Nuclear Information System (INIS)

    The usefulness and accuracy of PIXE as an analytical tool in the study of trace elements in environmental samples of the Brazilian Cerrado are discussed. The report lists actual and forthcoming publications resulting from the study. The mechanism of exchange of elements in solution in water to aerosols has been investigated. For details of the procedure the reader is referred to an earlier report

  10. Imaging cellular and molecular biological functions

    Energy Technology Data Exchange (ETDEWEB)

    Shorte, S.L. [Institut Pasteur, 75 - Paris (France). Plateforme d' Imagerie Dynamique PFID-Imagopole; Frischknecht, F. (eds.) [Heidelberg Univ. Medical School (Germany). Dept. of Parasitology

    2007-07-01

    'Imaging cellular and molecular biological function' provides a unique selection of essays by leading experts, aiming at scientist and student alike who are interested in all aspects of modern imaging, from its application and up-scaling to its development. Indeed the philosophy of this volume is to provide student, researcher, PI, professional or provost the means to enter this applications field with confidence, and to construct the means to answer their own specific questions. (orig.)

  11. Insights into the functional biology of schistosomes

    OpenAIRE

    Walker Anthony

    2011-01-01

    Abstract The need to discover new treatments for human schistosomiasis has been an important driver for molecular research on schistosomes, a major breakthrough being the publication of the Schistosoma mansoni and Schistosoma japonicum genomes in 2009. This 'Primer' considers recent advances in the understanding of schistosome biology by providing a snapshot of selected areas of contemporary functional schistosome research, including that on the genome, the tegument, cell signalling and devel...

  12. Biological Function of REE in Plants & Microbes

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    Rare earth elements (REE) and their compounds are widely applied in agronomic and medical fields for many years. The bioinorganic chemical research of REE during the past few years indicates that REE play important roles in the promotion of photosynthetic rate as well as root absorption, regulation of hormone and nitrogen metabolism, and suppression of microbes, etc. The metallic or non-metallic targets of key biomolecule in various physiological processes can be chosen by REE for the chelation or replacement, which enables REE to regulate the biological functions or behaviors of those biomolecule and consequently leads to significant embodiment of biological function of REE in plants and microbes.Overdose of REE, however, shows an inhibitory effect on living organisms. Therefore, this paper proposes two suggestions that will be available in the extension of full use of REE's biological function. One is to obey the dose law of REE and control REE concentrations within a safe range. The other is to further test the bioaccumulation and long-period influence of REE on organisms.

  13. Use of biological indicators to evaluate environmental stress

    International Nuclear Information System (INIS)

    This report examines the usefulness of biological analyses for evaluating environmental stress. All forms of stress are addressed; particular attention, however, is paid to the use of biological analyses to evaluate the impact on the environment from radioactive releases of the nuclear industry. First, we will review different biological analyses which are grouped into two approaches: the holistic approach (biotic and diversity indices) and the reductionist approach ('biological indicators' per se). Secondly, we will compare the usefulness of plants and animals as indicators based on the established criteria. This report ends with a compilation of letters received from different organizations which outline the present usage in Canada of biological indicators for evaluating environmental stress

  14. Use of biological indicators for evaluating environmental stress

    International Nuclear Information System (INIS)

    This report examines the usefulness of biological analyses for evaluating environmental stress. All forms of stress are addressed; particular attention, however, is paid to the use of biological analyses to evaluate the impact on the environment from radioactive releases of the nuclear industry. First, we will review different biological analyses which are grouped into two approaches: the holistic approach (biotic and diversity indices) and the reductionist approach ('biological indicators' per se). Secondly, we will compare the usefulness of plants and animals as indicators based on the established criteria. This report ends with a compilation of letters received from different organizations which outline the present use in Canada of biological indicators for evaluating environmental stress

  15. Biologic markers in risk assessment for environmental carcinogens

    Energy Technology Data Exchange (ETDEWEB)

    Perera, F.; Mayer, J.; Santella, R.M.; Brenner, D.; Jeffrey, A.; Latriano, L.; Smith, S.; Warburton, D.; Young, T.L.; Tsai, W.Y.; Brandt-Rauf, P. (Columbia Univ. School of Public Health, New York, NY (United States)); Hemminki, K. (Finnish School of Occupational Health, Helsinki (Finland))

    1991-01-01

    The potential of biologic markers to provide more timely and precise risk assessments for environmental carcinogens is viewed against the current state-of-the-art in biological monitoring/molecular epidemiology. Biologic markers such as carcinogen-DNA adducts and oncogene activation are currently considered valid qualitative indicators of potential risk, but for most chemical exposures research is needed to establish their validity as quantitative predictors of cancer risk. Biologic markers have, however, already provided valuable insights into the magnitude of interindividual variation in response to carcinogenic exposures, with major implications for risk assessment.

  16. Biologic markers in risk assessment for environmental carcinogens

    International Nuclear Information System (INIS)

    The potential of biologic markers to provide more timely and precise risk assessments for environmental carcinogens is viewed against the current state-of-the-art in biological monitoring/molecular epidemiology. Biologic markers such as carcinogen-DNA adducts and oncogene activation are currently considered valid qualitative indicators of potential risk, but for most chemical exposures research is needed to establish their validity as quantitative predictors of cancer risk. Biologic markers have, however, already provided valuable insights into the magnitude of interindividual variation in response to carcinogenic exposures, with major implications for risk assessment

  17. Biological functions of decorin in cancer

    Institute of Scientific and Technical Information of China (English)

    Xiu-Li Bi; Wancai Yang

    2013-01-01

    Decorin is a member of the extracellular matrix small leucine-rich proteoglycans family that exists and functions in stromal and epithelial cells.Accumulating evidence suggests that decorin affects the biology of various types of cancer by directly or indirectly targeting the signaling molecules involved in cell growth,survival,metastasis,and angiogenesis.More recent studies show that decorin plays important roles during tumor development and progression and is a potential cancer therapeutic agent.In this article,we summarize recent studies of decorin in cancer and discuss decorin's therapeutic and prognostic value.

  18. Department of Radiation and Environmental Biology - Overview

    International Nuclear Information System (INIS)

    californium 252 neutrons from KAERI source. The third part of our effort concerns an application of different radiation sources for clinical cancer therapy. In cooperation with dr Jacek Capala we have done experiments on Medical Research Reactor in Brookhaven Laboratory. We have also introduced a COMET assay in their laboratory. This is an excellent feeling when both cooperating sides may benefit from co-operation. The year 1998 was also very attractive in the sense of many interesting visits to our Department. All of them we enjoyed a lot. We were honored to host Dr Diana Anderson from BIBRA International, Carshalton, UK. We are happy to see that her visits have become a tradition so much profitable for both our friendship and programs. The end of the year was equally touching as the beginning when X-ray machine had arrived, at the beginning of December, I won myself, a prize from the International Mutagenesis Society for the outstanding presentation; on the 3rd International Conference of Mutagenesis in Human Populations. I really respect both, working issue of the Conference ''Understanding Gene and Environmental Interactions for Disease Prevention'' and a prize itself (Five-year-subscription of International Journal of Environmental and Molecular Mutagenesis). Whoop! I am proud of myself and of the people in my Department!!. (author)

  19. Flavonoids: Biosynthesis, Biological functions and Biotechnological applications

    Directory of Open Access Journals (Sweden)

    Maria Lorena eFalcone Ferreyra

    2012-09-01

    Full Text Available Flavonoids are widely distributed secondary metabolites with different metabolic functions in plants. The elucidation of the biosynthetic pathways, as well as their regulation by MYB, bHLH and WD40-type transcription factors, has allowed metabolic engineering of plants through the manipulation of the different final products with valuable applications. The present review describes the regulation of flavonoid biosynthesis, as well as the biological functions of flavonoids in plants, such as in defense against UV-B radiation and pathogen infection, nodulation, pollen fertility. In addition, we discuss different strategies and achievements through the genetic engineering of flavonoid biosynthesis with implication in the industry and the combinatorial biosynthesis in microorganisms by the reconstruction of the pathway to obtain high amounts of specific compounds.

  20. Environmental Noise and Nonlinear Relaxation in Biological Systems

    CERN Document Server

    Spagnolo, B; Spezia, S; Curcio, L; Pizzolato, N; Dubkov, A A; Fiasconaro, A; Adorno, D Persano; Bue, P Lo; Peri, E; Colazza, S

    2011-01-01

    We analyse the effects of environmental noise in three different biological systems: (i) mating behaviour of individuals of \\emph{Nezara viridula} (L.) (Heteroptera Pentatomidae); (ii) polymer translocation in crowded solution; (iii) an ecosystem described by a Verhulst model with a multiplicative L\\'{e}vy noise.

  1. Structure and biological functions of fungal cerebrosides

    Directory of Open Access Journals (Sweden)

    Barreto-Bergter Eliana

    2004-01-01

    Full Text Available Ceramide monohexosides (CMHs, cerebrosides are glycosphingolipids composed of a hydrophobic ceramide linked to one sugar unit. In fungal cells, CMHs are very conserved molecules consisting of a ceramide moiety containing 9-methyl-4,8-sphingadienine in amidic linkage to 2-hydroxyoctadecanoic or 2-hydroxyhexadecanoic acids, and a carbohydrate portion consisting of one residue of glucose or galactose. 9-Methyl 4,8-sphingadienine-containing ceramides are usually glycosylated to form fungal cerebrosides, but the recent description of a ceramide dihexoside (CDH presenting phytosphingosine in Magnaporthe grisea suggests the existence of alternative pathways of ceramide glycosylation in fungal cells. Along with their unique structural characteristics, fungal CMHs have a peculiar subcellular distribution and striking biological properties. In Pseudallescheria boydii, Candida albicans, Cryptococcus neoformans, Aspergillus nidulans, A. fumigatus, and Schizophyllum commune, CMHs are apparently involved in morphological transitions and fungal growth. The elucidation of structural and functional aspects of fungal cerebrosides may therefore contribute to the design of new antifungal agents inhibiting growth and differentiation of pathogenic species.

  2. Biological responses to environmental heterogeneity under future ocean conditions.

    Science.gov (United States)

    Boyd, Philip W; Cornwall, Christopher E; Davison, Andrew; Doney, Scott C; Fourquez, Marion; Hurd, Catriona L; Lima, Ivan D; McMinn, Andrew

    2016-08-01

    Organisms are projected to face unprecedented rates of change in future ocean conditions due to anthropogenic climate-change. At present, marine life encounters a wide range of environmental heterogeneity from natural fluctuations to mean climate change. Manipulation studies suggest that biota from more variable marine environments have more phenotypic plasticity to tolerate environmental heterogeneity. Here, we consider current strategies employed by a range of representative organisms across various habitats - from short-lived phytoplankton to long-lived corals - in response to environmental heterogeneity. We then discuss how, if and when organismal responses (acclimate/migrate/adapt) may be altered by shifts in the magnitude of the mean climate-change signal relative to that for natural fluctuations projected for coming decades. The findings from both novel climate-change modelling simulations and prior biological manipulation studies, in which natural fluctuations are superimposed on those of mean change, provide valuable insights into organismal responses to environmental heterogeneity. Manipulations reveal that different experimental outcomes are evident between climate-change treatments which include natural fluctuations vs. those which do not. Modelling simulations project that the magnitude of climate variability, along with mean climate change, will increase in coming decades, and hence environmental heterogeneity will increase, illustrating the need for more realistic biological manipulation experiments that include natural fluctuations. However, simulations also strongly suggest that the timescales over which the mean climate-change signature will become dominant, relative to natural fluctuations, will vary for individual properties, being most rapid for CO2 (~10 years from present day) to 4 decades for nutrients. We conclude that the strategies used by biota to respond to shifts in environmental heterogeneity may be complex, as they will have to

  3. Biological responses to environmental heterogeneity under future ocean conditions.

    Science.gov (United States)

    Boyd, Philip W; Cornwall, Christopher E; Davison, Andrew; Doney, Scott C; Fourquez, Marion; Hurd, Catriona L; Lima, Ivan D; McMinn, Andrew

    2016-08-01

    Organisms are projected to face unprecedented rates of change in future ocean conditions due to anthropogenic climate-change. At present, marine life encounters a wide range of environmental heterogeneity from natural fluctuations to mean climate change. Manipulation studies suggest that biota from more variable marine environments have more phenotypic plasticity to tolerate environmental heterogeneity. Here, we consider current strategies employed by a range of representative organisms across various habitats - from short-lived phytoplankton to long-lived corals - in response to environmental heterogeneity. We then discuss how, if and when organismal responses (acclimate/migrate/adapt) may be altered by shifts in the magnitude of the mean climate-change signal relative to that for natural fluctuations projected for coming decades. The findings from both novel climate-change modelling simulations and prior biological manipulation studies, in which natural fluctuations are superimposed on those of mean change, provide valuable insights into organismal responses to environmental heterogeneity. Manipulations reveal that different experimental outcomes are evident between climate-change treatments which include natural fluctuations vs. those which do not. Modelling simulations project that the magnitude of climate variability, along with mean climate change, will increase in coming decades, and hence environmental heterogeneity will increase, illustrating the need for more realistic biological manipulation experiments that include natural fluctuations. However, simulations also strongly suggest that the timescales over which the mean climate-change signature will become dominant, relative to natural fluctuations, will vary for individual properties, being most rapid for CO2 (~10 years from present day) to 4 decades for nutrients. We conclude that the strategies used by biota to respond to shifts in environmental heterogeneity may be complex, as they will have to

  4. The Structure and Function of Biological Networks

    Science.gov (United States)

    Wu, Daniel Duanqing

    2010-01-01

    Biology has been revolutionized in recent years by an explosion in the availability of data. Transforming this new wealth of data into meaningful biological insights and clinical breakthroughs requires a complete overhaul both in the questions being asked and the methodologies used to answer them. A major challenge in organizing and understanding…

  5. Molecular Sociology: Further Insights from Biological and Environmental Aspects

    Directory of Open Access Journals (Sweden)

    Ahed Jumah Mahmoud Al-Khatib

    2015-11-01

    Full Text Available The present study expanded our previous study in which features of molecular sociology were mentioned. In this study, we added the microbial dimensions in which it is thought that religiosity may be impacted by microbes that manipulate brains to create better conditions for their existence. This hypothesis is called “biomeme hypothesis”. We talked about other environmental impacts on human behaviors through three studies in which exposure to lead caused violent behaviors ending with arresting in prisons. By conclusion, the present study has expanded our horizon about interferences on various levels including biological and environmental impacts with our behaviors. Although we are convinced that behavior is a very diverse and complex phenomenon and cannot be understood within certain frame as either biologically or environmentally, but further new insights are possible to participate in better understanding of human behaviors. Many behaviors have their roots in religion, and we showed how religious rituals may be affected by some microbes that make to form a microenvironment within the host for microbial benefits.

  6. The use of self-determination theory to foster environmental motivation in an environmental biology course

    Science.gov (United States)

    Darner, Rebekka

    A scientifically literate person is one who understands the nature of science, its processes, products, and their appropriate application to decision-making contexts. The impetus to make informed decisions about environmental issues is environmental motivation. I examined students' environmental motivation, its relationship to scientific knowledge, and how environmental motivation can be fostered in a science classroom. This study took place in a college-level environmental biology course in which the instructor attempted to support students' basic psychological needs, as defined by self-determination theory (SDT). The first question was to what extent does an SDT-guided environmental biology course differ from a non-SDT-guided course in the degree to which it fostered self-determined motivation toward the environment. The administration of a well-validated scale to two sections before, after, and six months following the end of the course indicated that SDT-guided instruction is a plausible way to foster environmental motivation in the classroom. The second question was what are the multiple influences on fostering self-determined motivation toward the environment in an SDT-guided course. Path analysis indicated that environmental motivation can be partially accomplished in an environmental biology course by conveying to students that they are cared for, are connected to others, and can trust others while solving environmental problems. The third question sought to characterize students' scientific conceptualizations as they solve environmental problems and the extent to which their conceptualizations relate to the satisfaction of their need for competence. Students were videotaped during in-class problem-solving, after which stimulated-recall interviews were conducted. Grounded theory and an established coding scheme were combined to analyze these data, which resulted in three grounded hypotheses about what characterizes students' scientific knowledge when they

  7. Environmental chemicals and thyroid function: an update

    DEFF Research Database (Denmark)

    Boas, M.; Main, K.M.; Feldt-Rasmussen, U.

    2009-01-01

    PURPOSE OF REVIEW: To overview the effects of endocrine disrupters on thyroid function. RECENT FINDINGS: Studies in recent years have revealed thyroid-disrupting properties of many environmentally abundant chemicals. Of special concern is the exposure of pregnant women and infants, as thyroid......, epidemiological and exposure studies indicates that the ubiquitous human and environmental exposure to industrial chemicals may impose a serious threat to human and wildlife thyroid homeostasis. Currently, available evidence suggests that authorities need to regulate exposure to thyroid-disrupting chemicals...

  8. Gm crops: between biological risk and environmental and economic benefits

    International Nuclear Information System (INIS)

    The transgenic crops were the result of the application of recombinant DNA technology in agriculture. These crops were developed by transfer of foreign genes (transgenes) from any biological origin (animal, plant, microbial, viral) to the genome of cultivated species of plants. The crops genetically modified (GM) have been used in the world since 1996; up to December 2010 they counted to a billion hectares planted throughout the period. In just the past year 2010 148 million hectares were planted, grown by 15.4 million farmers in 29 countries. GM crops that are used in global agriculture are mainly soybean, cotton, corn and canola, which express transgenes derived from bacteria, and confer resistance to lepidopteron insects (ILR) or herbicide tolerance (HT; glyphosate and glufosinate ammonium). the first transgenic varieties containing only a single transgene, or simple event, while the current varieties express several transgenes, or stacked, conferring resistance to different species of Lepidoptera and coleopteran insects and tolerance to two different herbicides. In 2010 were planted in Colombia, 18.874 hectares of GM cotton, 16.793 hectares of GM corn, and 4 hectares of GM carnations and GM roses. GM corn and GM cotton were planted in Sucre, Cesar, Cordoba, Huila and Tolima. GM corn was planted in Antioquia, Valle del Cauca, Meta, Cundinamarca and Santander. Carnations and roses were planted in Cundinamarca. GM maize and GM cotton expressing ILR and HT features, as simple events or stacked. In the case of GM carnation and GM roses, these genotypes that express the color blue. Academia has tried to organize the debate on the adoption of GM crops around the analysis of biological risks and environmental vs environmental and economic benefits. Biological hazards are defined by the possible negative effects on human consumers or negative effects on the environment. The environmental benefits are related to reduce use of agrochemicals (insecticides and herbicides

  9. Biological monitoring and environmental assessment in the Alligator Rivers Region

    International Nuclear Information System (INIS)

    Mining projects in the Alligator Rivers Region can accumulate excess volumes of water from the heavy rains of the annual Wet season. Such water contains naturally-occurring substances (heavy metals, radionuclides, suspended solids) at concentrations greater than those in adjacent streams and could pose an environmental risk if allowed to drain freely from a site. Because transport by surface waters dominates dispersion of mine-derived material, much of the research carried out at the Alligator Rivers Region Research Institute has been centred on aquatic ecosystems. While chemical analysis of waters can be used to measure concentrations of selected constituents, only biological monitoring can be used to assess effects on organisms, a crucial aspect of environmental protection

  10. Marine Carotenoids: Biological Functions and Commercial Applications

    NARCIS (Netherlands)

    Vilchez, C.; Forján, E.; Cuaresma, M.; Bédmar, F.; Garbayo, I.; Vega, J.M.

    2011-01-01

    Carotenoids are the most common pigments in nature and are synthesized by all photosynthetic organisms and fungi. Carotenoids are considered key molecules for life. Light capture, photosynthesis photoprotection, excess light dissipation and quenching of singlet oxygen are among key biological functi

  11. Microbial Mat Compositional and Functional Sensitivity to Environmental Disturbance

    Science.gov (United States)

    Preisner, Eva C.; Fichot, Erin B.; Norman, Robert S.

    2016-01-01

    The ability of ecosystems to adapt to environmental perturbations depends on the duration and intensity of change and the overall biological diversity of the system. While studies have indicated that rare microbial taxa may provide a biological reservoir that supports long-term ecosystem stability, how this dynamic population is influenced by environmental parameters remains unclear. In this study, a microbial mat ecosystem located on San Salvador Island, The Bahamas was used as a model to examine how environmental disturbance affects the protein synthesis potential (PSP) of rare and abundant archaeal and bacterial communities and how these changes impact potential biogeochemical processes. This ecosystem experienced a large shift in salinity (230 to 65 g kg-1) during 2011–2012 following the landfall of Hurricane Irene on San Salvador Island. High throughput sequencing and analysis of 16S rRNA and rRNA genes from samples before and after the pulse disturbance showed significant changes in the diversity and PSP of abundant and rare taxa, suggesting overall compositional and functional sensitivity to environmental change. In both archaeal and bacterial communities, while the majority of taxa showed low PSP across conditions, the overall community PSP increased post-disturbance, with significant shifts occurring among abundant and rare taxa across and within phyla. Broadly, following the post-disturbance reduction in salinity, taxa within Halobacteria decreased while those within Crenarchaeota, Thaumarchaeota, Thermoplasmata, Cyanobacteria, and Proteobacteria, increased in abundance and PSP. Quantitative PCR of genes and transcripts involved in nitrogen and sulfur cycling showed concomitant shifts in biogeochemical cycling potential. Post-disturbance conditions increased the expression of genes involved in N-fixation, nitrification, denitrification, and sulfate reduction. Together, our findings show complex community adaptation to environmental change and help

  12. Triclosan: A Widespread Environmental Toxicant with Many Biological Effects.

    Science.gov (United States)

    Yueh, Mei-Fei; Tukey, Robert H

    2016-01-01

    Triclosan (TCS) is a broad-spectrum antimicrobial agent that has been added to personal care products, including hand soaps and cosmetics, and impregnated in numerous different materials ranging from athletic clothing to food packaging. The constant disposal of TCS into the sewage system is creating a major environmental and public health hazard. Owing to its chemical properties of bioaccumulation and resistance to degradation, TCS is widely detected in various environmental compartments in concentrations ranging from nanograms to micrograms per liter. Epidemiology studies indicate that significant levels of TCS are detected in body fluids in all human age groups. We document here the emerging evidence--from in vitro and in vivo animal studies and environmental toxicology studies--demonstrating that TCS exerts adverse effects on different biological systems through various modes of action. Considering the fact that humans are simultaneously exposed to TCS and many TCS-like chemicals, we speculate that TCS-induced adverse effects may be relevant to human health. PMID:26738475

  13. Tunable ultrasensitivity: functional decoupling and biological insights.

    Science.gov (United States)

    Wang, Guanyu; Zhang, Mengshi

    2016-01-01

    Sensitivity has become a basic concept in biology, but much less is known about its tuning, probably because allosteric cooperativity, the best known mechanism of sensitivity, is determined by rigid conformations of interacting molecules and is thus difficult to tune. Reversible covalent modification (RCM), owing to its systems-level ingenuity, can generate concentration based, tunable sensitivity. Using a mathematical model of regulated RCM, we find sensitivity tuning can be decomposed into two orthogonal modes, which provide great insights into vital biological processes such as tissue development and cell cycle progression. We find that decoupling of the two modes of sensitivity tuning is critical to fidelity of cell fate decision; the decoupling is thus important in development. The decomposition also allows us to solve the 'wasteful degradation conundrum' in budding yeast cell cycle checkpoint, which further leads to discovery of a subtle but essential difference between positive feedback and double negative feedback. The latter guarantees revocability of stress-induced cell cycle arrest; while the former does not. By studying concentration conditions in the system, we extend applicability of ultrasensitivity and explain the ubiquity of reversible covalent modification. PMID:26847155

  14. Hereditary and environmental influences on arterial function.

    Science.gov (United States)

    Hayward, C S; Benetos, A

    2007-07-01

    1. With the ageing population and increasing heart failure, arterial function has been shown to contribute to cardiovascular risk because of its adverse effects on ventriculovascular coupling. Population studies have confirmed independent prognostic information of arterial stiffening on cardiovascular survival. 2. The term 'arterial function' encompasses a range of phenotypes, including measures of arterial structure/remodelling, measures of arterial wall mechanics, surrogate measures of stiffness and of wave reflection. There exists significant interaction between these measures and none is truly independent of the others. Added to this complexity is the recognition that, although arterial function has a strong genetic component, quantification requires a range of techniques from twin to family and population studies. 3. The contribution of heritability is often derived from statistical models with input from genomic scanning and candidate gene studies. Studies to date confirm a significant heritable component for the majority of phenotypes examined. However, it has also been recognized that the factors involved in blood pressure maintenance are likely to be separate to those in arterial structural degeneration with ageing. Candidate genes for arterial function go beyond those of the sympathetic and renin-angiotensin systems and include genes involved in signalling pathways and extracellular matrix modulation. 4. The present review examines the evidence for heritability of the major arterial function phenotypes with environmental and ageing modulation. A brief overview of the impact of atherosclerotic risk factors on arterial function is included.

  15. Printable Bioelectronics To Investigate Functional Biological Interfaces.

    Science.gov (United States)

    Manoli, Kyriaki; Magliulo, Maria; Mulla, Mohammad Yusuf; Singh, Mandeep; Sabbatini, Luigia; Palazzo, Gerardo; Torsi, Luisa

    2015-10-19

    Thin-film transistors can be used as high-performance bioelectronic devices to accomplish tasks such as sensing or controlling the release of biological species as well as transducing the electrical activity of cells or even organs, such as the brain. Organic, graphene, or zinc oxide are used as convenient printable semiconducting layers and can lead to high-performance low-cost bioelectronic sensing devices that are potentially very useful for point-of-care applications. Among others, electrolyte-gated transistors are of interest as they can be operated as capacitance-modulated devices, because of the high capacitance of their charge double layers. Specifically, it is the capacitance of the biolayer, being lowest in a series of capacitors, which controls the output current of the device. Such an occurrence allows for extremely high sensitivity towards very weak interactions. All the aspects governing these processes are reviewed here. PMID:26420480

  16. Towards Integration of Biological and Physiological Functions at Multiple Levels

    Directory of Open Access Journals (Sweden)

    Taishin eNomura

    2010-12-01

    Full Text Available An aim of systems physiology today can be stated as to establish logical and quantitative bridges between phenomenological attributes of physiological entities such as cells and organs and physical attributes of biological entities, i.e., biological molecules, allowing us to describe and better understand physiological functions in terms of underlying biological functions. This article illustrates possible schema that can be used for promoting systems physiology by integrating quantitative knowledge of biological and physiological functions at multiple levels of time and space with the use of information technology infrastructure. Emphasis will be made for systematic, modular, hierarchical, and standardized descriptions of mathematical models of the functions and advantages for the use of them.

  17. Selenium: environmental significance, pollution, and biological treatment technologies.

    Science.gov (United States)

    Tan, Lea Chua; Nancharaiah, Yarlagadda V; van Hullebusch, Eric D; Lens, Piet N L

    2016-01-01

    Selenium is an essential trace element needed for all living organisms. Despite its essentiality, selenium is a potential toxic element to natural ecosystems due to its bioaccumulation potential. Though selenium is found naturally in the earth's crust, especially in carbonate rocks and volcanic and sedimentary soils, about 40% of the selenium emissions to atmospheric and aquatic environments are caused by various industrial activities such as mining-related operations. In recent years, advances in water quality and pollution monitoring have shown that selenium is a contaminant of potential environmental concern. This has practical implications on industry to achieve the stringent selenium regulatory discharge limit of 5μgSeL(-1) for selenium containing wastewaters set by the United States Environmental Protection Agency. Over the last few decades, various technologies have been developed for the treatment of selenium-containing wastewaters. Biological selenium reduction has emerged as the leading technology for removing selenium from wastewaters since it offers a cheaper alternative compared to physico-chemical treatments and is suitable for treating dilute and variable selenium-laden wastewaters. Moreover, biological treatment has the advantage of forming elemental selenium nanospheres which exhibit unique optical and spectral properties for various industrial applications, i.e. medical, electrical, and manufacturing processes. However, despite the advances in biotechnology employing selenium reduction, there are still several challenges, particularly in achieving stringent discharge limits, the long-term stability of biogenic selenium and predicting the fate of bioreduced selenium in the environment. This review highlights the significance of selenium in the environment, health, and industry and biotechnological advances made in the treatment of selenium contaminated wastewaters. The challenges and future perspectives are overviewed considering recent

  18. Selenium: environmental significance, pollution, and biological treatment technologies.

    Science.gov (United States)

    Tan, Lea Chua; Nancharaiah, Yarlagadda V; van Hullebusch, Eric D; Lens, Piet N L

    2016-01-01

    Selenium is an essential trace element needed for all living organisms. Despite its essentiality, selenium is a potential toxic element to natural ecosystems due to its bioaccumulation potential. Though selenium is found naturally in the earth's crust, especially in carbonate rocks and volcanic and sedimentary soils, about 40% of the selenium emissions to atmospheric and aquatic environments are caused by various industrial activities such as mining-related operations. In recent years, advances in water quality and pollution monitoring have shown that selenium is a contaminant of potential environmental concern. This has practical implications on industry to achieve the stringent selenium regulatory discharge limit of 5μgSeL(-1) for selenium containing wastewaters set by the United States Environmental Protection Agency. Over the last few decades, various technologies have been developed for the treatment of selenium-containing wastewaters. Biological selenium reduction has emerged as the leading technology for removing selenium from wastewaters since it offers a cheaper alternative compared to physico-chemical treatments and is suitable for treating dilute and variable selenium-laden wastewaters. Moreover, biological treatment has the advantage of forming elemental selenium nanospheres which exhibit unique optical and spectral properties for various industrial applications, i.e. medical, electrical, and manufacturing processes. However, despite the advances in biotechnology employing selenium reduction, there are still several challenges, particularly in achieving stringent discharge limits, the long-term stability of biogenic selenium and predicting the fate of bioreduced selenium in the environment. This review highlights the significance of selenium in the environment, health, and industry and biotechnological advances made in the treatment of selenium contaminated wastewaters. The challenges and future perspectives are overviewed considering recent

  19. Fibroblast Growth Factors: Biology, Function, and Application for Tissue Regeneration

    OpenAIRE

    Ye-Rang Yun; Jong Eun Won; Eunyi Jeon; Sujin Lee; Wonmo Kang; Hyejin Jo; Jun-Hyeog Jang; Ueon Sang Shin; Hae-Won Kim

    2010-01-01

    Fibroblast growth factors (FGFs) that signal through FGF receptors (FGFRs) regulate a broad spectrum of biological functions, including cellular proliferation, survival, migration, and differentiation. The FGF signal pathways are the RAS/MAP kinase pathway, PI3 kinase/AKT pathway, and PLCγ pathway, among which the RAS/MAP kinase pathway is known to be predominant. Several studies have recently implicated the in vitro biological functions of FGFs for tissue regeneration. However, to obtain opt...

  20. Genomic Functionalization: The Next Revolution In Biology.

    Energy Technology Data Exchange (ETDEWEB)

    Imbro, Paula; Schoeniger, Joseph S.; Anderson, Peter

    2014-07-01

    We have implemented a ligand-alignment algorithm into our developed computational pipeline for identifying specificity-determining features (SDFs) in protein-ligand complexes. Given a set of protein-ligand complex structures, the algorithm aligns the complexes by ligand rather than by the C -RMSD or standard approach, providing a single reference frame for extracting SDFs. We anticipate that this ligand-alignment capability will be highly useful for protein function prediction. We already have a database containing > 20 K ligand-protein complex crystal structures taken from the Protein Data Bank. By aligning these proteins to single reference frames using ligand alignment, we can submit the complexes to our pipeline for SDF extraction. The SDFs derived from this training procedure can be used as thumbprints that are hallmarks of individual enzyme classes. These SDF thumbprints may then serve as guides to the prediction of function of new unknown proteins. Page 4 of 17 PAGE INTENTIONALLY LEFT BLANK

  1. Genomic Functionalization: The Next Revolution In Biology

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Peter [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Schoeniger, Joseph S. [Sandia National Lab. (SNL-CA), Livermore, CA (United States); Imbro, Paula M. [Sandia National Lab. (SNL-CA), Livermore, CA (United States)

    2014-07-01

    We have implemented a ligand-alignment algorithm into our developed computational pipeline for identifying specificity-determining features (SDFs) in protein-ligand complexes. Given a set of protein-ligand complex structures, the algorithm aligns the complexes by ligand rather than by the C -RMSD or standard approach, providing a single reference frame for extracting SDFs. We anticipate that this ligand-alignment capability will be highly useful for protein function prediction. We already have a database containing > 20 K ligand-protein complex crystal structures taken from the Protein Data Bank. By aligning these proteins to single reference frames using ligand alignment, we can submit the complexes to our pipeline for SDF extraction. The SDFs derived from this training procedure can be used as thumbprints that are hallmarks of individual enzyme classes. These SDF thumbprints may then serve as guides to the prediction of function of new unknown proteins.

  2. Labeling and functionalizing amphipols for biological applications.

    Science.gov (United States)

    Le Bon, Christel; Popot, Jean-Luc; Giusti, Fabrice

    2014-10-01

    Amphipols (APols) are short amphipathic polymers developed as an alternative to detergents for handling membrane proteins (MPs) in aqueous solution. MPs are, as a rule, much more stable following trapping with APols than they are in detergent solutions. The best-characterized APol to date, called A8-35, is a mixture of short-chain sodium polyacrylates randomly derivatized with octylamine and isopropylamine. Its solution properties have been studied in detail, and it has been used extensively for biochemical and biophysical studies of MPs. One of the attractive characteristics of APols is that it is relatively easy to label them, isotopically or otherwise, without affecting their physical-chemical properties. Furthermore, several variously modified APols can be mixed, achieving multiple functionalization of MP/APol complexes in the easiest possible manner. Labeled or tagged APols are being used to study the solution properties of APols, their miscibility, their biodistribution upon injection into living organisms, their association with MPs and the composition, structure and dynamics of MP/APol complexes, examining the exchange of surfactants at the surface of MPs, labeling MPs to follow their distribution in fractionation experiments or to immobilize them, increasing the contrast between APols and solvent or MPs in biophysical experiments, improving NMR spectra, etc. Labeling or functionalization of APols can take various courses, each of which has its specific constraints and advantages regarding both synthesis and purification. The present review offers an overview of the various derivatives of A8-35 and its congeners that have been developed in our laboratory and discusses the pros and cons of various synthetic routes. PMID:24696186

  3. [Biological experiments in microgravity: equilibrium function].

    Science.gov (United States)

    Gorgiladze, G I; Shipov, A A; Horn, E

    2012-01-01

    The review deals with the investigations of structural and functional modifications in the equilibrium organ (EO) in invertebrates (coelenterates, shells, crustaceans and insects) and vertebrates (fishes, amphibians, rats, primates) on different ontogenetic stages in the condition of microgravity and during readaptation to the Earth's gravity. Results of the investigations detail the adaptive strategy of terrestrial organism in the environment lacking the gravitational components that leads to the discrepancy of an inner model of the body-environment schema constructed by the central nervous system at 1 g and the novel reality. It is manifested by ataxic behavior and increased graviceptors' afferentation against efferent system inactivation. The new condition is defined as a sensibilization phase ensued by the eluding phase: behavior obeys the innate motion strategy, whereas graviceptors' afferentation decreases due to activation of the efferent system. Readaptation to 1 G takes several to 50 days and proceeds as a sequence of slow in motion behavior, ataxia and vestibular sensitization. Reactivity of the gravitosensory system to microgravity was found to be age-dependent. Gain in the EO inertial mass in microgravity and reduction with return to 1 g indicates gravity relevance to EO genesis. PMID:23402139

  4. Evidence for a Role of Executive Functions in Learning Biology

    Science.gov (United States)

    Rhodes, Sinéad M.; Booth, Josephine N.; Campbell, Lorna Elise; Blythe, Richard A.; Wheate, Nial J.; Delibegovic, Mirela

    2014-01-01

    Research examining cognition and science learning has focused on working memory, but evidence implicates a broader set of executive functions. The current study examined executive functions and learning of biology in young adolescents. Fifty-six participants, aged 12-13?years, completed tasks of working memory (Spatial Working Memory), inhibition…

  5. Challenges for biological interpretation of environmental proteomics data in non-model organisms.

    Science.gov (United States)

    Dowd, W Wesley

    2012-11-01

    Environmental physiology, toxicology, and ecology and evolution stand to benefit substantially from the relatively recent surge of "omics" technologies into these fields. These approaches, and proteomics in particular, promise to elucidate novel and integrative functional responses of organisms to diverse environmental challenges, over a variety of time scales and at different levels of organization. However, application of proteomics to environmental questions suffers from several challenges--some unique to high-throughput technologies and some relevant to many related fields--that may confound downstream biological interpretation of the data. I explore three of these challenges in environmental proteomics, emphasizing the dependence of biological conclusions on (1) the specific experimental context, (2) the choice of statistical analytical methods, and (3) the degree of proteome coverage and protein identification rates, both of which tend to be much less than 100% (i.e., analytical incompleteness). I use both a review of recent publications and data generated from my previous and ongoing proteomics studies of coastal marine animals to examine the causes and consequences of these challenges, in one case analyzing the same multivariate proteomics data set using 29 different combinations of statistical techniques common in the literature. Although some of the identified issues await further critical assessment and debate, when possible I offer suggestions for meeting these three challenges.

  6. Evolutionary cell biology: functional insight from "endless forms most beautiful".

    Science.gov (United States)

    Richardson, Elisabeth; Zerr, Kelly; Tsaousis, Anastasios; Dorrell, Richard G; Dacks, Joel B

    2015-12-15

    In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking. PMID:26668171

  7. Evolutionary cell biology: functional insight from "endless forms most beautiful".

    Science.gov (United States)

    Richardson, Elisabeth; Zerr, Kelly; Tsaousis, Anastasios; Dorrell, Richard G; Dacks, Joel B

    2015-12-15

    In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking.

  8. Systematic Functional Annotation and Visualization of Biological Networks.

    Science.gov (United States)

    Baryshnikova, Anastasia

    2016-06-22

    Large-scale biological networks represent relationships between genes, but our understanding of how networks are functionally organized is limited. Here, I describe spatial analysis of functional enrichment (SAFE), a systematic method for annotating biological networks and examining their functional organization. SAFE visualizes the network in 2D space and measures the continuous distribution of functional enrichment across local neighborhoods, producing a list of the associated functions and a map of their relative positioning. I applied SAFE to annotate the Saccharomyces cerevisiae genetic interaction similarity network and protein-protein interaction network with gene ontology terms. SAFE annotations of the genetic network matched manually derived annotations, while taking less than 1% of the time, and proved robust to noise and sensitive to biological signal. Integration of genetic interaction and chemical genomics data using SAFE revealed a link between vesicle-mediate transport and resistance to the anti-cancer drug bortezomib. These results demonstrate the utility of SAFE for examining biological networks and understanding their functional organization. PMID:27237738

  9. Integrated Omics in Systems Biology: The New Frontier for Environmental Biotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Hazen, Terry C.

    2008-08-12

    Environmental biotechnology encompasses a wide range of characterization, monitoring and control for bioenergy and bioremediation technologies that are based on biological processes. Recent breakthroughs in our understanding of biogeochemical processes and genomics are leading to exciting new and cost effective ways to monitor and manipulate the environment and potentially produce bioenergy fuels as we also cleanup the environment. Indeed, our ability to sequence an entire microbial genome in just a few hours is leading to similar breakthroughs in characterizing proteomes, metabolomes, phenotypes, and fluxes for organisms, populations, and communities. Understanding and modeling functional microbial community structure and stress responses in subsurface environments has tremendous implications for our fundamental understanding of biogeochemistry and the potential for making biofuel breakthroughs. Monitoring techniques that inventory and monitor terminal electron acceptors and electron donors, enzyme probes that measure functional activity in the environment, functional genomic microarrays, phylogenetic microarrays, metabolomics, proteomics, and quantitative PCR are also being rapidly adapted for studies in environmental biotechnology. Integration of all of these new high throughput techniques using the latest advances in bioinformatics and modeling will enable break-through science in environmental biotechnology. A review of these techniques with examples from field studies and lab simulations will be discussed.

  10. Biomarkers of Aging: From Function to Molecular Biology

    OpenAIRE

    Karl-Heinz Wagner; David Cameron-Smith; Barbara Wessner; Bernhard Franzke

    2016-01-01

    Aging is a major risk factor for most chronic diseases and functional impairments. Within a homogeneous age sample there is a considerable variation in the extent of disease and functional impairment risk, revealing a need for valid biomarkers to aid in characterizing the complex aging processes. The identification of biomarkers is further complicated by the diversity of biological living situations, lifestyle activities and medical treatments. Thus, there has been no identification of a sing...

  11. Uncovering Biological Network Function via Graphlet Degree Signatures

    Directory of Open Access Journals (Sweden)

    Nataša Pržulj

    2008-01-01

    Full Text Available Motivation: Proteins are essential macromolecules of life and thus understanding their function is of great importance. The number of functionally unclassified proteins is large even for simple and well studied organisms such as baker’s yeast. Methods for determining protein function have shifted their focus from targeting specific proteins based solely on sequence homology to analyses of the entire proteome based on protein-protein interaction (PPI networks. Since proteins interact to perform a certain function, analyzing structural properties of PPI networks may provide useful clues about the biological function of individual proteins, protein complexes they participate in, and even larger subcellular machines.Results: We design a sensitive graph theoretic method for comparing local structures of node neighborhoods that demonstrates that in PPI networks, biological function of a node and its local network structure are closely related. The method summarizes a protein’s local topology in a PPI network into the vector of graphlet degrees called the signature of the protein and computes the signature similarities between all protein pairs. We group topologically similar proteins under this measure in a PPI network and show that these protein groups belong to the same protein complexes, perform the same biological functions, are localized in the same subcellular compartments, and have the same tissue expressions. Moreover, we apply our technique on a proteome-scale network data and infer biological function of yet unclassified proteins demonstrating that our method can provide valuable guidelines for future experimental research such as disease protein prediction.Availability: Data is available upon request.

  12. Functional and biological characteristics of asthma in cleaning workers.

    NARCIS (Netherlands)

    Vizcaya, D.; Mirabelli, M.C.; Orriols, R.; Antó, J.M.; Barreiro, E.; Burgos, F.; Arjona, L.; Gomez, F.; Zock, J.P.

    2013-01-01

    Objectives: Cleaning workers have an increased risk of asthma but the underlying mechanisms are largely unknown. We studied functional and biological characteristics in asthmatic cleaners and compared these to healthy cleaners. Methods: Forty-two cleaners with a history of asthma and/or recent respi

  13. Biological ensilage of fish - optimization of stability, safety and functionality

    NARCIS (Netherlands)

    Enes Dapkevicius, M.L.N.

    2002-01-01

    This thesis deals with stability, safety, and functionality aspects of biological fish silage (BFS) obtained by lactic acid fermentation. BFS may provide an economically viable, environment friendly way of upgrading fish waste.BFS has been found advantageous when compared to the so-called acid proce

  14. Applications of large-scale density functional theory in biology.

    Science.gov (United States)

    Cole, Daniel J; Hine, Nicholas D M

    2016-10-01

    Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality. PMID:27494095

  15. Applications of large-scale density functional theory in biology

    Science.gov (United States)

    Cole, Daniel J.; Hine, Nicholas D. M.

    2016-10-01

    Density functional theory (DFT) has become a routine tool for the computation of electronic structure in the physics, materials and chemistry fields. Yet the application of traditional DFT to problems in the biological sciences is hindered, to a large extent, by the unfavourable scaling of the computational effort with system size. Here, we review some of the major software and functionality advances that enable insightful electronic structure calculations to be performed on systems comprising many thousands of atoms. We describe some of the early applications of large-scale DFT to the computation of the electronic properties and structure of biomolecules, as well as to paradigmatic problems in enzymology, metalloproteins, photosynthesis and computer-aided drug design. With this review, we hope to demonstrate that first principles modelling of biological structure-function relationships are approaching a reality.

  16. Milk protein tailoring to improve functional and biological properties

    Directory of Open Access Journals (Sweden)

    JEAN-MARC CHOBERT

    2012-01-01

    Full Text Available Proteins are involved in every aspects of life: structure, motion, catalysis, recognition and regulation. Today's highly sophisticated science of the modifications of proteins has ancient roots. The tailoring of proteins for food and medical uses precedes the beginning of what is called biochemistry. Chemical modification of proteins was pursued early in the twentieth century as an analytical procedure for side-chain amino acids. Later, methods were developed for specific inactivation of biologically active proteins and titration of their essential groups. Enzymatic modifications were mainly developed in the seventies when many more enzymes became economically available. Protein engineering has become a valuable tool for creating or improving proteins for practical use and has provided new insights into protein structure and function. The actual and potential use of milk proteins as food ingredients has been a popular topic for research over the past 40 years. With today's sophisticated analytical, biochemical and biological research tools, the presence of compounds with biological activity has been demonstrated. Improvements in separation techniques and enzyme technology have enabled efficient and economic isolation and modification of milk proteins, which has made possible their use as functional foods, dietary supplements, nutraceuticals and medical foods. In this review, some chemical and enzymatic modifications of milk proteins are described, with particular focus on their functional and biological properties.

  17. Bigheaded carps : a biological synopsis and environmental risk assessment

    Science.gov (United States)

    Kolar, Cindy S.; Chapman, Duane C.; Courtenay, Walter R., Jr.; Housel, Christine M.; Williams, James D.; Jennings, Dawn P.

    2007-01-01

    The book is a detailed risk assessment and biological synopsis of the bigheaded carps of the genus Hypophthalmichthys, which includes the bighead, silver, and largescale silver carps. It summarizes the scientific literature describing their biology, ecology, uses, ecological effects, and risks to the environment.

  18. A structural biology perspective on NMDA receptor pharmacology and function.

    Science.gov (United States)

    Regan, Michael C; Romero-Hernandez, Annabel; Furukawa, Hiro

    2015-08-01

    N-methyld-aspartate receptors (NMDARs) belong to the large family of ionotropic glutamate receptors (iGluRs), which are critically involved in basic brain functions as well as multiple neurological diseases and disorders. The NMDARs are large heterotetrameric membrane protein complexes. The extensive extracellular domains recognize neurotransmitter ligands and allosteric compounds and translate the binding information to regulate activity of the transmembrane ion channel. Here, we review recent advances in the structural biology of NMDARs with a focus on pharmacology and function. Structural analysis of the isolated extracellular domains in combination with the intact heterotetrameric NMDAR structure provides important insights into how this sophisticated ligand-gated ion channel may function.

  19. Using Wetlands to Teach Ecology & Environmental Awareness in General Biology.

    Science.gov (United States)

    O'Neal, Lyman H.

    1995-01-01

    Presents advantages of using wetlands educationally and their relevance to local, national, and global environmental issues. Discusses field trips to mangrove forests and freshwater marshes. (Author/MKR)

  20. Morpho-chemistry and functionality of diseased biological tissues

    Science.gov (United States)

    Lange, Marta; Cicchi, Riccardo; Pavone, Francesco

    2014-09-01

    Heart and cardiovascular diseases are one of the most common in the world, in particular - arthrosclerosis. The aim of the research is to distinguish pathological and healthy tissue regions in biological samples, in this case - to distinguish collagen and lipid rich regions within the arterial wall. In the work a specific combination of such methods are used: FLIM and SHG in order to evaluate the biological tissue morphology and functionality, so that this research could give a contribution for creating a new biological tissue imaging standard in the closest future. During the study the most appropriate parameter for fluorescence lifetime decay was chosen in order to evaluate lifetime decay parameters and the isotropy of the arterial wall and deposition, using statistical methods FFT and GLCM. The research gives a contribution or the future investigations for evaluating lipid properties when it can de-attach from the arterial wall and cause clotting in the blood vessel or even a stroke.

  1. NMR-based Metabolomics Applications in Biological and Environmental Science

    Science.gov (United States)

    As a complimentary tool to other omics platforms, metabolomics is increasingly being used bybiologists to study the dynamic response of biological systems (cells, tissues, or wholeorganisms) under diverse physiological or pathological conditions. Metabolomics deals with the quali...

  2. Environmental DNA for wildlife biology and biodiversity monitoring

    DEFF Research Database (Denmark)

    Bohmann, Kristine; Evans, Alice; Gilbert, M. Thomas P.;

    2014-01-01

    Extraction and identification of DNA from an environmental sample has proven noteworthy recently in detecting and monitoring not only common species, but also those that are endangered, invasive, or elusive. Particular attributes of so-called environmental DNA (eDNA) analysis render it a potent...

  3. ENVIRONMENTAL ATTITUDES OF BIOLOGY TEACHER CANDIDATES AND THE ASSESSMENTS IN TERMS OF SOME VARIABLES

    OpenAIRE

    UĞULU, İlker; ERKOL, Sevilay

    2013-01-01

    Studying individuals and students' attitudes towards environment and factors affecting students to be responsible individuals towards their environment may provide help towards the solution of environmental problems. In this study, it is aimed to evaluate environmental attitudes of biology teacher candidates in terms of some variables. As a means of data collection, Environmental Attitude Scale and the personal information form have been used. Environmental Attitude Scale which has 35 items i...

  4. Biological collections and ecological/environmental research: a review, some observations and a look to the future.

    Science.gov (United States)

    Pyke, Graham H; Ehrlich, Paul R

    2010-05-01

    Housed worldwide, mostly in museums and herbaria, is a vast collection of biological specimens developed over centuries. These biological collections, and associated taxonomic and systematic research, have received considerable long-term public support. The work remaining in systematics has been expanding as the estimated total number of species of organisms on Earth has risen over recent decades, as have estimated numbers of undescribed species. Despite this increasing task, support for taxonomic and systematic research, and biological collections upon which such research is based, has declined over the last 30-40 years, while other areas of biological research have grown considerably, especially those that focus on environmental issues. Reflecting increases in research that deals with ecological questions (e.g. what determines species distribution and abundance) or environmental issues (e.g. toxic pollution), the level of research attempting to use biological collections in museums or herbaria in an ecological/environmental context has risen dramatically during about the last 20 years. The perceived relevance of biological collections, and hence the support they receive, should be enhanced if this trend continues and they are used prominently regarding such environmental issues as anthropogenic loss of biodiversity and associated ecosystem function, global climate change, and decay of the epidemiological environment. It is unclear, however, how best to use biological collections in the context of such ecological/environmental issues or how best to manage collections to facilitate such use. We demonstrate considerable and increasingly realized potential for research based on biological collections to contribute to ecological/environmental understanding. However, because biological collections were not originally intended for use regarding such issues and have inherent biases and limitations, they are proving more useful in some contexts than in others. Biological

  5. SU-E-T-54: Benefits of Biological Cost Functions

    Energy Technology Data Exchange (ETDEWEB)

    Demirag, N [Elekta CMS GmbH, Freiburg Im Breisgau, baden wurttemberg (Germany)

    2014-06-01

    Purpose: To verify the benefits of the biological cost functions. Methods: TG166 patients were used for the test case scenarios. Patients were planned using Monaco V5.0 (CMS/Elekta, St.Louis, MO) Monaco has 3 biological and 8 physical CFs. In this study the plans were optimized using 3 different scenarios. 1- Biological CFs only 2-Physical CFs only 3- Combination of Physical and Biological CFsMonaco has 3 biological CFs. Target EUD used for the targets, derived from the poisson cell kill model, has an α value that controls the cold spots inside the target. α values used in the optimization were 0.5 and 0.8. if cold spots needs to be penalized α value increased. Serial CF: it's called serial to mimic the behaviour of the serial organs, if a high k value like 12 or 14 is used it controls the maximum dose. Serial CF has a k parameter that is used to shape the whole dvh curve. K value ranges between 1–20. k:1 is used to control the mean dose, lower k value controls the mean dose, higher k value controls the higher dose, using 2 serial CFs with different k values controls the whole DVH. Paralel CF controls the percentage of the volume that tolerates higher doses than the reference dose to mimic the behaviour of the paralel organs. Results: It was possible to achive clinically accepted plans in all 3 scenarios. The benefit of the biological cost functions were to control the mean dose for target and OAR, to shape the DVH curve using one EUD value and one k value simplifies the optimization process. Using the biological CFs alone, it was hard to control the dose at a point. Conclusion: Biological CFs in Monaco doesn't require the ntcp/tcp values from the labs and useful to shape the whole dvh curve. I work as an applications support specialist for Elekta and I am a Ph.D. Student in Istanbul University for radiation therapy physics.

  6. Biological framework for soil aggregation: Implications for ecological functions.

    Science.gov (United States)

    Ghezzehei, Teamrat; Or, Dani

    2016-04-01

    Soil aggregation is heuristically understood as agglomeration of primary particles bound together by biotic and abiotic cementing agents. The organization of aggregates is believed to be hierarchical in nature; whereby primary particles bond together to form secondary particles and subsequently merge to form larger aggregates. Soil aggregates are not permanent structures, they continuously change in response to internal and external forces and other drivers, including moisture, capillary pressure, temperature, biological activity, and human disturbances. Soil aggregation processes and the resulting functionality span multiple spatial and temporal scales. The intertwined biological and physical nature of soil aggregation, and the time scales involved precluded a universally applicable and quantifiable framework for characterizing the nature and function of soil aggregation. We introduce a biophysical framework of soil aggregation that considers the various modes and factors of the genesis, maturation and degradation of soil aggregates including wetting/drying cycles, soil mechanical processes, biological activity and the nature of primary soil particles. The framework attempts to disentangle mechanical (compaction and soil fragmentation) from in-situ biophysical aggregation and provides a consistent description of aggregate size, hierarchical organization, and life time. It also enables quantitative description of biotic and abiotic functions of soil aggregates including diffusion and storage of mass and energy as well as role of aggregates as hot spots of nutrient accumulation, biodiversity, and biogeochemical cycles.

  7. Deducing protein function by forensic integrative cell biology.

    Directory of Open Access Journals (Sweden)

    William C Earnshaw

    2013-12-01

    Full Text Available Our ability to sequence genomes has provided us with near-complete lists of the proteins that compose cells, tissues, and organisms, but this is only the beginning of the process to discover the functions of cellular components. In the future, it's going to be crucial to develop computational analyses that can predict the biological functions of uncharacterised proteins. At the same time, we must not forget those fundamental experimental skills needed to confirm the predictions or send the analysts back to the drawing board to devise new ones.

  8. Functionalized Conjugated Polyelectrolytes for Biological Sensing and Imaging.

    Science.gov (United States)

    Zhan, Ruoyu; Liu, Bin

    2016-06-01

    Conjugated polyelectrolytes (CPEs) are macromolecules with highly delocalized π-conjugated backbones and charged side chains, which are unique types of active materials, with wide applications in optoelectronics, sensing, imaging, and therapy. By attaching specific groups (e.g., recognition elements, magnetic resonance (MR) contrast agents, gene carriers, and drugs) to the side chain or backbone of CPEs, functionalized CPEs have been developed and used for specific biological applications. In this account, we summarize the recent progress of functionalized CPEs with respect to their synthesis and biomedical applications. Future perspectives are also discussed at the end. PMID:27230631

  9. Deducing protein function by forensic integrative cell biology.

    Science.gov (United States)

    Earnshaw, William C

    2013-12-01

    Our ability to sequence genomes has provided us with near-complete lists of the proteins that compose cells, tissues, and organisms, but this is only the beginning of the process to discover the functions of cellular components. In the future, it's going to be crucial to develop computational analyses that can predict the biological functions of uncharacterised proteins. At the same time, we must not forget those fundamental experimental skills needed to confirm the predictions or send the analysts back to the drawing board to devise new ones.

  10. Environmental philosophy 2.0: ethics and conservation biology for the 21st century.

    Science.gov (United States)

    Odenbaugh, Jay

    2014-03-01

    In this essay, I critically engage Sahotra Sarkar's Environmental Philosophy. The several topics include the conceptual foundations of conservation biology and traditional philosophy of science, naturalism and its implications, and ethical theory and specifically the status of human welfare.

  11. Linking exposure to environmental pollutants with biological effects

    DEFF Research Database (Denmark)

    Sørensen, Mette; Autrup, Herman; Møller, Peter;

    2003-01-01

    Exposure to ambient air pollution has been associated with cancer. Ambient air contains a complex mixture of toxics, including particulate matter (PM) and benzene. Carcinogenic effects of PM may relate both to the content of PAH and to oxidative DNA damage generated by transition metals, benzene......, metabolism and inflammation. By means of personal monitoring and biomarkers of internal dose, biologically effective dose and susceptibility, it should be possible to characterize individual exposure and identify air pollution sources with relevant biological effects. In a series of studies, individual......, biological effects of air pollutants appear mainly related to oxidative stress via personal exposure and not to urban background levels. Future developments include personal time-resolved monitors for exposure to ultrafine PM and PM(2.5,) use of GPS, as well as genomics and proteomics based biomarkers....

  12. Annual rhythms that underlie phenology: biological time-keeping meets environmental change

    OpenAIRE

    Helm, Barbara; Ben Shlomo, Rachel; Sheriff, Michael J.; Hut, Roelof A.; Foster, Russell; Barnes, Brian M.; Dominoni, Davide

    2013-01-01

    Seasonal recurrence of biological processes (phenology) and its relationship to environmental change is recognized as being of key scientific and public concern, but its current study largely overlooks the extent to which phenology is based on biological time-keeping mechanisms. We highlight the relevance of physiological and neurobiological regulation for organisms’ responsiveness to environmental conditions. Focusing on avian and mammalian examples, we describe circannual rhythmicity of rep...

  13. Mnk kinase pathway: Cellular functions and biological outcomes

    Institute of Scientific and Technical Information of China (English)

    Sonali; Joshi; Leonidas; C; Platanias

    2014-01-01

    The mitogen-activated protein kinase(MAPK) interacting protein kinases 1 and 2(Mnk1 and Mnk2) play important roles in controlling signals involved in mRNA translation. In addition to the MAPKs(p38 or Erk), multiple studies suggest that the Mnk kinases can be regulated by other known kinases such as Pak2 and/or other unidentified kinases by phosphorylation of residues distinct from the sites phosphorylated by the MAPKs. Several studies have established multiple Mnk protein targets, including PSF, heterogenous nuclear ribonucleoprotein A1, Sprouty 2 and have lead to the identification of distinct biological functions and substrate specificity for the Mnk kinases. In this review we discuss the pathways regulating the Mnk kinases, their known substrates as well as the functional consequences of engagement of pathways controlled by Mnk kinases. These kinases play an important role in mRNA translation via their regulation of eukaryotic initiation factor 4E(eIF4E) and their functions have important implications in tumor biology as well as the regulation of drug resistance to anti-oncogenic therapies. Other studies have identified a role for the Mnk kinases in cap-independent mRNA translation, suggesting that the Mnk kinases can exert important functional effects independently of the phosphorylation of eIF4 E. The role of Mnk kinases in inflammation and inflammationinduced malignancies is also discussed.

  14. Systems analysis of biological networks in skeletal muscle function.

    Science.gov (United States)

    Smith, Lucas R; Meyer, Gretchen; Lieber, Richard L

    2013-01-01

    Skeletal muscle function depends on the efficient coordination among subcellular systems. These systems are composed of proteins encoded by a subset of genes, all of which are tightly regulated. In the cases where regulation is altered because of disease or injury, dysfunction occurs. To enable objective analysis of muscle gene expression profiles, we have defined nine biological networks whose coordination is critical to muscle function. We begin by describing the expression of proteins necessary for optimal neuromuscular junction function that results in the muscle cell action potential. That action potential is transmitted to proteins involved in excitation-contraction coupling enabling Ca(2+) release. Ca(2+) then activates contractile proteins supporting actin and myosin cross-bridge cycling. Force generated by cross-bridges is transmitted via cytoskeletal proteins through the sarcolemma and out to critical proteins that support the muscle extracellular matrix. Muscle contraction is fueled through many proteins that regulate energy metabolism. Inflammation is a common response to injury that can result in alteration of many pathways within muscle. Muscle also has multiple pathways that regulate size through atrophy or hypertrophy. Finally, the isoforms associated with fast muscle fibers and their corresponding isoforms in slow muscle fibers are delineated. These nine networks represent important biological systems that affect skeletal muscle function. Combining high-throughput systems analysis with advanced networking software will allow researchers to use these networks to objectively study skeletal muscle systems. PMID:23188744

  15. Biological properties of extracellular vesicles and their physiological functions

    Directory of Open Access Journals (Sweden)

    María Yáñez-Mó

    2015-05-01

    Full Text Available In the past decade, extracellular vesicles (EVs have been recognized as potent vehicles of intercellular communication, both in prokaryotes and eukaryotes. This is due to their capacity to transfer proteins, lipids and nucleic acids, thereby influencing various physiological and pathological functions of both recipient and parent cells. While intensive investigation has targeted the role of EVs in different pathological processes, for example, in cancer and autoimmune diseases, the EV-mediated maintenance of homeostasis and the regulation of physiological functions have remained less explored. Here, we provide a comprehensive overview of the current understanding of the physiological roles of EVs, which has been written by crowd-sourcing, drawing on the unique EV expertise of academia-based scientists, clinicians and industry based in 27 European countries, the United States and Australia. This review is intended to be of relevance to both researchers already working on EV biology and to newcomers who will encounter this universal cell biological system. Therefore, here we address the molecular contents and functions of EVs in various tissues and body fluids from cell systems to organs. We also review the physiological mechanisms of EVs in bacteria, lower eukaryotes and plants to highlight the functional uniformity of this emerging communication system.

  16. Probing the Xenopus laevis inner ear transcriptome for biological function

    Directory of Open Access Journals (Sweden)

    Powers TuShun R

    2012-06-01

    Full Text Available Abstract Background The senses of hearing and balance depend upon mechanoreception, a process that originates in the inner ear and shares features across species. Amphibians have been widely used for physiological studies of mechanotransduction by sensory hair cells. In contrast, much less is known of the genetic basis of auditory and vestibular function in this class of animals. Among amphibians, the genus Xenopus is a well-characterized genetic and developmental model that offers unique opportunities for inner ear research because of the amphibian capacity for tissue and organ regeneration. For these reasons, we implemented a functional genomics approach as a means to undertake a large-scale analysis of the Xenopus laevis inner ear transcriptome through microarray analysis. Results Microarray analysis uncovered genes within the X. laevis inner ear transcriptome associated with inner ear function and impairment in other organisms, thereby supporting the inclusion of Xenopus in cross-species genetic studies of the inner ear. The use of gene categories (inner ear tissue; deafness; ion channels; ion transporters; transcription factors facilitated the assignment of functional significance to probe set identifiers. We enhanced the biological relevance of our microarray data by using a variety of curation approaches to increase the annotation of the Affymetrix GeneChip® Xenopus laevis Genome array. In addition, annotation analysis revealed the prevalence of inner ear transcripts represented by probe set identifiers that lack functional characterization. Conclusions We identified an abundance of targets for genetic analysis of auditory and vestibular function. The orthologues to human genes with known inner ear function and the highly expressed transcripts that lack annotation are particularly interesting candidates for future analyses. We used informatics approaches to impart biologically relevant information to the Xenopus inner ear transcriptome

  17. Annual rhythms that underlie phenology : biological time-keeping meets environmental change

    NARCIS (Netherlands)

    Helm, Barbara; Ben-Shlomo, Rachel; Sheriff, Michael J; Hut, Roelof A; Foster, Russell; Barnes, Brian M; Dominoni, Davide

    2013-01-01

    Seasonal recurrence of biological processes (phenology) and its relationship to environmental change is recognized as being of key scientific and public concern, but its current study largely overlooks the extent to which phenology is based on biological time-keeping mechanisms. We highlight the rel

  18. Environmental Biology Programs at the University of Illinois, Urbana-Champaign.

    Science.gov (United States)

    Getz, Lowell L.

    1987-01-01

    Describes the programs of the Department of Ecology, Ethology, and Evolution at the University of Illinois (Urbana-Champaign). Focuses on the graduate degrees offered in environmental biology. Lists research interests and courses in plant biology, entomology, forestry, civil engineering, and landscape architecture. (TW)

  19. 75 FR 64984 - Availability of an Environmental Assessment for a Biological Control Agent for Hawkweeds

    Science.gov (United States)

    2010-10-21

    ... Assessment for a Biological Control Agent for Hawkweeds AGENCY: Animal and Plant Health Inspection Service... the control of hawkweeds (Hieracium spp.). The environmental assessment considers the effects of, and... States as a biological control agent to reduce the severity of infestations of hawkweeds. We are...

  20. A systems biology approach to understanding impacts of environmental contaminants on fish reproduction

    Science.gov (United States)

    Over the past decade, our research team at the US EPA Mid-Continent Ecology Division has employed systems biology approaches to examine and understand impacts of environmental contaminants on fish reproduction. Our systems biology approach is one in which iterations of model cons...

  1. Biological monitoring and selected trends in environmental quality. [Use of National Inventory of Selected Biological Monitoring Programs at ORNL to identify documented environmental trends

    Energy Technology Data Exchange (ETDEWEB)

    Suffern, J.S.; West, D.C.; Kemp, H.T.; Burgess, R.L.

    1976-10-01

    Under a contract with the President's Council on Environmental Quality, the National Inventory of Selected Biological Monitoring Programs at ORNL was used to identify documented environmental trends. Fish population trends were described for the Great Lakes and the Colorado River system. Trends in amphibian populations in the northeast were examined and correlated with acid precipitation. Increases in breeding success among large birds of prey were correlated with reductions in ambient levels of DDT and its residues. Geographic variation in PCB contamination was examined along with differences between aquatic and terrestrial contamination levels. Changes in air quality were documented, and their effects on plant viability were outlined. Trends in the biological effects of environmental deposition of lead were documented. Long-term changes in forest structure in the southeast were presented, and a general reduction in wildlife habitat, associated with land use practices, was documented for several areas in the US.

  2. Click Chemistry Mediated Functionalization of Vertical Nanowires for Biological Applications.

    Science.gov (United States)

    Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica; Buch-Månson, Nina; Bovet, Nicolas; Nygård, Jesper; Martinez, Karen L; Meldal, Morten

    2016-01-11

    Semiconductor nanowires (NWs) are gaining significant importance in various biological applications, such as biosensing and drug delivery. Efficient and controlled immobilization of biomolecules on the NW surface is crucial for many of these applications. Here, we present for the first time the use of the Cu(I) -catalyzed alkyne-azide cycloaddition and its strain-promoted variant for the covalent functionalization of vertical NWs with peptides and proteins. The potential of the approach was demonstrated in two complementary applications of measuring enzyme activity and protein binding, which is of general interest for biological studies. The attachment of a peptide substrate provided NW arrays for the detection of protease activity. In addition, green fluorescent protein was immobilized in a site-specific manner and recognized by antibody binding to demonstrate the proof-of-concept for the use of covalently modified NWs for diagnostic purposes using minute amounts of material.

  3. Phenological response of a key ecosystem function to biological invasion.

    Science.gov (United States)

    Alp, Maria; Cucherousset, Julien; Buoro, Mathieu; Lecerf, Antoine

    2016-05-01

    Although climate warming has been widely demonstrated to induce shifts in the timing of many biological events, the phenological consequences of other prominent global change drivers remain largely unknown. Here, we investigated the effects of biological invasions on the seasonality of leaf litter decomposition, a crucial freshwater ecosystem function. Decomposition rates were quantified in 18 temperate shallow lakes distributed along a gradient of crayfish invasion and a temperature-based model was constructed to predict yearly patterns of decomposition. We found that, through direct detritus consumption, omnivorous invasive crayfish accelerated decomposition rates up to fivefold in spring, enhancing temperature dependence of the process and shortening the period of major detritus availability in the ecosystem by up to 39 days (95% CI: 15-61). The fact that our estimates are an order of magnitude higher than any previously reported climate-driven phenological shifts indicates that some powerful drivers of phenological change have been largely overlooked. PMID:26931804

  4. Chemical and biological flocculation process to treat municipal sewage and analysis of biological function

    Institute of Scientific and Technical Information of China (English)

    XIA Si-qing; YANG Dian-hai; XU Bin; ZHAO Jian-fu

    2005-01-01

    The pilot-scale experimental apparatus and the procedure of the chemical and biological flocculation process to verify the feasibility in treating Shanghai municipal sewage were introduced in this paper. In addition, the biological function of the process was discussed. The results of optimal running showed that in the reaction tank, the concentration of mixed liquor suspended solid(MLSS) was2 g/L, hydraulic retention time(HRT) was 35 min, dosage of liquid polyaluminium chloride(PAC) was 60 mg/L, and the concentration of polyacrylamide(PAM) was 0.5 mg/L. The effluent average concentrations of CODcr, TP, SS and BOD5 were 50 mg/L, 0.62 mg/L, 18mg/L, and 17 mg/L, respectively. These were better than the designed demand. In addition, the existence of biological degradation in this system was proven by several methods. The removal efficiencies of the chemical and biological flocculation process were 20% higher than that of the chemical flocculation process above at the same coagulant dosage. The treatment process under different situations was evaluated on a pilot-scale experiment, and the results provided magnificent parameters and optimal condition for future operation of the plant.

  5. Lipids in the structure and functions of biological membranes

    Directory of Open Access Journals (Sweden)

    Kuznetsov V.I.

    2014-06-01

    Full Text Available Lipids are one of the main components of cellular membranes. Lipids make up 30-55% of the cell content depending on the types of cells. Phospholipids, sphingomyelins, cholesterol, etc. are characteristic to cellular membranes. The composition of lipids of the both sides of the membranes differs. This fact determines asymmetry of the structure of bili-pid layer. The reason for many pathologies is the changes in the properties of cellular membranes with the modification of their components. The study of structure and functioning of cellular biomembranes is essential for many researchers. The condition of membranes, their quality, their quantitative composition and modification under the influence of different factors as well as their interaction with carbohydrate and protein component are of great importance for the functioning of both membranes, cells and the body in general. Analysis and structuring of lipids and their functions in biological membranes are studied.

  6. Technologies for detecting botulinum neurotoxins in biological and environmental matrices

    Science.gov (United States)

    Biomonitoring of food and environmental matrices is critical for the rapid and sensitive diagnosis, treatment, and prevention of diseases caused by toxins. The United States Centers for Disease Control and Prevention (CDC) has noted that toxins from bacteria, fungi, algae, and plants present an ongo...

  7. The Impact of Collective Molecular Dynamics on Physiological and Biological Functionalities of Artificial and Biological Membranes

    Science.gov (United States)

    Rheinstadter, Maikel

    2008-03-01

    We use neutron, X-ray and light scattering techniques to determine dynamical and structural properties of artificial and biological membranes. The combination of various techniques enlarges the window to length scales from the nearest-neighbor distances of lipid molecules to more than 10-6m, covering time scales from about 0.1 ps to 1 s. The main research objective is to quantify collective molecular fluctuations in these systems and to establish relationships to physiological and biological functions of the bilayers, such as transmembrane transport. The motivation for this project is twofold: 1) By understanding fundamental properties of bilayers at the microscopic and mesoscopic level, we aim to tailor membranes with specific properties such as permeability and elasticity. 2) By relating dynamical fluctuations to physiological and biological functions, we can gain a deeper understanding of the bilayers on a molecular scale that may help optimizing the transmembrane transport of certain drugs. We show how bilayer permeability, elasticity and inter protein excitations can be determined from the experiments. M.C. Rheinstädter et al., Phys. Rev. Lett. 93, 108107 (2004); Phys. Rev. Lett. 97, 048103 (2006); Phys. Rev. E 75, 011907 (2007);J. Vac. Soc. Technol. A 24, 1191 (2006).

  8. 76 FR 78661 - Correction for Draft Vieques Report: An Evaluation of Environmental, Biological, and Health Data...

    Science.gov (United States)

    2011-12-19

    ... Draft Vieques Report: An Evaluation of Environmental, Biological, and Health Data From the Island of....gov . SUPPLEMENTARY INFORMATION: This report's principal focus is to review updated environmental data... HUMAN SERVICES Agency for Toxic Substances and Disease Registry Correction for Draft Vieques Report:...

  9. 76 FR 77234 - Availability of Draft Vieques Report: An Evaluation of Environmental, Biological, and Health Data...

    Science.gov (United States)

    2011-12-12

    ... availability of the Draft Vieques Report: An Evaluation of Environmental, Biological, and Health Data from the... environmental data on Vieques air, water, soil, seafood, and locally grown foods. In addition, this report.... This notice announces the availability of the draft Vieques Report: An Evaluation of...

  10. Natural environmental impacts on teleost immune function.

    Science.gov (United States)

    Makrinos, Daniel L; Bowden, Timothy J

    2016-06-01

    The environment in which teleosts exist can experience considerable change. Short-term changes can occur in relation to tidal movements or adverse weather events. Long-term changes can be caused by anthropogenic impacts such as climate change, which can result in changes to temperature, acidity, salinity and oxygen capacity of aquatic environments. These changes can have important impacts on the physiology of an animal, including its immune system. This can have consequences on the well-being of the animal and its ability to protect against pathogens. This review will look at recent investigations of these types of environmental change on the immune response in teleosts. PMID:26973022

  11. Functionalization of hydroxyl terminated polybutadiene with biologically active fluorescent molecule

    Indian Academy of Sciences (India)

    R Murali Sankar; Subhadeep Saha; K Seeni Meera; Tushar Jana

    2009-10-01

    A biologically active molecule, 2-chloro-4,6-bis(dimethylamino)-1,3,5-triazine (CBDT), has been covalently attached at the terminal carbon atoms of the hydroxyl terminated polybutadiene (HTPB) backbone. The modification of HTPB backbone by CBDT molecule does not affect the unique physico-chemical properties such as fluidity, hydroxyl value and microstructure of the parent HTPB. The formation of hydrogen bonding between the terminal hydroxyl groups and the nitrogen atoms of triazine moiety is the driving force for the terminal attachment chemistry. The functionalized HTPB (HTPB–CBDT) shows a strong fluorescence emission at 385 nm.

  12. Functionalization of polydopamine coated magnetic nanoparticles with biological entities

    Science.gov (United States)

    Mǎgeruşan, Lidia; Mrówczyński, Radosław; Turcu, Rodica

    2015-12-01

    New hybrid materials, obtained through introduction of cysteine, lysine and folic acid as biological entities into polydopamine-coated magnetite nanoparticles, are reported. The syntheses are straight forward and various methods were applied for structural and morphological characterization of the resulting nanoparticles. XPS proved a very powerful tool for surface chemical analysis and it evidences the functionalization of polydopamine coated magnetite nanoparticles. The superparamagnetic behavior and the high values of saturation magnetization recommend all products for further application where magnetism is important for targeting, separation, or heating by alternative magnetic fields.

  13. Environmental impacts of post-consumer material managements: recycling, biological treatments, incineration.

    Science.gov (United States)

    Valerio, F

    2010-11-01

    The environmental impacts of recycling, mechanical biological treatments (MBT) and waste-to-energy incineration, the main management strategies to respond to the increasing production of post-consumer materials are reviewed and compared. Several studies carried out according to life-cycle assessment (LCA) confirm that the lowest environmental impact, on a global scale, is obtained by recycling and by biological treatments (composting and anaerobic fermentations) if compost is used in agriculture. The available air emission factors suggest that, on a local scale, mechanical biological treatments with energy recovery of biogas, may be intrinsically safer than waste-to-energy incinerators. Several studies confirm the capability of biological treatments to degrade many toxic xenobiotic contaminating urban wastes such as dioxins and polycyclic aromatic hydrocarbons, an important property to be improved, for safe agricultural use of compost. Further LCA studies to compare the environmental impact of MBTs and of waste-to-energy incinerators are recommended.

  14. Transuranium analysis methodologies for biological and environmental samples

    International Nuclear Information System (INIS)

    Analytical procedures for the most abundant transuranium nuclides in the environment (i.e., plutonium and, to a lesser extent, americium) are available. There is a lack of procedures for doing sequential analysis for Np, Pu, Am, and Cm in environmental samples, primarily because of current emphasis on Pu and Am. Reprocessing requirements and waste disposal connected with the fuel cycle indicate that neptunium and curium must be considered in environmental radioactive assessments. Therefore it was necessary to develop procedures that determine all four of these radionuclides in the environment. The state of the art of transuranium analysis methodology as applied to environmental samples is discussed relative to different sample sources, such as soil, vegetation, air, water, and animals. Isotope-dilution analysis with 243Am (239Np) and 236Pu or 242Pu radionuclide tracers is used. Americium and curium are analyzed as a group, with 243Am as the tracer. Sequential extraction procedures employing bis(2-ethyl-hexyl)orthophosphoric acid (HDEHP) were found to result in lower yields and higher Am--Cm fractionation than ion-exchange methods

  15. Application of computational systems biology to explore environmental toxicity hazards

    DEFF Research Database (Denmark)

    Audouze, Karine Marie Laure; Grandjean, Philippe

    2011-01-01

    ) to ascertain their possible links to relevant adverse effects.Methods: We extracted chemical-protein association networks for each DDT isomer and its metabolites using ChemProt, a disease chemical biology database that includes both binding and gene expression data, and we explored protein-protein interactions...... diseases were linked to the two DDT isomers. Asthma was uniquely linked with p,p´-DDT, and autism with o,p´-DDT. Several reproductive and neurobehavioral outcomes and cancer types were linked to all three compounds.Conclusions: Computer-based modeling relies on available information. Although differences...

  16. Current studies on physiological functions and biological production of lactosucrose.

    Science.gov (United States)

    Mu, Wanmeng; Chen, Qiuming; Wang, Xiao; Zhang, Tao; Jiang, Bo

    2013-08-01

    Lactosucrose (O-β-D-galactopyranosyl-(1,4)-O-α-D-glucopyranosyl-(1,2)-β-D-fructofuranoside) is a trisaccharide formed from lactose and sucrose by enzymatic transglycosylation. This rare trisaccharide is a kind of indigestible carbohydrate, has good prebiotic effect, and promotes intestinal mineral absorption. It has been used as a functional ingredient in a range of food products which are approved as foods for specified health uses in Japan. Using lactose and sucrose as substrates, lactosucrose can be produced through transfructosylation by β-fructofuranosidase from Arthrobacter sp. K-1 or a range of levansucrases, or through transgalactosylation by β-galactosidase from Bacillus circulans. This article presented a review of recent studies on the physiological functions of lactosucrose and the biological production from lactose and sucrose by different enzymes.

  17. STAT6: its role in interleukin 4-mediated biological functions.

    Science.gov (United States)

    Takeda, K; Kishimoto, T; Akira, S

    1997-05-01

    Interleukin (IL) 4 is known to be a cytokine which plays a central role in the regulation of immune response. Studies on cytokine signal transduction have clarified the mechanism by which IL4 exerts its functions. Two cytoplasmic proteins, signal transducer and activator of transcription (STAT) 6 and IL4-induced phosphotyrosine substrate/insulin receptor substrate 2 (4PS/IRS2), are activated in IL4 signal transduction. Recent studies from STAT6-deficient mice have revealed the essential role of STAT6 in IL4-mediated biological actions. In addition, STAT6 has also been demonstrated to be important for the functions mediated by IL13, which is related to IL4. IL4 and IL13 have been shown to induce the production of IgE, which is a major mediator in an allergic response. These findings indicate that STAT6 activation is involved in IL4- and IL13-mediated disorders such as allergy.

  18. Functions of microRNAs in cardiovascular biology and disease.

    Science.gov (United States)

    Hata, Akiko

    2013-01-01

    In 1993, lin-4 was discovered as a critical modulator of temporal development in Caenorhabditis elegans and, most notably, as the first in the class of small, single-stranded noncoding RNAs now defined as microRNAs (miRNAs). Another eight years elapsed before miRNA expression was detected in mammalian cells. Since then, explosive advancements in the field of miRNA biology have elucidated the basic mechanism of miRNA biogenesis, regulation, and gene-regulatory function. The discovery of this new class of small RNAs has augmented the complexity of gene-regulatory programs as well as the understanding of developmental and pathological processes in the cardiovascular system. Indeed, the contributions of miRNAs in cardiovascular development and function have been widely explored, revealing the extensive role of these small regulatory RNAs in cardiovascular physiology. PMID:23157557

  19. Current studies on physiological functions and biological production of lactosucrose.

    Science.gov (United States)

    Mu, Wanmeng; Chen, Qiuming; Wang, Xiao; Zhang, Tao; Jiang, Bo

    2013-08-01

    Lactosucrose (O-β-D-galactopyranosyl-(1,4)-O-α-D-glucopyranosyl-(1,2)-β-D-fructofuranoside) is a trisaccharide formed from lactose and sucrose by enzymatic transglycosylation. This rare trisaccharide is a kind of indigestible carbohydrate, has good prebiotic effect, and promotes intestinal mineral absorption. It has been used as a functional ingredient in a range of food products which are approved as foods for specified health uses in Japan. Using lactose and sucrose as substrates, lactosucrose can be produced through transfructosylation by β-fructofuranosidase from Arthrobacter sp. K-1 or a range of levansucrases, or through transgalactosylation by β-galactosidase from Bacillus circulans. This article presented a review of recent studies on the physiological functions of lactosucrose and the biological production from lactose and sucrose by different enzymes. PMID:23828605

  20. Biological Monitoring Prospects in Occupational and Environmental Medicine

    CERN Document Server

    Angerer, Jürgen

    2003-01-01

    At the invitation of the Deutsche Forschungsgemeinschaft (DFG), a round-table discussion was held on 9 and 10 March 2000, dealing with future possibilities for biomonitoring in occupational and environmental medicine. Biomonitoring has reached a high standard in Germany over the past 30 years, not least due to the fact that the results of the Senate commission on materials hazardous to health at the workplace have been directly implemented as part of the jurisdiction relating to occupational safety. This book combines the expertise gathered from various areas within toxicology, occupational me

  1. Sucrose metabolism gene families and their biological functions.

    Science.gov (United States)

    Jiang, Shu-Ye; Chi, Yun-Hua; Wang, Ji-Zhou; Zhou, Jun-Xia; Cheng, Yan-Song; Zhang, Bao-Lan; Ma, Ali; Vanitha, Jeevanandam; Ramachandran, Srinivasan

    2015-11-30

    Sucrose, as the main product of photosynthesis, plays crucial roles in plant development. Although studies on general metabolism pathway were well documented, less information is available on the genome-wide identification of these genes, their expansion and evolutionary history as well as their biological functions. We focused on four sucrose metabolism related gene families including sucrose synthase, sucrose phosphate synthase, sucrose phosphate phosphatase and UDP-glucose pyrophosphorylase. These gene families exhibited different expansion and evolutionary history as their host genomes experienced differentiated rates of the whole genome duplication, tandem and segmental duplication, or mobile element mediated gene gain and loss. They were evolutionarily conserved under purifying selection among species and expression divergence played important roles for gene survival after expansion. However, we have detected recent positive selection during intra-species divergence. Overexpression of 15 sorghum genes in Arabidopsis revealed their roles in biomass accumulation, flowering time control, seed germination and response to high salinity and sugar stresses. Our studies uncovered the molecular mechanisms of gene expansion and evolution and also provided new insight into the role of positive selection in intra-species divergence. Overexpression data revealed novel biological functions of these genes in flowering time control and seed germination under normal and stress conditions.

  2. Event-based text mining for biology and functional genomics.

    Science.gov (United States)

    Ananiadou, Sophia; Thompson, Paul; Nawaz, Raheel; McNaught, John; Kell, Douglas B

    2015-05-01

    The assessment of genome function requires a mapping between genome-derived entities and biochemical reactions, and the biomedical literature represents a rich source of information about reactions between biological components. However, the increasingly rapid growth in the volume of literature provides both a challenge and an opportunity for researchers to isolate information about reactions of interest in a timely and efficient manner. In response, recent text mining research in the biology domain has been largely focused on the identification and extraction of 'events', i.e. categorised, structured representations of relationships between biochemical entities, from the literature. Functional genomics analyses necessarily encompass events as so defined. Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify the exact types of reactions to be retrieved. This article provides an overview of recent research into event extraction. We cover annotated corpora on which systems are trained, systems that achieve state-of-the-art performance and details of the community shared tasks that have been instrumental in increasing the quality, coverage and scalability of recent systems. Finally, several concrete applications of event extraction are covered, together with emerging directions of research.

  3. Environmental distribution and population biology of Candidatus Accumulibacter, a primary agent of Biological Phosphorus Removal

    OpenAIRE

    Peterson, S. Brook; Warnecke, Falk; Madejska, Julita; McMahon, Katherine D.; Hugenholtz, Philip

    2008-01-01

    Members of the uncultured bacterial genus Candidatus Accumulibacter are capable of intracellular accumulation of inorganic phosphate (Pi) in activated sludge wastewater treatment plants (WWTPs) performing enhanced biological phosphorus removal (EBPR), but were also recently shown to inhabit freshwater and estuarine sediments. Additionally, metagenomic sequencing of two bioreactor cultures enriched in Candidatus Accumulibacter, but housed on separate continents, revealed the potential for glob...

  4. DMPD: Type I interferon receptors: biochemistry and biological functions. [Dynamic Macrophage Pathway CSML Database

    Lifescience Database Archive (English)

    Full Text Available 17502368 Type I interferon receptors: biochemistry and biological functions. de Wee...(.html) (.csml) Show Type I interferon receptors: biochemistry and biological functions. PubmedID 17502368 T...itle Type I interferon receptors: biochemistry and biological functions. Authors

  5. Excitation functions and production of arsenic radioisotopes for environmental toxicology and biomedical purposes

    Energy Technology Data Exchange (ETDEWEB)

    Basile, D.; Birattari, C.; Bonard, M.; Salomone, A. (Istituto Nazionale di Fisica Nucleare, Milan (Italy)); Goetz, L.; Sabbioni, E. (Commission of the European Communities, Ispra (Italy). Joint Research Centre)

    1981-06-01

    Many arsenic radionuclides have come to be used as tracers in biology and in the study of environmental pollution of both water and soil. In nuclear medicine, radioactive /sup 74/As has been employed as a positron emitter for the localization of brain tumors, cerebral occlusive vascular lesions, arterious-venous malformations, etc. The aim of the work described was to study the excitation functions for the production of the arsenic radioisotopes from targets of natural germanium via nuclear reactions (p, xn).

  6. OMNIHAB - a controlled environmental system for application in gravitational biology

    Science.gov (United States)

    Anken, Ralf; Hilbig, Reinhard; Anken, Ralf; Lebert, Michael; Häder, Donat

    Several "closed" habitats have been designed in the past for experiments with unicellular organisms as well as with multicellular animals and plants under long-term microgravity. Some of these environmental systems were flown successfully. The bioregenerative C.E.B.A.S.- Minimodul allowed the maintenance of higher plants (Ceratophyllum sp.), mollusks (Biomphalaria glabrata) and fish (swordtail Xiphophorus helleri, cichlid fish Oreochromis mossambicus) under spaceflight conditions (STS-89, STS-90 Neurolab, STS-107). A much simpler and smaller system, the OMEGAHAB, was successfully employed on the FOTON M-3 flight, containing cichlid fish larvae and unicellular algae (Euglena gracilis). Further aquatic habitats are under development (e.g., AquaHab, another aquatic research module especially dedicated to ground based, application-oriented research). These systems tend to be specialized, minimal ecosystems with limited research potential. Therefore, we propose to develop a controlled, multi-modular hardware to increase the diversity of experimental species to be flown together. Currently, a variety of plant and animal species are used as model systems. Combining as many of them as possible (and conducting a most effective sample-sharing among the different working groups) will strongly improve the cost-benefit ratio and thus effectiveness of a space- flight experiment in utilising limited resources at the maximum. The concept of OMNIHAB, an aquatic life support system comprising exchangeable modules, will be presented at the meeting.

  7. Insights into IL-23 biology: From structure to function.

    Science.gov (United States)

    Floss, Doreen M; Schröder, Jutta; Franke, Manuel; Scheller, Jürgen

    2015-10-01

    Interleukin (IL-)23 is a central cytokine controlling TH17 development. Overshooting IL-23 signaling contribute to autoimmune diseases. Moreover, GWAS studies have identified several SNPs within the IL-23 receptor, which are associated with autoimmune diseases. IL-23 is a member of the IL-12-type cytokine family and consists of IL-23p19 and p40. Within the IL-12 family, IL-12 and IL-23 share the p40 cytokine subunit and the IL-12Rβ1 as one chain of the receptor complex. For signaling, IL-23 triggers heterodimerization of IL-12Rβ1 and the IL-23R. Subsequently, signal transduction pathways including JAK/STAT, MAPK and PI3K are activated. Most studies have investigated the biological relevance of IL-23 in the development of TH17 cells and autoimmunity, whereas less is known about the molecular context of IL-23 biology. Therefore, we focused on IL-23 receptor complex assembly, signal transduction and functional relevance of IL-23R SNPs in the context of IL-23-inhibitory principles.

  8. Linking biological soil crust diversity to ecological functions

    Science.gov (United States)

    Glaser, Karin; Borchhardt, Nadine; Schulz, Karoline; Mikhailyuk, Tatiana; Baumann, Karen; Leinweber, Peter; Ulf, Karsten

    2016-04-01

    Biological soil crusts (BSCs) are an association of different microorganisms and soil particles in the top millimeters of the soil. They are formed by algae, cyanobacteria, microfungi, bacteria, bryophytes and lichens in various compositions. Our aim was to determine and compare the biodiversity of all occurring organisms in biogeographically different habitats, ranging from polar (both Arctic and Antarctic), subpolar (Scandinavia), temperate (Germany) to dry regions (Chile). The combination of microscopy and molecular techniques (next-generation sequencing) revealed highly diverse crust communities, whose composition clustered by region and correlates with habitat characteristics such as water content. The BSC biodiversity was then linked to the ecological function of the crusts. The functional role of the BSCs in the biogeochemical cycles of carbon, nitrogen and phosphorous is evaluated using an array of state of the art soil chemistry methods including Py-FIMS (pyrolysis field ionization mass spectrometry) and XANES (x-ray absorbance near edge structure). Total P as well as P fractions were quantified in all BSCs, adjacent soil underneath and comparable nearby soil of BSC-free areas revealing a remarkable accumulation of total phosphorous and a distinct pattern of P fractions in the crust. Further, we observed an indication of a different P-speciation composition in the crust compared with BSC-free soil. The data allow answering the question whether BSCs act as sink or source for these compounds, and how biodiversity controls the biogeochemical function of BSCs.

  9. Genome-wide survey for biologically functional pseudogenes.

    Directory of Open Access Journals (Sweden)

    Orjan Svensson

    2006-05-01

    Full Text Available According to current estimates there exist about 20,000 pseudogenes in a mammalian genome. The vast majority of these are disabled and nonfunctional copies of protein-coding genes which, therefore, evolve neutrally. Recent findings that a Makorin1 pseudogene, residing on mouse Chromosome 5, is, indeed, in vivo vital and also evolutionarily preserved, encouraged us to conduct a genome-wide survey for other functional pseudogenes in human, mouse, and chimpanzee. We identify to our knowledge the first examples of conserved pseudogenes common to human and mouse, originating from one duplication predating the human-mouse species split and having evolved as pseudogenes since the species split. Functionality is one possible way to explain the apparently contradictory properties of such pseudogene pairs, i.e., high conservation and ancient origin. The hypothesis of functionality is tested by comparing expression evidence and synteny of the candidates with proper test sets. The tests suggest potential biological function. Our candidate set includes a small set of long-lived pseudogenes whose unknown potential function is retained since before the human-mouse species split, and also a larger group of primate-specific ones found from human-chimpanzee searches. Two processed sequences are notable, their conservation since the human-mouse split being as high as most protein-coding genes; one is derived from the protein Ataxin 7-like 3 (ATX7NL3, and one from the Spinocerebellar ataxia type 1 protein (ATX1. Our approach is comparative and can be applied to any pair of species. It is implemented by a semi-automated pipeline based on cross-species BLAST comparisons and maximum-likelihood phylogeny estimations. To separate pseudogenes from protein-coding genes, we use standard methods, utilizing in-frame disablements, as well as a probabilistic filter based on Ka/Ks ratios.

  10. Genome-wide survey for biologically functional pseudogenes.

    Science.gov (United States)

    Svensson, Orjan; Arvestad, Lars; Lagergren, Jens

    2006-05-01

    According to current estimates there exist about 20,000 pseudogenes in a mammalian genome. The vast majority of these are disabled and nonfunctional copies of protein-coding genes which, therefore, evolve neutrally. Recent findings that a Makorin1 pseudogene, residing on mouse Chromosome 5, is, indeed, in vivo vital and also evolutionarily preserved, encouraged us to conduct a genome-wide survey for other functional pseudogenes in human, mouse, and chimpanzee. We identify to our knowledge the first examples of conserved pseudogenes common to human and mouse, originating from one duplication predating the human-mouse species split and having evolved as pseudogenes since the species split. Functionality is one possible way to explain the apparently contradictory properties of such pseudogene pairs, i.e., high conservation and ancient origin. The hypothesis of functionality is tested by comparing expression evidence and synteny of the candidates with proper test sets. The tests suggest potential biological function. Our candidate set includes a small set of long-lived pseudogenes whose unknown potential function is retained since before the human-mouse species split, and also a larger group of primate-specific ones found from human-chimpanzee searches. Two processed sequences are notable, their conservation since the human-mouse split being as high as most protein-coding genes; one is derived from the protein Ataxin 7-like 3 (ATX7NL3), and one from the Spinocerebellar ataxia type 1 protein (ATX1). Our approach is comparative and can be applied to any pair of species. It is implemented by a semi-automated pipeline based on cross-species BLAST comparisons and maximum-likelihood phylogeny estimations. To separate pseudogenes from protein-coding genes, we use standard methods, utilizing in-frame disablements, as well as a probabilistic filter based on Ka/Ks ratios. PMID:16680195

  11. Structure, Function, and Biology of the Enterococcus faecalis Cytolysin

    Directory of Open Access Journals (Sweden)

    Daria Van Tyne

    2013-04-01

    Full Text Available Enterococcus faecalis is a Gram-positive commensal member of the gut microbiota of a wide range of organisms. With the advent of antibiotic therapy, it has emerged as a multidrug resistant, hospital-acquired pathogen. Highly virulent strains of E. faecalis express a pore-forming exotoxin, called cytolysin, which lyses both bacterial and eukaryotic cells in response to quorum signals. Originally described in the 1930s, the cytolysin is a member of a large class of lanthionine-containing bacteriocins produced by Gram-positive bacteria. While the cytolysin shares some core features with other lantibiotics, it possesses unique characteristics as well. The current understanding of cytolysin biosynthesis, structure/function relationships, and contribution to the biology of E. faecalis are reviewed, and opportunities for using emerging technologies to advance this understanding are discussed.

  12. Quality of environmental impact assessment (EIA) reports on biological pest control / Thea Henriette Carroll

    OpenAIRE

    Carroll, Thea Henriette

    2006-01-01

    Decision making regarding the release of biological control agents for invasive species such as lantana, Lantana camara, requires the consideration and evaluation of environmental impact assessment (EIA) reports by a competent authority. Although various biological control agents have been authorised for release into the environment for the control of lantana, the quality of the EIA reports that form the basis for decision making has never been evaluated. The evaluation of the ...

  13. Biological impact of environmental polycyclic aromatic hydrocarbons (ePAHs) as endocrine disruptors.

    Science.gov (United States)

    Zhang, Yanyan; Dong, Sijun; Wang, Hongou; Tao, Shu; Kiyama, Ryoiti

    2016-06-01

    Polycyclic aromatic hydrocarbons (PAHs) are often detected in the environment and are regarded as endocrine disruptors. We here designated mixtures of PAHs in the environment as environmental PAHs (ePAHs) to discuss their effects collectively, which could be different from the sum of the constituent PAHs. We first summarized the biological impact of environmental PAHs (ePAHs) found in the atmosphere, sediments, soils, and water as a result of human activities, accidents, or natural phenomena. ePAHs are characterized by their sources and forms, followed by their biological effects and social impact, and bioassays that are used to investigate their biological effects. The findings of the bioassays have demonstrated that ePAHs have the ability to affect the endocrine systems of humans and animals. The pathways that mediate cell signaling for the endocrine disruptions induced by ePAHs and PAHs have also been summarized in order to obtain a clearer understanding of the mechanisms responsible for these effects without animal tests; they include specific signaling pathways (MAPK and other signaling pathways), regulatory mechanisms (chromatin/epigenetic regulation, cell cycle/DNA damage control, and cytoskeletal/adhesion regulation), and cell functions (apoptosis, autophagy, immune responses/inflammation, neurological responses, and development/differentiation) induced by specific PAHs, such as benz[a]anthracene, benzo[a]pyrene, benz[l]aceanthrylene, cyclopenta[c,d]pyrene, 7,12-dimethylbenz[a]anthracene, fluoranthene, fluorene, 3-methylcholanthrene, perylene, phenanthrene, and pyrene as well as their derivatives. Estrogen signaling is one of the most studied pathways associated with the endocrine-disrupting activities of PAHs, and involves estrogen receptors and aryl hydrocarbon receptors. However, some of the actions of PAHs are contradictory, complex, and unexplainable. Although several possibilities have been suggested, such as direct interactions between PAHs and

  14. A Vital Legacy: Biological and Environmental Research in the Atomic Age

    Science.gov (United States)

    1997-09-01

    This booklet presents a summary of the five decades of biological and environmental research in the atomic age. It commemorates the contributions to science and society during these decades and concludes with a view to the years ahead. The Contents includes Safety First: in the Shadow of a New Technology; A Healthy Citizenry: Gifts of the New Era; and Environmental Concerns: From Meteorology to Ecology. The conclusion is titled An Enduring Mandate: Looking to the Future.

  15. A vital legacy: Biological and environmental research in the atomic age

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, D. [ed.

    1997-09-01

    This booklet presents a summary of the five decades of biological and environmental research in the atomic age. It commemorates the contributions to science and society during these decades and concludes with a view to the years ahead. The Contents includes `Safety First: in the Shadow of a New Technology; A Healthy Citizenry: Gifts of the New Era; and Environmental Concerns: From Meteorology to Ecology`. The conclusion is titled `An Enduring Mandate: Looking to the Future`.

  16. Home environmental problems and physical function in Taiwanese older adults.

    Science.gov (United States)

    Lan, Tzuo-Yun; Wu, Shwu-Chong; Chang, Wen-Chiung; Chen, Ching-Yu

    2009-01-01

    Environmental hazards play an important role in the disablement process. The purpose of this study was to investigate the relationship between home environmental problems and personal physical function. Data were based on a two-stage nationwide survey and evaluation on the needs of long-term care in Taiwan. A total of 10,596 individuals aged 65 and over were included in this study. These participants were identified with physical or cognitive problems at the screening interview and further evaluated at the second interview on health condition, functional status, needs of long-term care, and home environmental problems. Six items of environmental hazards were assessed at the participants' homes with direct observation. The prevalence rates of home environmental problems were similar among older adults with different levels of physical function. No grab bars (79.6-85.1%) and no protections against slip (81.9-92.8%) in the bathroom were two commonly present hazards in older adults' homes. Older adults with a higher income (Odds ratio=OR=0.75), without income information (OR=0.78) or living with other persons (OR=0.74) were less likely to experience environmental problems at home. Results from this study revealed that home environment condition was associated with factors other than personal disabling conditions for the elderly. Modifying home environment, especially the bathroom, should be attached with great importance for physically disabled older adults. PMID:19124167

  17. The functions of biological diversity in an age of extinction.

    Science.gov (United States)

    Naeem, Shahid; Duffy, J Emmett; Zavaleta, Erika

    2012-06-15

    Ecosystems worldwide are rapidly losing taxonomic, phylogenetic, genetic, and functional diversity as a result of human appropriation of natural resources, modification of habitats and climate, and the spread of pathogenic, exotic, and domestic plants and animals. Twenty years of intense theoretical and empirical research have shown that such biotic impoverishment can markedly alter the biogeochemical and dynamic properties of ecosystems, but frontiers remain in linking this research to the complexity of wild nature, and in applying it to pressing environmental issues such as food, water, energy, and biosecurity. The question before us is whether these advances can take us beyond merely invoking the precautionary principle of conserving biodiversity to a predictive science that informs practical and specific solutions to mitigate and adapt to its loss. PMID:22700920

  18. Biosynthesis and biological functions of terpenoids in plants.

    Science.gov (United States)

    Tholl, Dorothea

    2015-01-01

    Terpenoids (isoprenoids) represent the largest and most diverse class of chemicals among the myriad compounds produced by plants. Plants employ terpenoid metabolites for a variety of basic functions in growth and development but use the majority of terpenoids for more specialized chemical interactions and protection in the abiotic and biotic environment. Traditionally, plant-based terpenoids have been used by humans in the food, pharmaceutical, and chemical industries, and more recently have been exploited in the development of biofuel products. Genomic resources and emerging tools in synthetic biology facilitate the metabolic engineering of high-value terpenoid products in plants and microbes. Moreover, the ecological importance of terpenoids has gained increased attention to develop strategies for sustainable pest control and abiotic stress protection. Together, these efforts require a continuous growth in knowledge of the complex metabolic and molecular regulatory networks in terpenoid biosynthesis. This chapter gives an overview and highlights recent advances in our understanding of the organization, regulation, and diversification of core and specialized terpenoid metabolic pathways, and addresses the most important functions of volatile and nonvolatile terpenoid specialized metabolites in plants.

  19. Shaping Small Bioactive Molecules to Untangle Their Biological Function: A Focus on Fluorescent Plant Hormones.

    Science.gov (United States)

    Lace, Beatrice; Prandi, Cristina

    2016-08-01

    Modern biology overlaps with chemistry in explaining the structure and function of all cellular processes at the molecular level. Plant hormone research is perfectly located at the interface between these two disciplines, taking advantage of synthetic and computational chemistry as a tool to decipher the complex biological mechanisms regulating the action of plant hormones. These small signaling molecules regulate a wide range of developmental processes, adapting plant growth to ever changing environmental conditions. The synthesis of small bioactive molecules mimicking the activity of endogenous hormones allows us to unveil many molecular features of their functioning, giving rise to a new field, plant chemical biology. In this framework, fluorescence labeling of plant hormones is emerging as a successful strategy to track the fate of these challenging molecules inside living organisms. Thanks to the increasing availability of new fluorescent probes as well as advanced and innovative imaging technologies, we are now in a position to investigate many of the dynamic mechanisms through which plant hormones exert their action. Such a deep and detailed comprehension is mandatory for the development of new green technologies for practical applications. In this review, we summarize the results obtained so far concerning the fluorescent labeling of plant hormones, highlighting the basic steps leading to the design and synthesis of these compelling molecular tools and their applications. PMID:27378726

  20. Environmental and biological applications and implications of soft and condensed nanomaterials

    Science.gov (United States)

    Chen, Pengyu

    Recent innovations and growth of nanotechnology have spurred exciting technological and commercial developments of nanomaterails. Their appealing physical and physicochemical properties offer great opportunities in biological and environmental applications, while in the meantime may compromise human health and environmental sustainability through either unintentional exposure or intentional discharge. Accordingly, this dissertation exploits the physicochemical behavior of soft dendritic polymers for environmental remediation and condensed nano ZnO tetrapods for biological sensing (Chapter two-four), and further delineate the environmental implications of such nanomaterials using algae- the major constituent of the aquatic food chain-as a model system (Chapter five). This dissertation is presented as follows. Chapter one presents a general review of the characteristic properties, applications, forces dictating nanomaterials, and their biological and environmental implications of the most produced and studied soft and condensed nanomaterials. In addition, dendritic polymers and ZnO nanomaterials are thoroughly reviewed separately. Chapter two investigates the physicochemical properties of poly(amidoamine)-tris(hydroxymethyl)amidomethane- dendrimer for its potential applications in water purification. The binding mechanisms and capacities of this dendrimer in hosting major environmental pollutants including cationic copper, anionic nitrate, and polyaromatic phenanthrene are discussed. Chapter three exploits a promising use of dendrimers for removal of potentially harmful discharged nanoparticles (NPs). Specifically, fullerenols are used as a model nanomaterial, and their interactions with two different generations of dendrimers are studied using spectrophotometry and thermodynamics methods. Chapter four elucidates two novel optical schemes for sensing environmental pollutants and biological compounds using dendrimer-gold nanowire complex and gold-coated ZnO tetrapods

  1. Beyond the Golden Gate; oceanography, geology, biology, and environmental issues in the Gulf of the Farallones

    Science.gov (United States)

    Karl, Herman A., (Edited By); Chin, John L.; Ueber, Edward; Stauffer, Peter H.; Hendley, James W., II

    2001-01-01

    In the 1990's, the U.S. Geological Survey sponsored a multidisciplinary, multiagency investigation of the Gulf of the Farallones, which lies offshore of the San Francisco Bay region. This book discussess the results of the endeavor, covering the topics of oceanography and geology, biology and ecological niches, and issues of environmental management.

  2. 75 FR 28232 - Availability of an Environmental Assessment for a Biological Control Agent for Hemlock Woolly...

    Science.gov (United States)

    2010-05-20

    ... Control Agent for Hemlock Woolly Adelgid AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION... Plant Health Inspection Service has prepared an environmental assessment relative to the control of... a biological control agent to reduce the severity of hemlock woolly adelgid infestations. We...

  3. 77 FR 46373 - Availability of an Environmental Assessment for a Biological Control Agent for Hemlock Woolly...

    Science.gov (United States)

    2012-08-03

    ... Control Agent for Hemlock Woolly Adelgid AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION... prepared an environmental assessment relative to the release of Symnus coniferarum to control hemlock... of Symnus coniferarum into the eastern United States for use as a biological control agent to...

  4. Polymer biomaterial constructs for regenerative medicine and functional biological systems

    Science.gov (United States)

    Meng, Linghui

    The use of collagen as a biomaterial is currently undergoing a renaissance in the tissue engineering field. The excellent biocompatibility and safety due to its biological characteristics, such as biodegradability and weak antigenicity, make collagen a primary material resource in medical applications. Described herein is work towards the development of novel collagen-based matrices, with additional multi-functionality imparted through a novel in-situ crosslinking approach. The process of electrospinning has become a widely used technique for the creation of fibrous scaffolds for tissue engineering applications due to its ability to rapidly create structures composed of nano-scale polymer fibers closely resembling the architecture of the extracellular matrix (ECM). Collagen-PCL sheath-core bicomponent fibrous scaffolds were fabricated using a novel variation on traditional electrospinning, known as co-axial electrospinning. The results showed that the addition of a synthetic polymer core into collagen nanofibers remarkably increased the mechanical strength of collagen matrices spun from the benign solvent system. A novel single-step, in-situ collagen crosslink approach was developed in order to solve the problems dominating traditional collagen crosslinking methods, such as dimensional shrinking and loss of porous morphology, and to simplify the crosslinking procedure for electrospun collagen scaffolds. The excess amount of NHS present in the crosslinking mixture was found to delay the EDC/collagen coupling reaction in a controlled fashion. Fundamental investigations into the development and characterization of in-situ crosslinked collagen matrices such as fibrous scaffolds, gels and sponges, as well as their biomedical applications including cell culture substrates, wound dressings, drug delivery matrices and bone regeneration substitutes, were performed. The preliminary mice studies indicated that the in-situ crosslinked collagen matrices could be good candidates

  5. Modelling of environmental impacts from biological treatment of organic municipal waste in EASEWASTE

    DEFF Research Database (Denmark)

    Boldrin, Alessio; Neidel, Trine Lund; Damgaard, Anders;

    2011-01-01

    The waste-LCA model EASEWASTE quantifies potential environmental effects from biological treatment of organic waste, based on mass and energy flows, emissions to air, water, soil and groundwater as well as effects from upstream and downstream processes. Default technologies for composting......, anaerobic digestion and combinations hereof are available in the model, but the user can change all key parameters in the biological treatment module so that specific local plants and processes can be modelled. EASEWASTE is one of the newest waste LCA models and the biological treatment module was built...... partly on features of earlier waste-LCA models, but offers additional facilities, more flexibility, transparency and user-friendliness. The paper presents the main features of the module and provides some examples illustrating the capability of the model in environmentally assessing and discriminating...

  6. Annual rhythms that underlie phenology: biological time-keeping meets environmental change.

    Science.gov (United States)

    Helm, Barbara; Ben-Shlomo, Rachel; Sheriff, Michael J; Hut, Roelof A; Foster, Russell; Barnes, Brian M; Dominoni, Davide

    2013-08-22

    Seasonal recurrence of biological processes (phenology) and its relationship to environmental change is recognized as being of key scientific and public concern, but its current study largely overlooks the extent to which phenology is based on biological time-keeping mechanisms. We highlight the relevance of physiological and neurobiological regulation for organisms' responsiveness to environmental conditions. Focusing on avian and mammalian examples, we describe circannual rhythmicity of reproduction, migration and hibernation, and address responses of animals to photic and thermal conditions. Climate change and urbanization are used as urgent examples of anthropogenic influences that put biological timing systems under pressure. We furthermore propose that consideration of Homo sapiens as principally a 'seasonal animal' can inspire new perspectives for understanding medical and psychological problems. PMID:23825201

  7. Function and regulation of lipid biology in Caenorhabditis elegans aging

    Directory of Open Access Journals (Sweden)

    Nicole Shangming Hou

    2012-05-01

    Full Text Available Rapidly expanding aging populations and a concomitant increase in the prevalence of age-related diseases are global health problems today. Over the past three decades, a large body of work has led to the identification of genes and regulatory networks that affect longevity and health span, often benefitting from the tremendous power of genetics in vertebrate and invertebrate model organisms. Interestingly, many of these factors appear linked to lipids, important molecules that participate in cellular signaling, energy metabolism, and structural compartmentalization. Despite the putative link between lipids and longevity, the role of lipids in aging remains poorly understood. Emerging data from the model organism Caenorhabditis elegans suggest that lipid composition may change during aging, as several pathways that influence aging also regulate lipid metabolism enzymes; moreover, some of these enzymes apparently play key roles in the pathways that affect the rate of aging. By understanding how lipid biology is regulated during C. elegans aging, and how it impacts molecular, cellular and organismal function, we may gain insight into novel ways to delay aging using genetic or pharmacological interventions. In the present review we discuss recent insights into the roles of lipids in C. elegans aging, including regulatory roles played by lipids themselves, the regulation of lipid metabolic enzymes, and the roles of lipid metabolism genes in the pathways that affect aging.

  8. Environmental hexachlorobenzene exposure and human male reproductive function

    DEFF Research Database (Denmark)

    Specht, Ina Olmer; Bonde, Jens Peter; Toft, Gunnar;

    2015-01-01

    Hexachlorobenzene (HCB) is a persistent environmental fungicide that may disrupt androgen regulation. The aim of this study was to investigate associations between HCB levels and biomarkers of male reproductive function. 589 Spouses of pregnant women from Greenland, Poland and Ukraine were enroll...

  9. Principles of biological adaptation of microorganisms to the change of environmental factors in artificial ecosystems

    Science.gov (United States)

    Somova, L. A.; Pisman, T. I.

    Studying the matter transformations and biotic cycling in artificial ecosystems (AES), we need to know the principles of biological adaptation of active organisms to the change of environment. Microorganisms in AES of water purification are the most active transform and consumers of organic substances of wastes. Utilization of organic substances is directly connected with the energy fluxes used by AES. According to energy criteria, the energy fluxes used by biological system have trends to maximum values under stable conditions. Nonutilized substrate concentration decreases in result of biological adaptations. After sharp change of environmental factors, for example, after sharp increase of flow rate of organic substances, the biological system is not able to react quickly. The concentration of nonutilized substrate increases and the energy flux used by biological system decreases. The structure of microbial community also changes, having the decrease of biological diversity. Later, as a result of biological adaptation, the ecological and evolution processes bring to decreasing the concentration of nonutilized substrate and to energy fluxes increasing. To compare with natural ecosystems, AES allow to follow and to study these processes quickly and quantitatively.

  10. Phytochrome from Green Plants: Properties and biological Function

    Energy Technology Data Exchange (ETDEWEB)

    Quail, Peter H.

    2014-07-25

    Pfr conformer reverses this activity upon initial light exposure, inducing the switch to photomorphogenic development. This reversal involves light-triggered translocation of the photoactivated phy molecule into the nucleus where it interacts with PIF-family members, inducing rapid phosphorylation and degradation of the PIFs via the ubiquitin-proteasome system. This degradation in turn elicits rapid alterations in gene expression that drive the deetiolation transition. This project has made considerable progress in defining phy-PIF signaling activity in controlling the SAR. The biological functions of the multiple PIF-family members in controlling the SAR, including dissection of the relative contributions of the individual PIFs to this process, as well as to diurnal growth-control oscillations, have been investigated using higher-order pif-mutant combinations. Using microarray analysis of a quadruple pif mutant we have defined the shade-induced, PIF-regulated transcriptional network genome-wide. This has revealed that a dynamic antagonism between the phys and PIFs generates selective reciprocal responses during deetiolation and the SAR in a rapidly light-responsive transcriptional network. Using integrated RNA-seq and ChIP-seq analysis of higher order pif-mutant combinations, we have defined the direct gene-targets of PIF transcriptional regulation, and have obtained evidence that this regulation involves differential direct targeting of rapidly light-responsive genes by the individual PIF-family members. This project has provided significant advances in our understanding of the molecular mechanisms by which the phy-PIF photosensory signaling pathway regulates an important bioenergy-related plant response to the light environment. The identification of molecular targets in the primary transcriptional-regulatory circuitry of this pathway has the potential to enable genetic or reverse-genetic manipulation of the partitioning of carbon between reproductive and

  11. Challenges for environmental epidemiology research: are biomarker concentrations altered by kidney function or urine concentration adjustment?

    Science.gov (United States)

    Biological monitoring has become a standard approach to exposure assessment in occupational and environmental epidemiology. The use of biological effect markers to identify early adverse changes in target organs has also become widely adopted. Recently, nephrotoxicant research us...

  12. Principles of biological adaptation of organisms in artificial ecosystems to changes of environmental factors

    Science.gov (United States)

    Somova, L. A.; Pechurkin, N. S.; Pisman, T. I.

    Studying material transformations and biotic cycling in artificial ecosystems (AES), we need to know the principles of biological adaptation of active organisms to change in the environment. Microorganisms in AES for water purification are the most active transforming organisms and consumers of the organic substances contained in wastes. Utilization of organic substances is directly connected with the energy fluxes used by AES. According to energy criteria, the energy fluxes used by a biological system tend to reach maximum values under stable conditions. Unutilized substrate concentration decreases as a result of biological adaptations. After a dramatic change in environmental factors, for example, after a sharp increase in the flow rate of organic substances, the biological system is not able to react quickly. The concentration of unutilized substrate increases and the energy flux used by the biological system decreases. The structure of the microbial community also changes, with a decrease in biological diversity. The efficiency of energy use by simple terrestrial ecosystems depends on the energetic intensity and interactions between plants and rhizospheric microorganisms.

  13. Biological markers in animals can provide information on exposure and bioavailability of environmental contaminants

    International Nuclear Information System (INIS)

    Epidemiologic studies of agents present in the environment seek to identify the extent to which they contribute to the causation of a specific toxic, clinical, or pathological endpoint. The multifactorial nature of disease etiology, long latency periods and the complexity of exposure, all contribute to the difficulty of establishing associations and casual relationships between a specific exposure and an adverse outcome. These barriers to studies of exposures and subsequent risk assessment cannot generally be changed. However, the appropriate use of biological markers in animal species living in a contaminated habitat can provide a measure of potential damage from that exposure and, in some instances, act as a surrogate for human environmental exposures. Quantitative predictivity of the effect of exposure to environmental pollutants is being approached by employing an appropriate array of biological end points. 34 refs., 1 fig., 6 tabs

  14. Surface-enhanced Raman scattering detection of silver nanoparticles in environmental and biological samples.

    Science.gov (United States)

    Guo, Huiyuan; Xing, Baoshan; Hamlet, Leigh C; Chica, Andrea; He, Lili

    2016-06-01

    Growing concerns over the potential release and threat of silver nanoparticles (AgNPs) to environmental and biological systems urge researchers to investigate their fate and behavior. However, current analytical techniques cannot meet the requirements for rapidly, sensitively and reliably probing AgNPs in complex matrices. Surface-enhanced Raman spectroscopy (SERS) has shown great capability for rapid detection of AgNPs based on an indicator molecule that can bind on the AgNP surface. The objective of this study was to exploit SERS to detect AgNPs in environmental and biological samples through optimizing the Raman indicator for SERS. Seven indicator molecules were selected and determined to obtain their SERS signals at optimal concentrations. Among them, 1,2-di(4-pyridyl)ethylene (BPE), crystal violet and ferric dimethyl-dithiocarbamate (ferbam) produced the highest SERS intensities. Further experiments on binding competition between each two of the three candidates showed that ferbam had the highest AgNPs-binding ability. The underlying mechanism lies in the strong binding affinity of ferbam with AgNPs via multiple sulfur atoms. We further validated ferbam to be an effective indicator for SERS detection of as low as 0.1mg/L AgNPs in genuine surface water and 0.57 mg/L in spinach juice. Moreover, limited interference on SERS detection of AgNPs was found from environmentally relevant inorganic ions, organic matter, inorganic particles, as well as biologically relevant components, demonstrating the ferbam-assisted SERS is an effective and sensitive method to detect AgNPs in complex environmental and biological samples. PMID:26956173

  15. Surface-enhanced Raman scattering detection of silver nanoparticles in environmental and biological samples.

    Science.gov (United States)

    Guo, Huiyuan; Xing, Baoshan; Hamlet, Leigh C; Chica, Andrea; He, Lili

    2016-06-01

    Growing concerns over the potential release and threat of silver nanoparticles (AgNPs) to environmental and biological systems urge researchers to investigate their fate and behavior. However, current analytical techniques cannot meet the requirements for rapidly, sensitively and reliably probing AgNPs in complex matrices. Surface-enhanced Raman spectroscopy (SERS) has shown great capability for rapid detection of AgNPs based on an indicator molecule that can bind on the AgNP surface. The objective of this study was to exploit SERS to detect AgNPs in environmental and biological samples through optimizing the Raman indicator for SERS. Seven indicator molecules were selected and determined to obtain their SERS signals at optimal concentrations. Among them, 1,2-di(4-pyridyl)ethylene (BPE), crystal violet and ferric dimethyl-dithiocarbamate (ferbam) produced the highest SERS intensities. Further experiments on binding competition between each two of the three candidates showed that ferbam had the highest AgNPs-binding ability. The underlying mechanism lies in the strong binding affinity of ferbam with AgNPs via multiple sulfur atoms. We further validated ferbam to be an effective indicator for SERS detection of as low as 0.1mg/L AgNPs in genuine surface water and 0.57 mg/L in spinach juice. Moreover, limited interference on SERS detection of AgNPs was found from environmentally relevant inorganic ions, organic matter, inorganic particles, as well as biologically relevant components, demonstrating the ferbam-assisted SERS is an effective and sensitive method to detect AgNPs in complex environmental and biological samples.

  16. Some environmental and biological factors influencing the activity of entomopathogenic Bacillus on mosquito larvae in Brazil

    Directory of Open Access Journals (Sweden)

    R. A. G. B Consoli

    1995-02-01

    Full Text Available The influence of environmental and biological factors on the efficacy of Bacillus thuringiensis serovar israelensis and B. sphaericus as mosquito larvicides are reviewed. The importance of strain dependence, cultivating media/methods, mosquito species/specificity, formulations and their relation to mosquito feeding habits, as well as temperature, solar exposure, larval density and concomitant presence of other aquatic organisms are addressed with reference to the present status of knowledge in Brazil.

  17. Deposition rates in growing tissue: Implications for physiology, molecular biology, and response to environmental variation

    OpenAIRE

    Silk, Wendy K.; Bogeat-Triboulot, Marie-Béatrice

    2014-01-01

    Net rates of biosynthesis and mineral deposition are needed to understand the physiology and molecular biology of growth and plant responses to environmental variation. Many popular models ignore cell expansion and displacement. In contrast, the continuity equation, used with empirical data on growth velocity and concentration, allows computation of biosynthesis and deposition rates in growing tissue. This article describes data and methods needed to calculate deposition rates and reviews som...

  18. Molecular Biology for the Environment: an EC-US hands-on Course in Environmental Biotechnology

    Energy Technology Data Exchange (ETDEWEB)

    Victor de Lorenzo; Juan Luis Ramos; Jerome Kukor; Gerben J. Zylstra

    2004-02-15

    One of the central goals of this activity is to bring together young scientists (at the late Ph.D. or early postdoctoral stages of their careers) in a forum that should result in future collaborations. The course is designed to give scientists hands-on experience in modern, up-to-date biotechnological methods at the interface between molecular biology and environmental biotechnology for the analysis of microorganisms and their activities with regard to the remediation of pollutants in the environment.

  19. Relevance of Crop Biology for Environmental Risk Assessment of Genetically Modified Crops in Africa

    OpenAIRE

    Akinbo, Olalekan; Hancock, James F.; Makinde, Diran

    2015-01-01

    Knowledge about the crop biology of economic crops in Africa is needed for regulators to accurately review dossiers and conduct comprehensive environmental risk assessments (ERAs). This information allows regulators to decide whether biotech crops present a risk to biodiversity, since crossing between domesticated crops and their wild relatives could affect the adaptations of the wild species. The criteria that should be used in the evaluation of African crops for ERA include growth habit, ce...

  20. The functioning of coral reef communities along environmental gradients

    OpenAIRE

    Plass-Johnson, Jeremiah

    2015-01-01

    One of the primary challenges in ecology is to understand how environmental disturbance affects diversity and community structure, and what are the subsequent consequences on ecosystem functioning. Coral reefs are some of the most diverse ecosystems on the planet resulting in complex sets of interactions between benthic, habitat-forming constituents and mobile fish consumers. However, scleractinian corals, the primary habitat engineers, are dependent on high-light, low-nutrient water conditio...

  1. Proposal for a biological environmental monitoring approach to be used in libraries and archives.

    Science.gov (United States)

    Pasquarella, Cesira; Saccani, Elisa; Sansebastiano, Giuliano Ezio; Ugolotti, Manuela; Pasquariello, Giovanna; Albertini, Roberto

    2012-01-01

    In cultural-heritage-related indoor environments, biological particles represent a hazard not only for cultural property, but also for operators and visitors. Reliable environmental monitoring methods are essential for examining each situation and assessing the effectiveness of preventive measures. We propose an integrated approach to the study of biological pollution in indoor environments such as libraries and archives. This approach includes microbial air and surface sampling, as well as an investigation of allergens and pollens. Part of this monitoring plan has been applied at the Palatina Library in Parma, Italy. However, wider collections of data are needed to fully understand the phenomena related with biological contamination, define reliable contamination threshold values, and implement appropriate preventive measures.

  2. Molecular eco-systems biology: towards an understanding of community function

    OpenAIRE

    Raes, J.; Bork, P.

    2008-01-01

    Systems-biology approaches, which are driven by genome sequencing and high-throughput functional genomics data, are revolutionizing single-cell-organism biology. With the advent of various high-throughput techniques that aim to characterize complete microbial ecosystems (metagenomics, meta-transcriptomics and meta-metabolomics), we propose that the time is ripe to consider molecular systems biology at the ecosystem level (eco-systems biology). Here, we discuss the necessary data types that ar...

  3. Grand Challenges for Biological and Environmental Research: A Long-Term Vision

    Energy Technology Data Exchange (ETDEWEB)

    Arkin, A.; Baliga, N.; Braam, J.; Church, G.; Collins, J; ; Cottingham, R.; Ecker, J.; Gerstein, M.; Gilna, P.; Greenberg, J.; Handelsman, J.; Hubbard, S.; Joachimiak, A.; Liao, J.; Looger, L.; Meyerowitz, E.; Mjolness, E.; Petsko, G.; Sayler, G.; Simpson, M.; Stacey, G.; Sussman, M.; Tiedje, J.; Bader, D.; Cessi, P.; Collins, W.; Denning, S.; Dickinson, R.; Easterling, D.; Edmonds, J.; Feddema, J.; Field, C.; Fridlind, A.; Fung, I.; Held, I.; Jackson, R.; Janetos, A.; Large, W.; Leinen, M.; Leung, R.; Long, S.; Mace, G.; Masiello, C.; Meehl, G.; Ort, D.; Otto-Bliesner, B.; Penner, J.; Prather, M.; Randall, D.; Rasch, P.; Schneider, E.; Shugart, H.; Thornton, P.; Washington, W.; Wildung, R.; Wiscombe, W.; Zak, D.; Zhang, M.; Bielicki, J.; Buford, M.; Cleland, E.; Dale, V.; Duke, C.; Ehleringer, J.; Hecht, A.; Kammen, D.; Marland, G.; Pataki, D.; Riley, M. Robertson, P.; Hubbard, S.

    2010-12-01

    The interactions and feedbacks among plants, animals, microbes, humans, and the environment ultimately form the world in which we live. This world is now facing challenges from a growing and increasingly affluent human population whose numbers and lifestyles are driving ever greater energy demand and impacting climate. These and other contributing factors will make energy and climate sustainability extremely difficult to achieve over the 20-year time horizon that is the focus of this report. Despite these severe challenges, there is optimism that deeper understanding of our environment will enable us to mitigate detrimental effects, while also harnessing biological and climate systems to ensure a sustainable energy future. This effort is advanced by scientific inquiries in the fields of atmospheric chemistry and physics, biology, ecology, and subsurface science - all made possible by computing. The Office of Biological and Environmental Research (BER) within the Department of Energy's (DOE) Office of Science has a long history of bringing together researchers from different disciplines to address critical national needs in determining the biological and environmental impacts of energy production and use, characterizing the interplay of climate and energy, and collaborating with other agencies and DOE programs to improve the world's most powerful climate models. BER science focuses on three distinct areas: (1) What are the roles of Earth system components (atmosphere, land, oceans, sea ice, and the biosphere) in determining climate? (2) How is the information stored in a genome translated into microbial, plant, and ecosystem processes that influence biofuel production, climate feedbacks, and the natural cycling of carbon? (3) What are the biological, geochemical, and physical forces that govern the behavior of Earth's subsurface environment? Ultimately, the goal of BER science is to support experimentation and modeling that can reliably predict the

  4. REE incorporation and behaviour in aquatic turtles as a consequence of environmental exposure and biological processes

    Science.gov (United States)

    Censi, P.; Randazzo, L. A.; D'Angelo, S.; Cuttitta, A.; Saiano, F.

    2012-04-01

    Rare Earth Elements (REE) contents in Emys trinacris have been investigated for the first time in order to recognise effects of the chemistry of the environment on the composition of biological fluids. Representing radionuclides a potential health risk for living organisms in case of incorporation in tissues and being REE geochemical analogues of actinides in hydrosphere, this study was focused on investigation of REE behaviour in whole blood and esoskeleton of selected individuals of Emys trinacris. The choice of this species is related to its amphibian character that allowed us to evidence environmental stress in terms of composition of environmental freshwaters whose REE compositions were investigated and compared with blood samples. Moreover effects induced by different environmental conditions were investigated collecting samples in two sites characterised by absence of an anthropogenic signature (GT site) and subjected to strong anthropogenic pressure in terms of wastewater input (SIC site), respectively. In both sites REE contents in whole blood samples of studied turtles are quite similar even if in GT site the highest REE contents have been recognised. Shale-normalised REE patterns show very similar REE behaviour with light REE (LREE) enrichments with respect to heavier REE (HREE), mainly in samples from anthropized site. If REE concentrations in whole blood are normalised to the composition of environmental waters, calculated REE patterns show upward concave shapes centred on Gd that are more pronounced in samples from GT site because their patterns are more enriched in LREE. The last features observed in blood samples from GT can be related to larger REE contents occurred in environmental water from this site with respect to waters collected in SIC site, suggesting that a relationship occurs between REE contents in environmental and biological fluids. Since MREE depletions were observed in waters experiencing phosphate crystallization, observed REE

  5. A "weight of evidence" approach for the integration of environmental "triad" data to assess ecological risk and biological vulnerability.

    Science.gov (United States)

    Dagnino, Alessandro; Sforzini, Susanna; Dondero, Francesco; Fenoglio, Stefano; Bona, Elisa; Jensen, John; Viarengo, Aldo

    2008-07-01

    A new Expert Decision Support System (EDSS) that can integrate Triad data for assessing environmental risk and biological vulnerability at contaminated sites has been developed. Starting with ecosystem relevance, the EDSS assigns different weights to the results obtained from Triad disciplines. The following parameters have been employed: 1) chemical soil analyses (revealing the presence of potentially dangerous substances), 2) ecotoxicological bioassays (utilizing classical endpoints such as survival and reproduction rates), 3) biomarkers (showing sublethal pollutant effects), and 4) ecological parameters (assessing changes in community structure and functions). For each Triad discipline, the EDSS compares the data obtained at the studied field sites with reference values and calculates different 0-1 indexes (e.g., Chemical Risk Index, Ecotoxicological Risk Index, and Ecological Risk Index). The EDSS output consists of 3 indexes: 1) Environmental Risk index (EnvRI), quantifying the levels of biological damage at population-community level, 2) Biological Vulnerability Index (BVI), assessing the potential threats to biological equilibriums, and 3) Genotoxicity Index (GTI), screening genotoxicity effects. The EDSS has been applied in the integration of a battery of Triad data obtained during the European Union-funded Life Intervention in the Fraschetta Area (LINFA) project, which has been carried out in order to estimate the potential risk from soils of a highly anthropized area (Alessandria, Italy) mainly impacted by deposition of atmospheric pollutants. Results obtained during 4 seasonal sampling campaigns (2004-2005) show maximum values of EnvRI in sites A and B (characterized by industrial releases) and lower levels in site D (affected by vehicular traffic emissions). All 3 potentially polluted sites have shown high levels of BVI and GTI, suggesting a general change from reference conditions (site C). PMID:18393577

  6. A "weight of evidence" approach for the integration of environmental "triad" data to assess ecological risk and biological vulnerability.

    Science.gov (United States)

    Dagnino, Alessandro; Sforzini, Susanna; Dondero, Francesco; Fenoglio, Stefano; Bona, Elisa; Jensen, John; Viarengo, Aldo

    2008-07-01

    A new Expert Decision Support System (EDSS) that can integrate Triad data for assessing environmental risk and biological vulnerability at contaminated sites has been developed. Starting with ecosystem relevance, the EDSS assigns different weights to the results obtained from Triad disciplines. The following parameters have been employed: 1) chemical soil analyses (revealing the presence of potentially dangerous substances), 2) ecotoxicological bioassays (utilizing classical endpoints such as survival and reproduction rates), 3) biomarkers (showing sublethal pollutant effects), and 4) ecological parameters (assessing changes in community structure and functions). For each Triad discipline, the EDSS compares the data obtained at the studied field sites with reference values and calculates different 0-1 indexes (e.g., Chemical Risk Index, Ecotoxicological Risk Index, and Ecological Risk Index). The EDSS output consists of 3 indexes: 1) Environmental Risk index (EnvRI), quantifying the levels of biological damage at population-community level, 2) Biological Vulnerability Index (BVI), assessing the potential threats to biological equilibriums, and 3) Genotoxicity Index (GTI), screening genotoxicity effects. The EDSS has been applied in the integration of a battery of Triad data obtained during the European Union-funded Life Intervention in the Fraschetta Area (LINFA) project, which has been carried out in order to estimate the potential risk from soils of a highly anthropized area (Alessandria, Italy) mainly impacted by deposition of atmospheric pollutants. Results obtained during 4 seasonal sampling campaigns (2004-2005) show maximum values of EnvRI in sites A and B (characterized by industrial releases) and lower levels in site D (affected by vehicular traffic emissions). All 3 potentially polluted sites have shown high levels of BVI and GTI, suggesting a general change from reference conditions (site C).

  7. The IWOP Technique and Wigner-Function Approach to Quantum Effect of Mesoscopic Biological Cell

    Science.gov (United States)

    Wang, Xiu-Xia

    2014-09-01

    Using the IWOP technique, Wigner function theory and TFD theory, the quantization of a mesoscopic biological cell equivalent circuit is proposed, The quantum fluctuations of the mesoscopic biological cell are researched in thermal vacuum state and vacuum state. It is shown that the IWOP technique, Wigner function theory and Umezawa-Takahashi's TFD theory play the key role in quantizing a mesoscopic biological cell at finite temperature and the fluctuations and uncertainty increase with increasing temperature and decrease with prolonged time.

  8. Lipid polymorphism and the functional roles of lipids in biological membranes

    NARCIS (Netherlands)

    Cullis, P.R.; Kruijff, B. de

    1979-01-01

    The reasons for the great variety of lipids found in biological membranes, and the relations between lipid composition and membrane function pose major unsolved problems in membrane biology. Perhaps the only major functional role of lipids which may be regarded as firmly established involves the bil

  9. Functional-environmental assessment of Chernozems' technogenic changes in the Central-Chernozem Region of Russia

    Science.gov (United States)

    Deviatova, Tatiana; Jablonskikh, Lidiia; Alaeva, Liliia; Negrobova, Elena

    2015-04-01

    Long-term research revealed the significant changes in Chernozems of the recreational, urban, industrial and transport areas in the eastern part of the Central-Chernozem Region of Russia. They are reflected in the soil properties and regimes disturbances that determine their environmental functions. The level of the Chernozems' anthropogenic degradation is usually determined not only by their pollutants composition and quantity but by landscape, microclimatic, hydrological and soil features too. The Chernozems strongest degradation has been observed in the industrial zone and central part of Voronezh, and also in the 20-m zone of the highway "Don" with maximum technogenic input intensity and depth. The Chernozems' resistance to contamination is determined by their texture, organic matter content and quality, microbial activity and biochemical processes, pH and redox power. The level of the pollution impact on the organic substances decomposition can be evaluated according to the extracellular biological processes changes from their standard rates: 50% - very hazardous (ecotoxicological scale). The investigated soil types and subtypes have essentially different resistance to their contamination. In case of the gray forest soils already medium input of pollutants often results in irreversible changes in their biocenosis functions. In case of the leached Chernozems 50%-drop in their biological state occurs only at high levels of pollution. The developed criteria reflect the man-made ecosystems' soil principal changes and can be useful in prediction of their environmental functions.

  10. Genes and environment - striking the fine balance between sophisticated biomonitoring and true functional environmental genomics.

    Science.gov (United States)

    Steinberg, Christian E W; Stürzenbaum, Stephen R; Menzel, Ralph

    2008-08-01

    This article provides an overview how the application of the gene profiling (mainly via microarray technology) can be used in different organisms to address issues of environmental importance. Only recently, environmental sciences, including ecotoxicology, and molecular biology have started to mutually fertilize each other. This conceptual blend has enabled the identification of the interaction between molecular events and whole animal and population responses. Likewise, striking the fine balance between biomonitoring and functional environmental genomics will allow legislative and administrative measures to be based on a more robust platform. The application of DNA microarrays to ecotoxicogenomics links ecotoxicological effects of exposure with expression profiles of several thousand genes. The gene expression profiles are altered during toxicity, as either a direct or indirect result of toxicant exposure and the comparison of numerous specific expression profiles facilitates the differentiation between intoxication and true responses to environmental stressors. Furthermore, the application of microarrays provides the means to identify complex pathways and strategies that an exposed organism applies in response to environmental stressors. This review will present evidence that the widespread phenomenon of hormesis has a genetic basis that goes beyond an adaptive response. Some more practical advantages emerge: the toxicological assessment of complex mixtures, such as effluents or sediments, as well as drugs seems feasible, especially when classical ecotoxicological tests have failed. The review of available information demonstrates the advantages of microarray application to environmental issues spanning from bacteria, over algae and spermatophytes, to invertebrates (nematode Caenorhabditis elegans, crustacea Daphnia spp., earthworms), and various fish species. Microarrays have also highlighted why populations of a given species respond differently to similar

  11. Click chemistry mediated functionalization of vertical nanowires for biological applications

    DEFF Research Database (Denmark)

    Vutti, Surendra; Schoffelen, Sanne; Bolinsson, Jessica;

    2016-01-01

    is of general interest for biological studies. The attachment of a peptide substrate provided NW arrays for the detection of protease activity. In addition, green fluorescent protein was immobilized in a site-specific manner and recognized by antibody binding to demonstrate the proof-of-concept for the use...

  12. Limiting similarity and functional diversity along environmental gradients

    Science.gov (United States)

    Schwilk, D.W.; Ackerly, D.D.

    2005-01-01

    Recent developments in community models emphasize the importance of incorporating stochastic processes (e.g. ecological drift) in models of niche-structured community assembly. We constructed a finite, spatially explicit, lottery model to simulate the distribution of species in a one-dimensional landscape with an underlying gradient in environmental conditions. Our framework combines the potential for ecological drift with environmentally-mediated competition for space in a heterogeneous environment. We examined the influence of niche breadth, dispersal distances, community size (total number of individuals) and the breadth of the environmental gradient on levels of species and functional trait diversity (i.e. differences in niche optima). Three novel results emerge from this model: (1) niche differences between adjacent species (e.g. limiting similarity) increase in smaller communities, because of the interaction of competitive effects and finite population sizes; (2) immigration from a regional species pool, stochasticity and niche-assembly generate a bimodal distribution of species residence times ('transient' and 'resident') under a heterogeneous environment; and (3) the magnitude of environmental heterogeneity has a U-shaped effect on diversity, because of shifts in species richness of resident vs. transient species. These predictions illustrate the potential importance of stochastic (although not necessarily neutral) processes in community assembly. ??2005 Blackwell Publishing Ltd/CNRS.

  13. In search of lipid translocases and their biological functions

    NARCIS (Netherlands)

    Hoekstra, D; van Ijzendoorn, SCD

    2003-01-01

    In plasma membranes, lipids distribute asymmetrically across the bilayer, a process that requires proteins. Recent work identified novel lipid translocators in yeast, and their activity was functionally correlated to endocytosis, thus boosting investigations on identity, mechanism, and function of l

  14. Biological and environmental reference materials for trace elements, nuclides and organic microcontaminants

    International Nuclear Information System (INIS)

    This report has been produced from a database on analytical reference materials of biological and environmental origin, which is maintained at the International Atomic Energy Agency. It is an updated version of an earlier report, published in 1985, which focussed mainly on reference materials for trace elements. In the present version of the report, reference materials for trace elements still constitute the major part of the data; however, information is also now included on a number of other selected analytes of relevance to IAEA programmes, i.e. radionuclides, stable isotopes and organic microcontaminants. The database presently contains 2,694 analyte values for 117 analytes in 116 biological and 77 environmental (non-biological) reference materials produced by 20 different suppliers. Additional information on the cost of the material, the unit size supplied, (weight or volume), and the minimum weight of material recommended for analysis is also provided (if available to the authors). It is expected that this report will help analysts to select the reference material that matches as closely as possible, with respect to matrix type and concentrations of the analytes of interest, the ''real'' samples that are to be analysed. Refs, 12 tabs

  15. Cerenkov Radiation: A Multi-functional Approach for Biological Sciences

    Directory of Open Access Journals (Sweden)

    Xiaowei eMa

    2014-02-01

    Full Text Available Cerenkov radiation (CR has been used in various biological research fields, which has aroused lots of attention in recent years. Combining optical imaging instruments and most of nuclear medicine imaging or radiotherapy probes, the CR was developed as a new imaging modality for biology studies, called Cerenkov luminescence imaging (CLI. On the other hand, it was novelly used as an internal excitation source to activate some fluorophores for energy transfer imaging. However, it also has some shortages such as relatively weak luminescence intensity and low penetration in tissue. Thus some scientific groups demonstrated to optimize the CLI and demonstrated it to three-dimension tomography. In this article, we elaborate on its principle, history, and applications and discuss a number of directions for technical improvements. Then concluded some advantages and shortages of CR and discuss some prospects of it.

  16. Biological activity of Cryptococcus neoformans and Cryptococcus gattii from clinical and environmental isolates

    Directory of Open Access Journals (Sweden)

    Antonio Marcio Barbosa Junior

    2013-06-01

    Full Text Available INTRODUCTION: Cryptococcus neoformans and Cryptococcus gattii are encapsulated basidiomycetous yeasts with worldwide distribution. They cause cryptococcosis with features of systemic infection, affecting the central nervous system, lungs and skin in humans and animals. These fungi present numerous virulence factors that allow them to invade the host and multiply, among which extracellular enzyme capacity and microbial adaptation to different temperatures are worth mentioning. OBJECTIVE: To evaluate the production of protease and investigate possible differences in thermotolerance and urease activity in clinical and environmental yeast isolates. MATERIAL AND METHODS: Culture methods and Pz analysis were applied to assess urease and protease, whereas the optical density method was used to analyze biological activity in thermotolerance. RESULTS: There was no significant results as to microbial growth at the tested temperatures (25º, 37º and 42ºC. It was observed that clinical specimens grew better than environmental ones at elevated temperatures. As to C. neoformans, the moderate production of urease enzyme prevailed in both clinical and environmental isolates within 24h or 48h. Moreover, there was significant production on the seventh day of reading. The best reading time for viewing protease production in both isolates and species was the seventh day: 96% clinical samples and 94% environmental isolates. CONCLUSION: Further studies are required in order to investigate the virulence factors of C. neoformans and C. gattii cerebrospinal isolates from patients with meningoencephalitis and environmental samples from Sergipe. Furthermore, a higher technical accuracy and statistical precision are indispensable.

  17. Consequences of Environmental Service Payments for Forest Retention and Recruitment in a Costa Rican Biological Corridor

    Directory of Open Access Journals (Sweden)

    Steven J. Hollenhorst

    2009-06-01

    Full Text Available Compensation to landowners for forest-derived environmental services has gained international recognition as a mechanism to combat forest loss and fragmentation. This approach is widely promoted, although there is little evidence demonstrating that environmental service payments encourage forest stewardship and conservation. Costa Rica provides a unique case study in which a 1996 Forestry Law initiated environmental service payments and prohibited forest conversion to other land uses. We examined these novel policies to determine their influence on landowner decisions that affect forest change, carbon services, and connectivity in a 2425 km² biological corridor. We used Landsat images to compare land-cover changes before and after 1996, and linked these data to landowner surveys investigating land-use decisions. Carbon stocks and storage in secondary forests were also examined. Forest change observations were corroborated by landowner survey data, indicating that the 1996 Forestry Law and environmental service payments contributed positively to forest retention and recruitment. Socioeconomic conditions also favored forest protection. Rates of natural forest loss declined from -1.43% to -0.10%/yr after 1996. Forest cover and connectivity were maintained through tree plantations and secondary forest recruitment, although forest heterogeneity increased as these forest types sometimes replaced natural forest. Carbon storage in secondary forest approached levels in primary forest after 25–30 yr of succession, although few landowners retained natural regeneration. Secondary forests will persist as minor landscape components without legal or financial incentives. The Costa Rican experience provides evidence that environmental service payments can be effective in retaining natural forest and recruiting tree cover within biological corridors.

  18. Chemical Dissolution Pathways of MoS2 Nanosheets in Biological and Environmental Media.

    Science.gov (United States)

    Wang, Zhongying; von dem Bussche, Annette; Qiu, Yang; Valentin, Thomas M; Gion, Kyle; Kane, Agnes B; Hurt, Robert H

    2016-07-01

    Material stability and dissolution in aqueous media are key issues to address in the development of a new nanomaterial intended for technological application. Dissolution phenomena affect biological and environmental persistence; fate, transport, and biokinetics; device and product stability; and toxicity pathways and mechanisms. This article shows that MoS2 nanosheets are thermodynamically and kinetically unstable to O2-oxidation under ambient conditions in a variety of aqueous media. The oxidation is accompanied by nanosheet degradation and release of soluble molybdenum and sulfur species, and generates protons that can colloidally destabilize the remaining sheets. The oxidation kinetics are pH-dependent, and a kinetic law is developed for use in biokinetic and environmental fate modeling. MoS2 nanosheets fabricated by chemical exfoliation with n-butyl-lithium are a mixture of 1T (primary) and 2H (secondary) phases and oxidize rapidly with a typical half-life of 1-30 days. Ultrasonically exfoliated sheets are in pure 2H phase, and oxidize much more slowly. Cytotoxicity experiments on MoS2 nanosheets and molybdate ion controls reveal the relative roles of the nanosheet and soluble fractions in the biological response. These results indicate that MoS2 nanosheets will not show long-term persistence in living systems and oxic natural waters, with important implications for biomedical applications and environmental risk. PMID:27267956

  19. Functional Analytic Multisensory Environmental Therapy for People with Dementia

    Directory of Open Access Journals (Sweden)

    Jason A. Staal

    2012-01-01

    Full Text Available This paper introduces Functional Analytic Multisensory Environmental Therapy (FAMSET for use with elders with dementia while using a multisensory environment/snoezelen room. The model introduces behavioral theory and practice to the multisensory environment treatment, addressing assessment, and, within session techniques, integrating behavioral interventions with emotion-oriented care. A modular approach is emphasized to delineate different treatment phases for multisensory environment therapy. The aim of the treatment is to provide a safe and effective framework for reducing the behavioral disturbance of the disease process, increasing elder well-being, and to promote transfer of positive effects to other environments outside of the multisensory treatment room.

  20. Computational Exploration of the Biological Basis of Black-Scholes Expected Utility Function

    OpenAIRE

    Sukanto Bhattacharya; Kuldeep Kumar

    2007-01-01

    It has often been argued that there exists an underlying biological basis of utility functions. Taking this line of argument a step further in this paper, we have aimed to computationally demonstrate the biological basis of the Black-Scholes functional form as applied to classical option pricing and hedging theory. The evolutionary optimality of the classical Black-Scholes function has been computationally established by means of a haploid genetic algorithm model. The objective was to minimiz...

  1. Computational Exploration of the Biological Basis of Black-Scholes Expected Utility Function

    OpenAIRE

    Kuldeep Kumar; Sukanto Bhattacharya

    2007-01-01

    It has often been argued that there exists an underlying biological basis of utility functions. Taking this line of argument a step further in this paper, we have aimed to computationally demonstrate the biological basis of the Black-Scholes functional form as applied to classical option pricing and hedging theory. The evolutionary optimality of the classical Black-Scholes function has been computationally established by means of a haploid genetic algorithm model. The objective was to mi...

  2. MECHANISTIC INDICATORS OF CHILDHOOD ASTHMA (MICA): A SYSTEMS BIOLOGY APPROACH FOR THE INTEGRATION OF MULTIFACTORIAL EXPOSURE AND ENVIRONMENTAL HEALTH DATA

    Science.gov (United States)

    Modem methods in molecular biology and advanced computational tools show promise in elucidating complex interactions that occur between genes and environmental factors in diseases such as asthma. However, appropriately designed studies are critical for these methods to reach the...

  3. Deciphering Diseases and Biological Targets for Environmental Chemicals using Toxicogenomics Networks

    DEFF Research Database (Denmark)

    Audouze, Karine Marie Laure; Juncker, Agnieszka; Roque, Francisco José Sousa Simões Almeida;

    2010-01-01

    Exposure to environmental chemicals and drugs may have a negative effect on human health. A better understanding of the molecular mechanism of such compounds is needed to determine the risk. We present a high confidence human protein-protein association network built upon the integration...... of chemical toxicology and systems biology. This computational systems chemical biology model reveals uncharacterized connections between compounds and diseases, thus predicting which compounds may be risk factors for human health. Additionally, the network can be used to identify unexpected potential...... associations between chemicals and proteins. Examples are shown for chemicals associated with breast cancer, lung cancer and necrosis, and potential protein targets for di-ethylhexyl-phthalate, 2,3,7,8-tetrachlorodibenzo-p-dioxin, pirinixic acid and permethrine. The chemical-protein associations are supported...

  4. Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach.

    Science.gov (United States)

    Li, Jun; Zhao, Patrick X

    2016-01-01

    Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/. PMID:27446133

  5. Mining Functional Modules in Heterogeneous Biological Networks Using Multiplex PageRank Approach.

    Science.gov (United States)

    Li, Jun; Zhao, Patrick X

    2016-01-01

    Identification of functional modules/sub-networks in large-scale biological networks is one of the important research challenges in current bioinformatics and systems biology. Approaches have been developed to identify functional modules in single-class biological networks; however, methods for systematically and interactively mining multiple classes of heterogeneous biological networks are lacking. In this paper, we present a novel algorithm (called mPageRank) that utilizes the Multiplex PageRank approach to mine functional modules from two classes of biological networks. We demonstrate the capabilities of our approach by successfully mining functional biological modules through integrating expression-based gene-gene association networks and protein-protein interaction networks. We first compared the performance of our method with that of other methods using simulated data. We then applied our method to identify the cell division cycle related functional module and plant signaling defense-related functional module in the model plant Arabidopsis thaliana. Our results demonstrated that the mPageRank method is effective for mining sub-networks in both expression-based gene-gene association networks and protein-protein interaction networks, and has the potential to be adapted for the discovery of functional modules/sub-networks in other heterogeneous biological networks. The mPageRank executable program, source code, the datasets and results of the presented two case studies are publicly and freely available at http://plantgrn.noble.org/MPageRank/.

  6. Underwater linear polarization: physical limitations to biological functions

    OpenAIRE

    Shashar, Nadav; Johnsen, Sönke; Lerner, Amit; Sabbah, Shai; Chiao, Chuan-Chin; Mäthger, Lydia M; Hanlon, Roger T

    2011-01-01

    Polarization sensitivity is documented in a range of marine animals. The variety of tasks for which animals can use this sensitivity, and the range over which they do so, are confined by the visual systems of these animals and by the propagation of the polarization information in the aquatic environment. We examine the environmental physical constraints in an attempt to reveal the depth, range and other limitations to the use of polarization sensitivity by marine animals. In clear oceanic wat...

  7. Inferring biological functions of guanylyl cyclases with computational methods

    KAUST Repository

    Alquraishi, May Majed

    2013-09-03

    A number of studies have shown that functionally related genes are often co-expressed and that computational based co-expression analysis can be used to accurately identify functional relationships between genes and by inference, their encoded proteins. Here we describe how a computational based co-expression analysis can be used to link the function of a specific gene of interest to a defined cellular response. Using a worked example we demonstrate how this methodology is used to link the function of the Arabidopsis Wall-Associated Kinase-Like 10 gene, which encodes a functional guanylyl cyclase, to host responses to pathogens. © Springer Science+Business Media New York 2013.

  8. The SHP-2 tyrosine phosphatase: Signaling mechanisms and biological functions

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Cellular biological activities are tightly controlled by intracellular signaling processes initiated by extracellular signals.Protein tyrosine phosphatases, which remove phosphate groups from phosphorylated signaling molecules, play equally important tyrosine roles as protein tyrosine kinases in signal transduction.SHP-2, a cytoplasmic SH2 domain containing protein tyrosine phosphatase, is involved in the signaling pathways of a variety of growth factors and cytokines. Recent studies have clearly demonstrated that this phosphatase plays an important role in transducing signal relay from the cell surface to the nucleus, and is a critical intracellular regulator in mediating cell proliferation and differentiation.

  9. Environmental and biological monitoring in a lead acid battery manufacturing unit in India.

    Science.gov (United States)

    Ravichandran, B; Ravibabu, K; Raghavan, S; Krishnamurthy, V; Rajan, B K; Rajmohan, H R

    2005-07-01

    An environmental and biological monitoring of a lead acid battery manufacturing unit was carried out to measure the respirable particulate matter, lead content in working atmosphere and blood lead levels of workers employed in different sections. The results showed high mean air lead concentration in buffing (1444.45 microg/m(3)), plate cutting (430.14 microg/m(3)) and pasting (277.48 microg/m(3)) sections. The mean blood lead levels of employees in these sections were also higher than the values prescribed by ACGIH.

  10. Global environmental change and the biology of arbuscular mycorrhizas: gaps and challenges

    DEFF Research Database (Denmark)

    Fitter, A.H.; Heinemeyer, A.; Husband, R.;

    2004-01-01

    Our ability to make predictions about the impact of global environmental change on arbuscular mycorrhizal (AM) fungi and on their role in regulating biotic response to such change is seriously hampered by our lack of knowledge of the basic biology of these ubiquitous organisms. Current information...... in determining the structure of the AM fungal community. Nevertheless, the direct response of AM fungi to temperature may have large implications for rates of C cycling. New evidence shows that AM fungal hyphae may be very short lived, potentially acting as a rapid route by which C may cycle back......, and if the number of species is much greater than the number currently described (150), as seems almost certain, then there is the potential for several new fields of study, including community ecology and biogeography of AM fungi, and these will give us new insights into the impacts of global environmental change...

  11. Non-coding RNAs: Classification, Biology and Functioning.

    Science.gov (United States)

    Hombach, Sonja; Kretz, Markus

    2016-01-01

    One of the long-standing principles of molecular biology is that DNA acts as a template for transcription of messenger RNAs, which serve as blueprints for protein translation. A rapidly growing number of exceptions to this rule have been reported over the past decades: they include long known classes of RNAs involved in translation such as transfer RNAs and ribosomal RNAs, small nuclear RNAs involved in splicing events, and small nucleolar RNAs mainly involved in the modification of other small RNAs, such as ribosomal RNAs and transfer RNAs. More recently, several classes of short regulatory non-coding RNAs, including piwi-associated RNAs, endogenous short-interfering RNAs and microRNAs have been discovered in mammals, which act as key regulators of gene expression in many different cellular pathways and systems. Additionally, the human genome encodes several thousand long non-protein coding RNAs >200 nucleotides in length, some of which play crucial roles in a variety of biological processes such as epigenetic control of chromatin, promoter-specific gene regulation, mRNA stability, X-chromosome inactivation and imprinting. In this chapter, we will introduce several classes of short and long non-coding RNAs, describe their diverse roles in mammalian gene regulation and give examples for known modes of action. PMID:27573892

  12. 76 FR 13597 - Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological...

    Science.gov (United States)

    2011-03-14

    ...; ] DEPARTMENT OF AGRICULTURE Animal and Plant Health Inspection Service Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological Control Agent for Hawkweeds AGENCY: Animal... subterminalis, into the continental United States as a biological control agent to reduce the severity...

  13. Simplivariate Models: Uncovering the Underlying Biology in Functional Genomics Data

    OpenAIRE

    Edoardo Saccenti; Westerhuis, Johan A.; Smilde, Age K.; van der Werf, Mariët J; Jos A Hageman; Hendriks, Margriet M. W. B.

    2011-01-01

    One of the first steps in analyzing high-dimensional functional genomics data is an exploratory analysis of such data. Cluster Analysis and Principal Component Analysis are then usually the method of choice. Despite their versatility they also have a severe drawback: they do not always generate simple and interpretable solutions. On the basis of the observation that functional genomics data often contain both informative and non-informative variation, we propose a method that finds sets of va...

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

    OpenAIRE

    Narayanasamy, Shaman; Muller, Emilie; Sheik, Abdul; 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 functionalitie...

  15. 76 FR 4859 - Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological...

    Science.gov (United States)

    2011-01-27

    ... Animal and Plant Health Inspection Service Availability of an Environmental Assessment and Finding of No Significant Impact for a Biological Control Agent for Asian Citrus Psyllid AGENCY: Animal and Plant Health... Health Inspection Service has prepared an environmental assessment and finding of no significant...

  16. Molecular structure and biological function of proliferating cell nuclear antigen

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Proliferating cell nuclear antigen (PCNA) is the core component of replication complex in eukaryote.As a processive factor of DNA polymerase delta, PCNA coordinates the replication process by interacting with various replication proteins. PCNA appears to play an essential role in many cell events, such as DNA damage repair, cell cycle regulation, and apoptosis, through the coordination or organization of different partners. PCNA is an essential factor in cell proliferation, and has clinical significance in tumor research. In this article we review the functional structure of PCNA, which acts as a function switch in different cell events.

  17. Novel ESCRT functions in cell biology: spiraling out of control?

    Science.gov (United States)

    Campsteijn, Coen; Vietri, Marina; Stenmark, Harald

    2016-08-01

    The endosomal sorting complex required for transport (ESCRT), originally identified for its role in endosomal protein sorting and biogenesis of multivesicular endosomes (MVEs), has proven to be a versatile machinery for involution and scission of narrow membrane invaginations filled with cytosol. Budding of enveloped viruses and cytokinetic abscission were early described functions for the ESCRT machinery, and recently a number of new ESCRT functions have emerged. These include cytokinetic abscission checkpoint control, plasma membrane repair, exovesicle release, quality control of nuclear pore complexes, neuron pruning, and sealing of the newly formed nuclear envelope. Here we review these novel ESCRT mechanisms and discuss similarities and differences between the various ESCRT-dependent activities.

  18. Analysis of Boolean Functions based on Interaction Graphs and their influence in System Biology

    OpenAIRE

    Das, Jayanta Kumar; Rout, Ranjeet Kumar; Choudhury, Pabitra Pal

    2014-01-01

    Interaction graphs provide an important qualitative modeling approach for System Biology. This paper presents a novel approach for construction of interaction graph with the help of Boolean function decomposition. Each decomposition part (Consisting of 2-bits) of the Boolean functions has some important significance. In the dynamics of a biological system, each variable or node is nothing but gene or protein. Their regulation has been explored in terms of interaction graphs which are generate...

  19. Environmental routes for platinum group elements to biological materials--a review.

    Science.gov (United States)

    Ek, Kristine H; Morrison, Gregory M; Rauch, Sebastien

    2004-12-01

    The increased use of platinum group elements (PGE) in automobile catalysts has led to concern over potential environmental and biological accumulation. Platinum (Pt), palladium (Pd) and rhodium (Rh) concentrations have increased in the environment since the introduction of automobile catalysts. This review summarises current knowledge concerning the environmental mobility, speciation and bioavailability of Pt, Pd and Rh. The greater proportion of PGE emissions is from automobile catalysts, in the form of nanometer-sized catalyst particles, which deposit on roadside surfaces, as evidenced in samples of road dust, grass and soil. In soil, PGE can be transformed into more mobile species through complexation with organic matter and can be solubilised in low pH rainwater. There are indications that environmentally formed Pd species are more soluble and hence more mobile in the environment than Rh and Pt. PGE can reach waterbodies through stormwater transport and deposition in sediments. Besides external contamination of grass close to roads, internal PGE uptake has been observed for plants growing on soil contaminated with automobile catalyst PGE. Fine particles of PGE were also detected on the surface of feathers sampled from passerines and raptors in their natural habitat, and internal organs of these birds also contained PGE. Uptake has been observed in sediment-dwelling invertebrates, and laboratory studies have shown an uptake of PGE in eel and fish exposed to water containing road dust. The available evidence indicates that the PGE, especially Pd, are transported to biological materials through deposition in roots by binding to sulphur-rich low molecular weight species in plants. PGE uptake to exposed animals have uptake rates in the following order: Pd>Pt>Rh. The liver and kidney accumulate the highest levels of PGE, especially Pd. Urinary Pd and Rh, but not Pt, levels are correlated with traffic intensity. Dental alloys may lead to elevated urinary Pt levels

  20. Environmental routes for platinum group elements to biological materials. A review

    Energy Technology Data Exchange (ETDEWEB)

    Ek, Kristine H.; Morrison, Gregory M. [Water Environment Transport, Chalmers University of Technology, SE 412 96 Goteborg (Sweden); Rauch, Sebastien [R.M. Parsons Laboratory 48-108, Massachusetts Institute of Technology, Cambridge, MA 02139 (United States)

    2004-12-01

    The increased use of platinum group elements (PGE) in automobile catalysts has led to concern over potential environmental and biological accumulation. Platinum (Pt), palladium (Pd) and rhodium (Rh) concentrations have increased in the environment since the introduction of automobile catalysts. This review summarises current knowledge concerning the environmental mobility, speciation and bioavailability of Pt, Pd and Rh. The greater proportion of PGE emissions is from automobile catalysts, in the form of nanometer-sized catalyst particles, which deposit on roadside surfaces, as evidenced in samples of road dust, grass and soil. In soil, PGE can be transformed into more mobile species through complexation with organic matter and can be solubilised in low pH rainwater. There are indications that environmentally formed Pd species are more soluble and hence more mobile in the environment than Rh and Pt. PGE can reach waterbodies through stormwater transport and deposition in sediments. Besides external contamination of grass close to roads, internal PGE uptake has been observed for plants growing on soil contaminated with automobile catalyst PGE. Fine particles of PGE were also detected on the surface of feathers sampled from passerines and raptors in their natural habitat, and internal organs of these birds also contained PGE. Uptake has been observed in sediment-dwelling invertebrates, and laboratory studies have shown an uptake of PGE in eel and fish exposed to water containing road dust.The available evidence indicates that the PGE, especially Pd, are transported to biological materials through deposition in roots by binding to sulphur-rich low molecular weight species in plants. PGE uptake to exposed animals have uptake rates in the following order: Pd>Pt>Rh. The liver and kidney accumulate the highest levels of PGE, especially Pd. Urinary Pd and Rh, but not Pt, levels are correlated with traffic intensity. Dental alloys may lead to elevated urinary Pt levels

  1. MicroRNA function in NK cell biology

    OpenAIRE

    Beaulieu, AM; Bezman, NA; Lee, JE; Matloubian, M; Sun, JC; Lanier, LL

    2013-01-01

    The important role of microRNAs in directing immune responses has become increasingly clear. Here, we highlight discoveries uncovering the role of specific microRNAs in regulating the development and function of natural killer (NK) cells. Furthermore, we discuss the impact of NK cells on the entire immune system during global and specific microRNA ablation in the settings of inflammation, infection, and immune dysregulation. © 2013 John Wiley & Sons A/S.

  2. Functional Nanostructured Platforms for Chemical and Biological Sensing

    Energy Technology Data Exchange (ETDEWEB)

    Letant, S E

    2006-03-20

    The central goal of our work is to combine semiconductor nanotechnology and surface functionalization in order to build platforms for the selective detection of bio-organisms ranging in size from bacteria (micron range) down to viruses, as well as for the detection of chemical agents (nanometer range). We will show on three porous silicon platforms how pore geometry and pore wall chemistry can be combined and optimized to capture and detect specific targets. We developed a synthetic route allowing to directly anchor proteins on silicon surfaces and illustrated the relevance of this technique by immobilizing live enzymes onto electrochemically etched luminescent nano-porous silicon. The powerful association of the specific enzymes with the transducing matrix led to a selective hybrid platform for chemical sensing. We also used light-assisted electrochemistry to produce periodic arrays of through pores on pre-patterned silicon membranes with controlled diameters ranging from many microns down to tens of nanometers. We demonstrated the first covalently functionalized silicon membranes and illustrated their selective capture abilities with antibody-coated micro-beads. These engineered membranes are extremely versatile and could be adapted to specifically recognize the external fingerprints (size and coat composition) of target bio-organisms. Finally, we fabricated locally functionalized single nanopores using a combination of focused ion beam drilling and ion beam assisted oxide deposition. We showed how a silicon oxide ring can be grown around a single nanopore and how it can be functionalized with DNA probes to detect single viral-sized beads. The next step for this platform is the detection of whole viruses and bacteria.

  3. Language: A Typological, Functional, Cognitive, Biological and Evolutionary Approach.

    OpenAIRE

    Kirtchuk, Pablo

    2009-01-01

    The paper shows the inadequacy of the structuralist method with its climax in generative grammar method when applied to our understanding of langauge. It shows the adequation of the cognitive, typological and functional approach. based on croslinguistically empirical data, i show the intrinsically human nature of language, which distinguishes it from other communication sysrtemss, viz. animal, computer and artificial ones,. Points treated in some detail are : Iconicity, Deixis, Multiple encod...

  4. Functionalization of carbon nanotube and nanofiber electrodes with biological macromolecules: Progress toward a nanoscale biosensor

    Science.gov (United States)

    Baker, Sarah E.

    The integration of nanoscale carbon-based electrodes with biological recognition and electrical detection promises unparalleled biological detection systems. First, biologically modified carbon-based materials have been shown to have superior long-term chemical stability when compared to other commonly used materials for biological detection such as silicon, gold, and glass surfaces. Functionalizing carbon electrodes for biological recognition and using electrochemical methods to transduce biological binding information will enable real-time, hand-held, lower cost and stable biosensing devices. Nanoscale carbon-based electrodes allow the additional capability of fabricating devices with high densities of sensing elements, enabling multi-analyte detection on a single chip. We have worked toward the integration of these sensor components by first focusing on developing and characterizing the chemistry required to functionalize single-walled carbon nanotubes and vertically aligned carbon nanofibers with oligonucleotides and proteins for specific biological recognition. Chemical, photochemical and electrochemical methods for functionalizing these materials with biological molecules were developed. We determined, using fluorescence and colorimetric techniques, that these biologically modified nanoscale carbon electrodes are biologically active, selective, and stable. A photochemical functionalization method enabled facile functionalization of dense arrays vertically aligned carbon nanofiber forests. We found that much of the vertically aligned carbon nanofiber sidewalls were functionalized and biologically accessible by this method---the absolute number of DNA molecules hybridized to DNA-functionalized nanofiber electrodes was ˜8 times higher than the number of DNA molecules hybridized to flat glassy carbon electrodes and implies that nanofiber forest sensors may facilitate higher sensitivity to target DNA sequences per unit area. We also used the photochemical method

  5. Underwater linear polarization: physical limitations to biological functions.

    Science.gov (United States)

    Shashar, Nadav; Johnsen, Sönke; Lerner, Amit; Sabbah, Shai; Chiao, Chuan-Chin; Mäthger, Lydia M; Hanlon, Roger T

    2011-03-12

    Polarization sensitivity is documented in a range of marine animals. The variety of tasks for which animals can use this sensitivity, and the range over which they do so, are confined by the visual systems of these animals and by the propagation of the polarization information in the aquatic environment. We examine the environmental physical constraints in an attempt to reveal the depth, range and other limitations to the use of polarization sensitivity by marine animals. In clear oceanic waters, navigation that is based on the polarization pattern of the sky appears to be limited to shallow waters, while solar-based navigation is possible down to 200-400 m. When combined with intensity difference, polarization sensitivity allows an increase in target detection range by 70-80% with an upper limit of 15 m for large-eyed animals. This distance will be significantly smaller for small animals, such as plankton, and in turbid waters. Polarization-contrast detection, which is relevant to object detection and communication, is strongly affected by water conditions and in clear waters its range limit may reach 15 m as well. We show that polarization sensitivity may also serve for target distance estimation, when examining point source bioluminescent objects in the photic mesopelagic depth range.

  6. Comparative Study on Human Risk by Ionizing Radiation and Pesticide as Biological Information about Environmental Disaster

    International Nuclear Information System (INIS)

    Environmental risk factors such as ionizing radiations, heavy metals, and pesticides can cause environmental disasters when they exist in excess. The increases in use of ionizing radiation and agricultural pesticide are somewhat related to the possibility of the disaster. The risk of radiation and pesticide was evaluated by means of the Single Cell Gel Electrophoresis (SCGE) assay on the human blood lymphocytes. The lymphocytes were irradiated with 0∼2.0 Gy of 60Co gamma ray. Another groups of lymphocytes were exposed to various concentrations of parathion. Significantly increased tail moment, which was a marker of DNA strand breaks in SCGE assay, showed a clear dose- or concentration-response relationship. Parathion of a recommended concentration for agricultural use ( 1 mg l-1) has a strong cytotoxic effect on lymphocytes, which is equivalent to damage induced by 0.1 Gy of γ-ray. Furthermore, 2 mg l-1 of parathion can give rise to DNA damage equivalent to that induced by 0.25 Gy at which the radiation-induced damage can start to develop into clinical symptoms. The comparative results of this study can provide an experimental basis and biological information for the prevention of environmental disaster

  7. DataONE: Enabling Data-Intensive Biological and Environmental Research through Cyberinfrastructure

    Science.gov (United States)

    Cook, R. B.; Michener, W. K.; Frame, M. T.; Hampton, S. E.; Vision, T. J.

    2009-12-01

    Addressing the Earth's environmental problems requires that we change the ways that we do science; harness the enormity of existing data; develop new methods to combine, analyze, and visualize diverse data resources; create new, long-lasting cyberinfrastructure; and re-envision many of our longstanding institutions. DataONE (Observation Network for Earth) represents a new virtual organization whose goal is to enable new science and knowledge creation through universal access to data about life on Earth and the environment that sustains it. DataONE is designed to be the foundation of new innovative environmental science through a distributed framework and sustainable cyberinfrastructure that meets the needs of science and society for open, persistent, robust, and secure access to well-described and easily discovered Earth observational data. Supported by the U.S. National Science Foundation, DataONE will ensure the preservation and access to multi-scale, multi-discipline, and multi-national science data. DataONE is transdisciplinary, making biological data available from the genome to the ecosystem; making environmental data available from atmospheric, ecological, hydrological, and oceanographic sources; providing secure and long-term preservation and access; and engaging scientists, land-managers, policy makers, students, educators, and the public through logical access and intuitive visualizations. Most importantly, DataONE will serve a broader range of science domains both directly and through the interoperability with the DataONE distributed network.

  8. Decreased functional diversity and biological pest control in conventional compared to organic crop fields.

    Directory of Open Access Journals (Sweden)

    Jochen Krauss

    Full Text Available Organic farming is one of the most successful agri-environmental schemes, as humans benefit from high quality food, farmers from higher prices for their products and it often successfully protects biodiversity. However there is little knowledge if organic farming also increases ecosystem services like pest control. We assessed 30 triticale fields (15 organic vs. 15 conventional and recorded vascular plants, pollinators, aphids and their predators. Further, five conventional fields which were treated with insecticides were compared with 10 non-treated conventional fields. Organic fields had five times higher plant species richness and about twenty times higher pollinator species richness compared to conventional fields. Abundance of pollinators was even more than one-hundred times higher on organic fields. In contrast, the abundance of cereal aphids was five times lower in organic fields, while predator abundances were three times higher and predator-prey ratios twenty times higher in organic fields, indicating a significantly higher potential for biological pest control in organic fields. Insecticide treatment in conventional fields had only a short-term effect on aphid densities while later in the season aphid abundances were even higher and predator abundances lower in treated compared to untreated conventional fields. Our data indicate that insecticide treatment kept aphid predators at low abundances throughout the season, thereby significantly reducing top-down control of aphid populations. Plant and pollinator species richness as well as predator abundances and predator-prey ratios were higher at field edges compared to field centres, highlighting the importance of field edges for ecosystem services. In conclusion organic farming increases biodiversity, including important functional groups like plants, pollinators and predators which enhance natural pest control. Preventative insecticide application in conventional fields has only short

  9. Decreased functional diversity and biological pest control in conventional compared to organic crop fields.

    Science.gov (United States)

    Krauss, Jochen; Gallenberger, Iris; Steffan-Dewenter, Ingolf

    2011-01-01

    Organic farming is one of the most successful agri-environmental schemes, as humans benefit from high quality food, farmers from higher prices for their products and it often successfully protects biodiversity. However there is little knowledge if organic farming also increases ecosystem services like pest control. We assessed 30 triticale fields (15 organic vs. 15 conventional) and recorded vascular plants, pollinators, aphids and their predators. Further, five conventional fields which were treated with insecticides were compared with 10 non-treated conventional fields. Organic fields had five times higher plant species richness and about twenty times higher pollinator species richness compared to conventional fields. Abundance of pollinators was even more than one-hundred times higher on organic fields. In contrast, the abundance of cereal aphids was five times lower in organic fields, while predator abundances were three times higher and predator-prey ratios twenty times higher in organic fields, indicating a significantly higher potential for biological pest control in organic fields. Insecticide treatment in conventional fields had only a short-term effect on aphid densities while later in the season aphid abundances were even higher and predator abundances lower in treated compared to untreated conventional fields. Our data indicate that insecticide treatment kept aphid predators at low abundances throughout the season, thereby significantly reducing top-down control of aphid populations. Plant and pollinator species richness as well as predator abundances and predator-prey ratios were higher at field edges compared to field centres, highlighting the importance of field edges for ecosystem services. In conclusion organic farming increases biodiversity, including important functional groups like plants, pollinators and predators which enhance natural pest control. Preventative insecticide application in conventional fields has only short-term effects on aphid

  10. ISSEBETS 2009. 7. International Symposium on Speciation of Elements in Biological, Environmental and Toxicological Sciences

    International Nuclear Information System (INIS)

    The 7th ISSEBETS was held in August 2009 in city of Eger, Hungary. The main topics were: speciation of essential and toxic elements in food, in traditional drugs, designing functional foods through applied speciation, metallomics and metalloproteomics, metal species in health and disease, cycling of elemental species in the environment, speciation related regulations and legislation, metal environmental, bioremediation, quality assurance of speciation analysis. (S.I.)

  11. Recent advances in alveolar biology: evolution and function of alveolar proteins.

    Science.gov (United States)

    Orgeig, Sandra; Hiemstra, Pieter S; Veldhuizen, Edwin J A; Casals, Cristina; Clark, Howard W; Haczku, Angela; Knudsen, Lars; Possmayer, Fred

    2010-08-31

    This review is focused on the evolution and function of alveolar proteins. The lung faces physical and environmental challenges, due to changing pressures/volumes and foreign pathogens, respectively. The pulmonary surfactant system is integral in protecting the lung from these challenges via two groups of surfactant proteins - the small molecular weight hydrophobic SPs, SP-B and -C, that regulate interfacial adsorption of the lipids, and the large hydrophilic SPs, SP-A and -D, which are surfactant collectins capable of inhibiting foreign pathogens. Further aiding pulmonary host defence are non-surfactant collectins and antimicrobial peptides that are expressed across the biological kingdoms. Linking to the first symposium session, which emphasised molecular structure and biophysical function of surfactant lipids and proteins, this review begins with a discussion of the role of temperature and hydrostatic pressure in shaping the evolution of SP-C in mammals. Transitioning to the role of the alveolus in innate host defence we discuss the structure, function and regulation of antimicrobial peptides, the defensins and cathelicidins. We describe the recent discovery of novel avian collectins and provide evidence for their role in preventing influenza infection. This is followed by discussions of the roles of SP-A and SP-D in mediating host defence at the alveolar surface and in mediating inflammation and the allergic response of the airways. Finally we discuss the use of animal models of lung disease including knockouts to develop an understanding of the role of these proteins in initiating and/or perpetuating disease with the aim of developing new therapeutic strategies. PMID:20433956

  12. Is kinase activity essential for biological functions of BRI1?

    Institute of Scientific and Technical Information of China (English)

    Weihui Xu; Juan Huang; Baohua Li; Jiayang Li; Yonghong Wang

    2008-01-01

    Brassinosteroids (BRs) are a major group of plant hormones that regulate plant growth and development. BRI1, a protein localized to the plasma membrane, functions as a BR receptor and it has been proposed that its kinase activity has an essential role in BR-regulated plant growth and development. Here we report the isolation and molecular characterization of a new allele of bril, bril-301, which shows moderate morphological phenotypes and a reduced response to BRs under normal growth conditions. Sequence analysis identified a two-base alteration from GG to AT, resulting in a conversion of 989G to 9891 in the BRI1 kinase domain. An in vitro assay of kinase activity showed that bril-301 has no detectable autophosphorylation activity or phosphorylation activity towards the BRI1 substrates TTL and BAK1. Furthermore, our results suggest that bril-301, even with extremely impaired kinase activity, still retains partial function in regulating plant growth and development, which raises the question of whether BRI1 kinase activity is essential for BR-mediated growth and development in higher plants.

  13. [Dialectic of the interrelationship between structure and function in biology and medicine].

    Science.gov (United States)

    Strukov, A I; Kakturskiĭ, L V

    1977-01-01

    The paper deals with some aspects of the dialectics of structure and function relationships in biological objects normally and pathologically. Idealistic and metaphysical concepts of the structure-function relationships (morphological idealism, holism, physiological idealism, functionalism) are critisized, and historical premises of these concepts are characterized. The principle of indissoluble unity and interconnection of changes in structure and function is emphasized, while the thesis of the primacy of function in the shaping of the form and the concept of functional diseases are rejected. Much attention is paid to the methodological principles of the study of structure and function based on the systemic approach to the investigation of biological objects from the point of view of structural levels and integratism. The groundlessness of the principles of reductionism and organicism in the solution of this problem is indicated. The connection of the concepts of structure and function with categories and laws of materialistic dialectics is dwelt on. PMID:880057

  14. [Adipogenic function and other biologic effects of insulin].

    Science.gov (United States)

    Pankov, Y A

    2016-01-01

    Studies on experimental animals with knockout of the insulin receptor gene Insr (in the whole body or in certain tissues) and/or related genes encoding proteins involved in realization of insulin signal transduction in target cells, have made an important contribution to the elucidation of insulin regulation of metabolism, particularly fat metabolism. Since the whole insulin secreted by b-cells, together with the products of gastrointestinal tract digestion of proteins, fats, and carbohydrates reach the liver, the latter is the first organ on which this hormone acts. The liver employs released amino acids for synthesis of proteins, including apoproteins for various lipoproteins. Glucose is used for synthesis of glycogen, fatty acids, and triglycerides, which enter all the organs in very low density lipoproteins (VLDL). The LIRKO mice with knockout of the Insr gene in the liver demonstrated inhibition of synthesis of macromolecular compounds from amino acids, glucose, and fatty acids. Low molecular weight substances demonstrated increased entry to circulation, and together with other disorders induced hyperglycemia. In LIRKO mice blood glucose levels and glucose tolerance demonstrated time-dependent normalization and at later stages the increase in glucose levels was replaced by hypoglycemia. These changes can be well explained if we take into consideration that one of the main functions of insulin consists in stimulation of energy accumulation by means of activation of triglyceride deposition in adipose tissue. FIRKO mice with selective knockout of adipose tissue Insr were characterized by decreased uptake of glucose in adipocytes, and its transformation into lipids. However, the level of body fat in animals remained normal, possibly due to preserved insulin receptor in the liver and insulin-induced activation of triglyceride production which maintained normal levels of body fat stores, the effective functioning of adipose tissue and secretion of leptin by

  15. Development of biological functional material and product from Nelumbo nucifera

    International Nuclear Information System (INIS)

    The solvent extracts of Nelumbo nucifera G. were investigated for the activities of antioxidant, whitening, anti-wrinkle and antimicrobial effects to apply as a functional ingredient for cosmetic products. The electron donating ability of irradiated NN-L extract was above 85% at the concentration of 50ppm. The superoxide dismutase(SOD)-like activity of irradiated NN-L extract was about 76% at 1,000ppm concentration. The xanthine oxidase inhibitory effect of irradiated NN-L extract was about 15% at 1,000ppm. The tyrosinase inhibitory effect of irradiated NN-L extract was about 18% at 1,000ppm. Anti-wrinkle effect, the elastase inhibition activity of irradiated NN-L extract was about 45% at 1,000ppm concentration. All these findings suggested that Nelumbo nucifera G. has a great potential as a cosmeceutical ingredient

  16. The biology and function of exosomes in cancer.

    Science.gov (United States)

    Kalluri, Raghu

    2016-04-01

    Humans circulate quadrillions of exosomes at all times. Exosomes are a class of extracellular vesicles released by all cells, with a size range of 40-150 nm and a lipid bilayer membrane. Exosomes contain DNA, RNA, and proteins. Exosomes likely remove excess and/or unnecessary constituents from the cells, functioning like garbage bags, although their precise physiological role remains unknown. Additionally, exosomes may mediate specific cell-to-cell communication and activate signaling pathways in cells they fuse or interact with. Exosomes are detected in the tumor microenvironment, and emerging evidence suggests that they play a role in facilitating tumorigenesis by regulating angiogenesis, immunity, and metastasis. Circulating exosomes can be used as liquid biopsies and noninvasive biomarkers for early detection, diagnosis, and treatment of cancer patients.

  17. Development of biological functional material and product from Nelumbo nucifera

    Energy Technology Data Exchange (ETDEWEB)

    Jeong, Il Yun; Park, Yong Dae; Jin, Chang Hyun; Choi, Dae Seong

    2008-01-15

    The solvent extracts of Nelumbo nucifera G. were investigated for the activities of antioxidant, whitening, anti-wrinkle and antimicrobial effects to apply as a functional ingredient for cosmetic products. The electron donating ability of irradiated NN-L extract was above 85% at the concentration of 50ppm. The superoxide dismutase(SOD)-like activity of irradiated NN-L extract was about 76% at 1,000ppm concentration. The xanthine oxidase inhibitory effect of irradiated NN-L extract was about 15% at 1,000ppm. The tyrosinase inhibitory effect of irradiated NN-L extract was about 18% at 1,000ppm. Anti-wrinkle effect, the elastase inhibition activity of irradiated NN-L extract was about 45% at 1,000ppm concentration. All these findings suggested that Nelumbo nucifera G. has a great potential as a cosmeceutical ingredient.

  18. The biology and function of exosomes in cancer.

    Science.gov (United States)

    Kalluri, Raghu

    2016-04-01

    Humans circulate quadrillions of exosomes at all times. Exosomes are a class of extracellular vesicles released by all cells, with a size range of 40-150 nm and a lipid bilayer membrane. Exosomes contain DNA, RNA, and proteins. Exosomes likely remove excess and/or unnecessary constituents from the cells, functioning like garbage bags, although their precise physiological role remains unknown. Additionally, exosomes may mediate specific cell-to-cell communication and activate signaling pathways in cells they fuse or interact with. Exosomes are detected in the tumor microenvironment, and emerging evidence suggests that they play a role in facilitating tumorigenesis by regulating angiogenesis, immunity, and metastasis. Circulating exosomes can be used as liquid biopsies and noninvasive biomarkers for early detection, diagnosis, and treatment of cancer patients. PMID:27035812

  19. Biological function of activation-induced cytidine deaminase (AID

    Directory of Open Access Journals (Sweden)

    Ritu Kumar

    2014-10-01

    Full Text Available Activation-induced Cytidine Deaminase (AID is an essential regulator of B cell diversification, but its full range of action has until recently been an enigma. Based on homology, it was originally proposed to be an RNA-editing enzyme, but so far, no RNA substrates are known. Rather, it functions by deaminating cytidine, and in this manner, coupled with base-excision repair or mismatch repair machinery, it is a natural mutator. This allows it to play a central role in adaptive immunity, whereby it initiates the processes of class switch recombination and somatic hypermutation to help generate a diverse and high-affinity repertoire of immunoglobulin isotypes. More recently, it has been appreciated that methylated cytidine, already known as a key epigenetic mark on DNA controlling gene expression, can also be a target for AID modification. Coupled with repair machinery, this can facilitate the active removal of methylated DNA. This activity can impact the process of cellular reprogramming, including transition of a somatic cell to pluripotency, which requires major reshuffling of epigenetic memory. Thus, seemingly disparate roles for AID in controlling immune diversity and epigenetic memory have a common mechanistic basis. However, the very activity that is so useful for B cell diversity and cellular reprogramming is dangerous for the integrity of the genome. Thus, AID expression and activity is tightly regulated, and deregulation is associated with diseases including cancer. Here, we review the range of AID functions with a focus on its mechanisms of action and regulation. Major questions remain to be answered concerning how and when AID is targeted to specific loci and how this impacts development and disease.

  20. GSK-3: functional insights from cell biology and animal models

    Directory of Open Access Journals (Sweden)

    Oksana eKaidanovich-Beilin

    2011-11-01

    Full Text Available Glycogen synthase kinase-3 (GSK-3 is a widely expressed and highly conserved serine/threonine protein kinase encoded in mammals by two genes that generate two related proteins: GSK-3α and GSK-3β. GSK-3 is active in cells under resting conditions and is primarily regulated through inhibition or diversion of its activity. While GSK-3 is one of the few protein kinases that can be inactivated by phosphorylation, the mechanisms of GSK-3 regulation are more varied and not fully understood. Precise control appears to be achieved by a combination of phosphorylation, localization, and sequestration by a number of GSK-3-binding proteins. GSK-3 lies downstream of several major signaling pathways including the phosphatidylinositol 3’ kinase pathway, the Wnt pathway, Hedgehog signaling and Notch. Specific pools of GSK-3, which differ in intracellular localization, binding partner affinity and relative amount are differentially sensitized to several distinct signaling pathways and these sequestration mechanisms contribute to pathway insulation and signal specificity. Dysregulation of signaling pathways involving GSK-3 is associated with the pathogenesis of numerous neurological and psychiatric disorders and there are data suggesting GSK-3 isoform-selective roles in several of these. Here, we review the current knowledge of GSK-3 regulation and targets and discuss the various animal models that have been employed to dissect the functions of GSK-3 in brain development and function through the use of conventional or conditional knock-out mice as well as transgenic mice. These studies have revealed fundamental roles for these protein kinases in memory, behavior and neuronal fate determination and provide insights into possible therapeutic interventions.

  1. Biological function of activation-induced cytidine deaminase (AID).

    Science.gov (United States)

    Kumar, Ritu; DiMenna, Lauren J; Chaudhuri, Jayanta; Evans, Todd

    2014-01-01

    Activation-induced Cytidine Deaminase (AID) is an essential regulator of B cell diversification, but its full range of action has until recently been an enigma. Based on homology, it was originally proposed to be an RNA-editing enzyme, but so far, no RNA substrates are known. Rather, it functions by deaminating cytidine, and in this manner, coupled with base-excision repair or mismatch repair machinery, it is a natural mutator. This allows it to play a central role in adaptive immunity, whereby it initiates the processes of class switch recombination and somatic hypermutation to help generate a diverse and high-affinity repertoire of immunoglobulin isotypes. More recently, it has been appreciated that methylated cytidine, already known as a key epigenetic mark on DNA controlling gene expression, can also be a target for AID modification. Coupled with repair machinery, this can facilitate the active removal of methylated DNA. This activity can impact the process of cellular reprogramming, including transition of a somatic cell to pluripotency, which requires major reshuffling of epigenetic memory. Thus, seemingly disparate roles for AID in controlling immune diversity and epigenetic memory have a common mechanistic basis. However, the very activity that is so useful for B cell diversity and cellular reprogramming is dangerous for the integrity of the genome. Thus, AID expression and activity is tightly regulated, and deregulation is associated with diseases including cancer. Here, we review the range of AID functions with a focus on its mechanisms of action and regulation. Major questions remain to be answered concerning how and when AID is targeted to specific loci and how this impacts development and disease.

  2. Functional group based Ligand binding affinity scoring function at atomic environmental level

    Science.gov (United States)

    Varadwaj, Pritish Kumar; Lahiri, Tapobrata

    2009-01-01

    Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the environmental effect of the atom under consideration. We have developed a novel knowledge-based statistical energy function for protein-ligand complexes which takes atomic environment in to account hence functional group as a singular entity. The proposed knowledge based scoring function is fast, simple to construct, easy to use and moreover it tackle the existing problem of handling molecular orientation in active site pocket. We have designed and used Functional group based Ligand retrieval (FBLR) system which can identify and detect the orientation of functional groups in ligand. This decoy searching was used to build the above KBSF to quantify the activity and affinity of high resolution protein-ligand complexes. We have proposed the probable use of these decoys in molecular build-up as a de-novo drug designing approach. We have also discussed the possible use of the said KSBF in pharmacophore fragment detection and pseudo center based fragment alignment procedure. PMID:19255647

  3. The biology and functional morphology of Macoma biota (Bivalvia: Tellinidae: Macominae

    Directory of Open Access Journals (Sweden)

    Pedro Ribeiro Piffer

    2011-06-01

    Full Text Available Macoma biota Arruda & Domaneschi, 2005, is a recently described species known only from the intertidal zone of Praia da Cidade, Caraguatatuba Bay, in the state of São Paulo, southeastern Brazil. The main purpose of the present paper is to describe the biology of M. biota, beginning with a detailed analysis of its anatomy and functional morphology and how these attributes are correlated with its habitat and life history. The morphology of the organs in the pallial cavity and their sorting devices indicate that this species has efficient mechanisms to process large amounts of particles that enter this cavity via the inhalant current. M. biota can rapidly select the material suitable for ingestion and direct the undesired excess to the rejection mantle tracts. These characteristics along with the siphon's behavior and the digestive tract configuration reveal that this species can be classified primarily as a deposit feeder, like other species of the genus; however, it can also behave as a suspension feeder, depending on the environmental conditions.

  4. Global Environmental Change and Biological Invading%全球环境变化与生物入侵

    Institute of Scientific and Technical Information of China (English)

    王静; 黄正文; 王寻

    2012-01-01

    全球环境变化将对地球生态系统的物种多样性及其分布产生重要而深远的影响:一方面可能使部分地区的生态系统对外来物种的抗性弱化;另一方面将激活外来物种的活性,导致外来生物的快速扩散和大规模入侵,进而排挤和“杀死”当地乡土物种,减少生物多样性,改变原有生态系统的组成、结构和功能.提出了加强对入侵物种的预测、监控,以及立足于生态系统和整个社会来应对生物入侵的策略,以期为预防和控制生物入侵提供参考。%Global environmental change will heavily impact the species diversity of global ecosystem and its distribution. Global environmental change may lead to weakening resistance to adventive species in some parts of the ecosystem. Moreover, it may activate the activity of invasive species and lead to the rapid prolif- eration of alien organisms and large-scale invasion, which can exclude and kill native species, even reduce biological diversity and change the composition, structure and functions of original ecosystem. Strategies were suggested to enhance the prediction and supervision of invasive species and cope with them based on the whole ecosystem and society, which will provide references for prediction and control of biological inva- sion.

  5. The Biology of Behaviour.

    Science.gov (United States)

    Broom, D. M.

    1981-01-01

    Discusses topics to aid in understanding animal behavior, including the value of the biological approach to psychology, functional systems, optimality and fitness, universality of environmental effects on behavior, and evolution of social behavior. (DS)

  6. Department of Energy's Biological and Environmental Research Strategic Data Roadmap for Earth System Science

    Energy Technology Data Exchange (ETDEWEB)

    Williams, Dean N. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Palanisamy, Giri [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Shipman, Galen [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Boden, Thomas A. [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Voyles, Jimmy W. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2014-04-25

    Rapid advances in experimental, sensor, and computational technologies and techniques are driving exponential growth in the volume, acquisition rate, variety, and complexity of scientific data. This wealth of scientifically meaningful data has tremendous potential to lead to scientific discovery. However, to achieve scientific breakthroughs, these data must be exploitable—they must be analyzed effectively and efficiently and the results shared and communicated easily within the wider Department of Energy’s (DOE’s) Biological and Environmental Research (BER) Climate and Environmental Sciences Division (CESD) community. The explosion in data complexity and scale makes these tasks exceedingly difficult to achieve, particularly given that an increasing number of disciplines are working across techniques, integrating simulation and experimental or observational results (see Table 5 in Appendix 2). Consequently, we need new approaches to data management, analysis, and visualization that provide research teams with easy-to-use and scalable end-to-end solutions. These solutions must facilitate (and where feasible, automate and capture) every stage in the data lifecycle (shown in Figure 1), from collection to management, annotation, sharing, discovery, analysis, and visualization. In addition, the core functionalities are the same across climate science communities, but they require customization to adapt to specific needs and fit into research and analysis workflows. To this end, the mission of CESD’s Data and Informatics Program is to integrate all existing and future distributed CESD data holdings into a seamless and unified environment for the acceleration of Earth system science.

  7. The reflection of life functional entailment and imminence in relational biology

    CERN Document Server

    Louie, A H

    2013-01-01

    A. H. Louie’s The Reflection of Life: Functional Entailment and Imminence in Relational Biology is a continuation of the exploratory journey in relational biology which began with his 2009 monograph More Than Life Itself: A Synthetic Continuation in Relational Biology. The theme of his first book was ‘What is life?’; the theme of this sequel is “How do two life forms interact?” Biology is a subject concerned with organization of relations. Relational biology is the approach that advocates ‘function dictates structure”, rather than ‘structure implies function’. It is mathematics decoded into biological realizations. The book demonstrates some of the powers of the approach of relational biology, and illustrates how pertinent problems in biology can be better addressed this way. In the first volume the theory was developed by using partially ordered sets, lattices, simulations, models, Aristotle’s four causes, graphs, categories, simple and complex systems, anticipatory systems, and metabolis...

  8. Functionalized diamond nanopowder for phosphopeptides enrichment from complex biological fluids

    Energy Technology Data Exchange (ETDEWEB)

    Hussain, Dilshad [Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800 (Pakistan); Najam-ul-Haq, Muhammad, E-mail: najamulhaq@bzu.edu.pk [Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800 (Pakistan); Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, A-6020 Innsbruck (Austria); Jabeen, Fahmida; Ashiq, Muhammad N.; Athar, Muhammad [Division of Analytical Chemistry, Institute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800 (Pakistan); Rainer, Matthias; Huck, Christian W.; Bonn, Guenther K. [Institute of Analytical Chemistry and Radiochemistry, Leopold-Franzens University, Innrain 80-82, A-6020 Innsbruck (Austria)

    2013-05-02

    Graphical abstract: -- Highlights: •Derivatization of diamond nanopowder as IMAC and RP. •Characterization with SEM, EDX and FT-IR. •Phosphopeptide enrichment from standard as well as real samples. •Desalting and human serum profiling with reproducible results. •MALDI-MS analysis with database identification. -- Abstract: Diamond is known for its high affinity and biocompatibility towards biomolecules and is used exclusively in separation sciences and life science research. In present study, diamond nanopowder is derivatized as Immobilized Metal Ion Affinity Chromatographic (IMAC) material for the phosphopeptides enrichment and as Reversed Phase (C-18) media for the desalting of complex mixtures and human serum profiling through MALDI-TOF-MS. Functionalized diamond nanopowder is characterized by Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy. Diamond-IMAC is applied to the standard protein (β-casein), spiked human serum, egg yolk and non-fat milk for the phosphopeptides enrichment. Results show the selectivity of synthesized IMAC-diamond immobilized with Fe{sup 3+} and La{sup 3+} ions. To comprehend the elaborated use, diamond-IMAC is also applied to the serum samples from gall bladder carcinoma for the potential biomarkers. Database search is carried out by the Mascot program ( (www.matrixscience.com)) for the assignment of phosphorylation sites. Diamond nanopowder is thus a separation media with multifunctional use and can be applied to cancer protein profiling for the diagnosis and biomarker identification.

  9. Functionalized diamond nanopowder for phosphopeptides enrichment from complex biological fluids.

    Science.gov (United States)

    Hussain, Dilshad; Najam-ul-Haq, Muhammad; Jabeen, Fahmida; Ashiq, Muhammad N; Athar, Muhammad; Rainer, Matthias; Huck, Christian W; Bonn, Guenther K

    2013-05-01

    Diamond is known for its high affinity and biocompatibility towards biomolecules and is used exclusively in separation sciences and life science research. In present study, diamond nanopowder is derivatized as Immobilized Metal Ion Affinity Chromatographic (IMAC) material for the phosphopeptides enrichment and as Reversed Phase (C-18) media for the desalting of complex mixtures and human serum profiling through MALDI-TOF-MS. Functionalized diamond nanopowder is characterized by Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy. Diamond-IMAC is applied to the standard protein (β-casein), spiked human serum, egg yolk and non-fat milk for the phosphopeptides enrichment. Results show the selectivity of synthesized IMAC-diamond immobilized with Fe(3+) and La(3+) ions. To comprehend the elaborated use, diamond-IMAC is also applied to the serum samples from gall bladder carcinoma for the potential biomarkers. Database search is carried out by the Mascot program (www.matrixscience.com) for the assignment of phosphorylation sites. Diamond nanopowder is thus a separation media with multifunctional use and can be applied to cancer protein profiling for the diagnosis and biomarker identification. PMID:23601977

  10. Towards understanding the biological function of hopanoids (Invited)

    Science.gov (United States)

    Doughty, D. M.; Hunter, R.; Summons, R. E.; Newman, D. K.

    2010-12-01

    Rhodopseudomonas palustris TIE-1 expresses bacterial hopanoid lipids that are structurally similar and evolutionarily related to eukaryotic sterols. The genome of R. palustris TIE-1 contains two copies of the hpnN gene (hpnN1 and hpnN2) that are orthologs of genes encoding eukaryotic sterol and lipid transporters. Hopanoid localization to the outer membrane was found to be dependent upon hpnN1. Since the cell cycle of R. palustris TIE-1 is obligately bimodal with each cell division resulting in the generation of one mother and one swarmer cell, evidence was obtained that hopanoids where specifically localized to the outer membrane of mother cells. The sequestration of hopanoids to the mother cells was also disrupted by the deletion of the hpnN1 gene. Mutants lacking the hopanoid transporters were able to grow normally at 30 °C but showed decreased growth at 38 °C. The hopanoid transporter mutant formed cellular filaments when grown at elevated temperature. Because sedimentary steranes and hopanes comprise some of the earliest evidence for the emergence of distinct bacteria and eukaryotic phyla, a better appreciation of the function of hopanoids will improve our ability to interpret the evolution of life on Earth.

  11. The biological effect and medical functions of the Infrared Rays

    Institute of Scientific and Technical Information of China (English)

    PANG Xiao-feng

    2001-01-01

    The quantum vibrational energy-spectra including high excited states of the protein molecules have been calculated by new theory of bio-energy transport along the protein molecules and its dynamic equation, discrete nonlinear Schrodinger equation, appropriate to the protein molecules on the basis of the level of molecular structure. This energy-spectra obtained are basically consistent with the experimental values by infrared absorption and radiated measurement of person's hands and laser-Raman spectrum from metabolically active E. Coli.. From this energy-spectra we know that the infrared lights with (1-3)x1000nm and (5-7)x1000nm wavelength can be absorbed by the protein molecules in the living systems.In accordance with the non-linear theory of the bio-energy transport we know that the energy of the infrared light absorbed by the proteins can result in vibrations of amide-I in amino acids and can facilitate the bio-energy transport along the protein molecular chains from one place to other for the growth of living bodies. This processe is non-thermal. This is just non-thermal effect of the infrared lights. According to the mechanism we explained further the medical functions of the infrared lights absorbed.

  12. Functionalized diamond nanopowder for phosphopeptides enrichment from complex biological fluids

    International Nuclear Information System (INIS)

    Graphical abstract: -- Highlights: •Derivatization of diamond nanopowder as IMAC and RP. •Characterization with SEM, EDX and FT-IR. •Phosphopeptide enrichment from standard as well as real samples. •Desalting and human serum profiling with reproducible results. •MALDI-MS analysis with database identification. -- Abstract: Diamond is known for its high affinity and biocompatibility towards biomolecules and is used exclusively in separation sciences and life science research. In present study, diamond nanopowder is derivatized as Immobilized Metal Ion Affinity Chromatographic (IMAC) material for the phosphopeptides enrichment and as Reversed Phase (C-18) media for the desalting of complex mixtures and human serum profiling through MALDI-TOF-MS. Functionalized diamond nanopowder is characterized by Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and energy dispersive X-ray (EDX) spectroscopy. Diamond-IMAC is applied to the standard protein (β-casein), spiked human serum, egg yolk and non-fat milk for the phosphopeptides enrichment. Results show the selectivity of synthesized IMAC-diamond immobilized with Fe3+ and La3+ ions. To comprehend the elaborated use, diamond-IMAC is also applied to the serum samples from gall bladder carcinoma for the potential biomarkers. Database search is carried out by the Mascot program ( (www.matrixscience.com)) for the assignment of phosphorylation sites. Diamond nanopowder is thus a separation media with multifunctional use and can be applied to cancer protein profiling for the diagnosis and biomarker identification

  13. Biological catalysis of the hydrological cycle: life's thermodynamic function

    Directory of Open Access Journals (Sweden)

    K. Michaelian

    2011-01-01

    Full Text Available Darwinian theory depicts life as being overwhelmingly consumed by a fight for survival in a hostile environment. However, from a thermodynamic perspective, life is a dynamic out of equilibrium process, stabilizing and coevolving in concert with its abiotic environment. The living component of the biosphere on the surface of the Earth of greatest biomass, the plants and cyanobacteria, are involved in the transpiration of a vast amount of water. Transpiration is part of the global water cycle, and it is this cycle that distinguishes Earth from its apparently life barren neighboring planets, Venus and Mars. The dissipation of sunlight into heat by organic molecules in the biosphere and its coupling to the water cycle (as well as other abiotic processes, is by far the greatest entropy producing process occurring on Earth. Life, from this perspective, can be viewed as performing an important thermodynamic function; acting as a dynamic catalyst by aiding irreversible abiotic process such as the water cycle, hurricanes, and ocean and wind currents to produce entropy. The role of animals in this view is that of unwitting but dedicated servants of the plants and cyanobacteria, helping them to grow and to spread into initially inhospitable areas.

  14. Trace Level Arsenic Quantification through Cloud Point Extraction: Application to Biological and Environmental Samples

    Directory of Open Access Journals (Sweden)

    Kempahanumakkagari Suresh Kumar

    2012-01-01

    Full Text Available A sensitive solvent-free extraction protocol for the quantification of arsenic at trace level has been described. It is based on the reaction of arsenic (V with molybdate in acidic medium in presence of antimony (III and ascorbic acid as a reducing agent to form a blue-colored arsenomolybdenum blue complex. The complex has been extracted into surfactant phase using Triton X-114, and its absorbance was measured at 690 nm. The detection limit, working range, and the relative standard deviation were found to be 1 ng mL−1, 10–200 ng mL−1, and 1.2%, respectively. The effect of common ions was studied, and the method has been applied to determine trace levels of As(III and As(V from a variety of samples like environmental, biological, and commercially procured chemicals.

  15. Biological reference materials from the National Institute for Environmental Studies (Japan)

    Energy Technology Data Exchange (ETDEWEB)

    Okamoto, Kensaku

    1988-12-01

    The National Institute for Environmental Studies has recently undertaken the development of two new biological reference materials, Sargasso and Rice Flour-Unpolished, for trace element analysis. The sargasso seaweed (Sargassum felvellum) reference material contains high levels of alkali, alkaline earth elements and As, together with low concentrations of heavy metals. The rice flour-unpolished reference material was prepared from unpolished rice collected from three different locations in Japan. This reference material consists of three samples, each containing different levels (low, medium, high) of Cd. This paper presents the preparation and elemental composition of NIES Sargasso and Rice Flour-Unpolished reference materials, following a brief description of each of the currently available NIES certified reference materials.

  16. Determination of rhenium in biological and environmental samples by radiochemical neutron activation analysis

    International Nuclear Information System (INIS)

    Radiochemical neutron activation procedures using liquid-liquid extraction with tetraphenylarsonium chloride in chloroform from 1 M HCl and solid extraction with ALIQUAT 336 incorporated in a polyacrylonitrile binding matrix from 0.1 M HCl were developed for accurate determination of rhenium in biological and environmental samples at the sub-ng.g-1 level. Concentrations of Re in the range of 0.1 to 2.4 ng.g-1 were determined in several botanical reference materials (RM), while in a RM of road dust a value of approx. 10 ng.g-1 was found. Significantly elevated values of Re, up to 90 ng.g-1, were found in seaweed (brown algae). Results for Re in the brown algae Fucus vesiculosus in which elevated 99Tc values had previously been determined suggest possible competition between Re and Tc in the accumulation process. (author)

  17. Genomic Insights into the Biomineralization and Environmental Function of Magnetotactic Bacteria

    Science.gov (United States)

    Lin, W.; Pan, Y.

    2015-12-01

    Microorganisms have populated the Earth for billions of years and their activities are important biologic forces shaping our planetary environments. Microbial biomineralization that selectively take up environmental elements (e.g., C, S, P, Fe) and synthesize minerals either intracellularly or extracellularly is of great interest. One of the most interesting examples of these types of organisms are magnetotactic bacteria (MTB), a polyphyletic group of prokaryotes that uptake iron from aquatic habitats and biomineralize intracellular nano-sized iron minerals of magnetite (Fe3O4) and/or greigite (Fe3S4), known as magnetosomes, and orientate and swim along the Earth's magnetic field. However, our knowledge on the biomineralization mechanisms of MTB and their environmental function remains very limited because the genomic information of most MTB is still not fully understood. By using metagenomic approaches, we have acquired genomic sequences of environmental MTB communities and discovered several conserved genomic fragments containing gene operons for magnetite or greigite biomineralization from Proteobacteria and Nitrospirae MTB. The comparison of these gene clusters has provided valuable insights into the origin and evolution of magnetosome biomineralization. We further obtained several draft genomes of uncultivated MTB belonging to the phylum Nitrospirae, which reveals a metabolic flexibility of this poorly understood magnetotactic group and indicates their considerable roles in the biogeochemical cycles of iron and sulfur.

  18. Determination of gadolinium-based MRI contrast agents in biological and environmental samples: A review

    Energy Technology Data Exchange (ETDEWEB)

    Telgmann, Lena [University of Münster, Institute of Inorganic and Analytical Chemistry, Münster (Germany); Sperling, Michael [University of Münster, Institute of Inorganic and Analytical Chemistry, Münster (Germany); European Virtual Institute for Speciation Analysis (EVISA), Münster (Germany); Karst, Uwe, E-mail: uk@uni-muenster.de [University of Münster, Institute of Inorganic and Analytical Chemistry, Münster (Germany)

    2013-02-18

    Highlights: ► All major methods for the analysis of Gd-based MRI contrast agents are discussed. ► Biological and environmental samples are covered. ► Pharmacokinetics and species transformation can be investigated. ► The figures of merit as limit of detection and analysis time are described. -- Abstract: The development of analytical methods and strategies to determine gadolinium and its complexes in biological and environmental matrices is evaluated in this review. Gadolinium (Gd) chelates are employed as contrast agents for magnetic resonance imaging (MRI) since the 1980s. In general they were considered as safe and well-tolerated, when in 2006, the disease nephrogenic systemic fibrosis (NSF) was connected to the administration of MRI contrast agents based on Gd. Pathogenesis and etiology of NSF are yet unclear and called for the development of several analytical methods to obtain elucidation in this field. Determination of Gd complex stability in vitro and in vivo, as well as the quantification of Gd in body fluids like blood and urine was carried out. Separation of the Gd chelates was achieved with high performance liquid chromatography (HPLC) and capillary electrophoresis (CE). For detection, various methods were employed, including UV–vis absorbance and fluorescence spectroscopy, electrospray ionization mass spectrometry (ESI-MS) and inductively coupled plasma mass spectrometry (ICP-MS). A second challenge for analysts was the discovery of high concentrations of anthropogenic Gd in surface waters draining populated areas. The source could soon be determined to be the increasing administration of Gd complexes during MRI examinations. Identification and quantification of the contrast agents was carried out in various surface and groundwater samples to determine the behavior and fate of the Gd chelates in the environment. The improvement of limits of detection (LOD) and limits of quantification (LOQ) was and still is the goal of past and ongoing

  19. Magnetically responsive polycaprolactone nanoparticles for progesterone screening in biological and environmental samples using gas chromatography.

    Science.gov (United States)

    Es'haghi, Zarrin; Nezhadali, Azizollah; Khatibi, Aram-Dokht

    2016-08-01

    A new Fe3O4/poly(є-caprolactone) (PCL) magnetite nanocomposite was fabricated and used as a sorbent for magnetically mediated PCL microspheres solid-phase extraction (MM-PCL-SPE) followed by gas chromatography-flame ionization detection (GC-FID) for monitoring of progesterone (PGN) hormone in biological and environmental matrices, namely blood serum, tap water, urine, and hospital wastewater. The nanomagnetite core of the sorbent was synthesized by a co-precipitation method. Magnetic nanoparticles (MNPs) were then microencapsulated with PCL microspheres using emulsion polymerization. The nanocomposite was characterized by scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR). The magnetite sorbent can be effectively dispersed in aqueous solution and attracted to an external magnetic field. The MM-PCL-SPE process for PGN assay involved (a) dispersion of the sorbent in the donor phase aqueous solution with sonication, (b) exposure to a magnetic field to collect sorbent that had adsorbed the analyte, and (c) solvent desorption of extracted PGN for GC-FID analysis. The work demonstrates the usefulness of MM-PCL-SPE in the rapid and sensitive monitoring of trace amounts of PGN in real samples. The limit of detection (LOD) and limit of quantification (LOQ) were 1.00 and 3.30 ng/mL, respectively. The relative recoveries in real samples were adequate. Linearity was observed over a wide range of 2.2-10,000.0 ng/mL in aqueous media and urine and 0.01-70.0 μg/mL in blood serum. Graphical Abstract In this research new Fe3O4/poly(є-caprolactone) (PCL) magnetite microspheres were developed as an efficient sorbent for solid-phase extraction of progesterone hormone in biological and environmental matrices. PMID:27299775

  20. Horns Rev offshore wind farm. Environmental impact assessment of sea bottom and marine biology

    Energy Technology Data Exchange (ETDEWEB)

    Leonhard, S.B.

    2000-03-15

    An Environmental Impact Assessment (EIA) of a planned 150 MW offshore wind farm at Horns Rev has been carried out for the marine biology and sea bottom in the area, and includes vegetation and benthic fauna. The study forms part of a total EIA of the planned offshore wind farm. This EIA study has been drawn up in accordance with the guidelines laid down by the Ministry of Environment and Energy in the publication, 'Guidelines for preparation of EIAstudies for offshore wind farms. Horns Rev is situated off Blaevands Huk, which is Denmark's most westerly point. It is a shallow reef with water depths between 2 and 9 metres and is primarily composed of sand, gravel and pebbles. The area designated for the wind farm lies directly south of Horns Rev and is dominated by sand with a median particle size of 0.3 mm. Along the edges, towards areas of greater depth, the particle size increases. There are areas of fine sand in the deepest area, and in isolated pockets within the proposed wind farm site. The sediment is characterised by a very low (<1%) organic matter content. On the basis of the expected impact from the establishment of the wind farm, it is not deemed necessary to carry out special programmes during the construction phase for monitoring of the environmental-biological conditions. A monitoring and control programme is recommended during the production phase in order to follow the copper concentration in bivalves, or alternatively to initiate recovery or elimination of the copper-laden waste. A control programme is recommended during the production phase in order to follow the establishment and succession of the fouling community on the wind turbine foundations and scour-protecting revetments. (BA)

  1. Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

    Science.gov (United States)

    Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

    2016-10-20

    The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

  2. Identification of biological and environmental risk factors for language delay: The Let's Talk STEPS study.

    Science.gov (United States)

    Korpilahti, Pirjo; Kaljonen, Anne; Jansson-Verkasalo, Eira

    2016-02-01

    The aim of this population-based study was to identify demographic factors for language delays at an early age. The risk analysis covered 11 biological and 8 environmental factors. The mothers' concerns regarding language development were also examined. A total of 226 children from a Finnish cohort study were invited to participate in language assessments at 36 months. The test results for word finding and language comprehension were compared with parental questionnaires about children's vocabulary at 13 and 24 months. Regression analysis revealed that the father's social class (t=-2.79, p=0.006) and working full time (t=-2.86, p=0.005) significantly predicted children's language delay. In addition, language comprehension was significantly predicted by the mother's social class (t=-2.06, p=0.041) and by gender, with an advantage to girls (t=-2.71, p=0.008). Vocabulary at 24 months was a powerful predictor for lexical development (t=4.58, pparents needed special education during school years. At the population-level, gender was the most powerful biological factor in predicting language delays. Similarly, both parents' social status had predictive value for the child's language development. In addition, it was found that the mother's concern about her child's slow language acquisition should be taken into account when making decisions regarding special support. PMID:26700576

  3. Engineering scalable biological systems

    OpenAIRE

    Lu, Timothy K.

    2010-01-01

    Synthetic biology is focused on engineering biological organisms to study natural systems and to provide new solutions for pressing medical, industrial, and environmental problems. At the core of engineered organisms are synthetic biological circuits that execute the tasks of sensing inputs, processing logic, and performing output functions. In the last decade, significant progress has been made in developing basic designs for a wide range of biological circuits in bacteria, yeast, and mammal...

  4. Effect of environmental exposure to mercury on the functioning of the human body

    Directory of Open Access Journals (Sweden)

    Maciej Cyran

    2013-09-01

    Full Text Available Mercury is classified as a heavy metal and thus is commonly referred to as a death metal due to its high toxicity. In the environment it occurs in metallic form or in combination with other compounds. Amidst the sources of exposure to mercury, the most important environmental sources are dental amalgam and mercury vapor from the production of chlorine which is the most important source of occupational exposure. Mercury is easily soluble in fats, so it penetrates through biological membranes. Both - acute and chronic mercury poisoning causes characteristic clinical symptoms. There are several connections between exposure to this metal and toxic effects on the nervous system, cardiovascular system, endocrine system and kidneys. Thus mercury damages the structure of many organs and impairs their function

  5. Applications of High Resolution Laser Induced Breakdown Spectroscopy for Environmental and Biological Samples

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Madhavi Z [ORNL; Labbe, Nicole [ORNL; Wagner, Rebekah J. [Pennsylvania State University, University Park, PA

    2013-01-01

    This chapter details the application of LIBS in a number of environmental areas of research such as carbon sequestration and climate change. LIBS has also been shown to be useful in other high resolution environmental applications for example, elemental mapping and detection of metals in plant materials. LIBS has also been used in phytoremediation applications. Other biological research involves a detailed understanding of wood chemistry response to precipitation variations and also to forest fires. A cross-section of Mountain pine (pinceae Pinus pungen Lamb.) was scanned using a translational stage to determine the differences in the chemical features both before and after a fire event. Consequently, by monitoring the elemental composition pattern of a tree and by looking for abrupt changes, one can reconstruct the disturbance history of a tree and a forest. Lastly we have shown that multivariate analysis of the LIBS data is necessary to standardize the analysis and correlate to other standard laboratory techniques. LIBS along with multivariate statistical analysis makes it a very powerful technology that can be transferred from laboratory to field applications with ease.

  6. Microwave-accelerated bioassay technique for rapid and quantitative detection of biological and environmental samples.

    Science.gov (United States)

    Mohammed, Muzaffer; Syed, Maleeha F; Aslan, Kadir

    2016-01-15

    Quantitative detection of molecules of interest from biological and environmental samples in a rapid manner, particularly with a relevant concentration range, is imperative to the timely assessment of human diseases and environmental issues. In this work, we employed the microwave-accelerated bioassay (MAB) technique, which is based on the combined use of circular bioassay platforms and microwave heating, for rapid and quantitative detection of Glial Fibrillary Acidic Protein (GFAP) and Shiga like toxin (STX 1). The proof-of-principle use of the MAB technique with the circular bioassay platforms for the rapid detection of GFAP in buffer based on colorimetric and fluorescence readouts was demonstrated with a 900W kitchen microwave. We also employed the MAB technique with a new microwave system (called the iCrystal system) for the detection of GFAP from mice with brain injuries and STX 1 from a city water stream. Control bioassays included the commercially available gold standard bioassay kits run at room temperature. Our results show that the lower limit of detection (LLOD) of the colorimetric and fluorescence based bioassays for GFAP was decreased by ~1000 times using the MAB technique and our circular bioassay platforms as compared to the commercially available bioassay kits. The overall bioassay time for GFAP and STX 1 was reduced from 4h using commercially available bioassay kits to 10min using the MAB technique.

  7. Single-stranded DNA phages: from early molecular biology tools to recent revolutions in environmental microbiology.

    Science.gov (United States)

    Székely, Anna J; Breitbart, Mya

    2016-03-01

    Single-stranded DNA (ssDNA) phages are profoundly different from tailed phages in many aspects including the nature and size of their genome, virion size and morphology, mutation rate, involvement in horizontal gene transfer, infection dynamics and cell lysis mechanisms. Despite the importance of ssDNA phages as molecular biology tools and model systems, the environmental distribution and ecological roles of these phages have been largely unexplored. Viral metagenomics and other culture-independent viral diversity studies have recently challenged the perspective of tailed, double-stranded DNA (dsDNA) phages, dominance by demonstrating the prevalence of ssDNA phages in diverse habitats. However, the differences between ssDNA and dsDNA phages also substantially limit the efficacy of simultaneously assessing the abundance and diversity of these two phage groups. Here we provide an overview of the major differences between ssDNA and tailed dsDNA phages that may influence their effects on bacterial communities. Furthermore, through the analysis of 181 published metaviromes we demonstrate the environmental distribution of ssDNA phages and present an analysis of the methodological biases that distort their study through metagenomics. PMID:26850442

  8. Esthetic-functional recovery of permanent posterior tooth using autogenous biological restoration

    Directory of Open Access Journals (Sweden)

    A M Botelho

    2012-01-01

    Full Text Available Occlusal morphology and difficult access for cleaning permanent molars result in the buildup of bacterial plaque and the development of caries. One method known as biological restoration was carried out. This technique known as biological restoration, has as main restorative material a fragment obtained from a duly donated extracted human tooth. This case report describes the restoration of an extensively decayed molar through the bonding of a fragment obtained from a third molar extracted from the patient himself. Biological restoration is a low-cost option that offers satisfactory aesthetic, morphological and functional results.The morphological/functional reestablishment of posterior teeth can be obtained through biological restoration, which allows the recovery of properties inherent to the dental structure, offers satisfactory aesthetic results and low cost.

  9. N-acylation of phosphatidylethanolamine and its biological functions in mammals

    DEFF Research Database (Denmark)

    Wellner, Niels; Diep, Thi Ai; Janfelt, Christian;

    2013-01-01

    N-acylphosphatidylethanolamine (NAPE) and N-acylplasmenylethanolamine (pNAPE) are widely found phospholipids, and they are precursors for N-acylethanolamines, a group of compounds that has a variety of biological effects and encompasses the endocannabinoid anandamide. NAPE and pNAPE are synthesiz...... reviews the metabolism, occurrence and assay of NAPE and pNAPE, and discusses the putative biological functions in mammals of these phospholipids. This article is part of a Special Issue entitled Phospholipids and Phospholipid Metabolism....

  10. Social inclusion enhances biological motion processing: A functional near-infrared spectroscopy study

    OpenAIRE

    Bolling, Danielle Z.; Pelphrey, Kevin A.; Kaiser, Martha D.

    2012-01-01

    Humans are especially tuned to the movements of other people. Neural correlates of this social attunement have been proposed to lie in and around the right posterior superior temporal sulcus (STS) region, which robustly responds to biological motion in contrast to a variety of non-biological motions. This response persists even when no form information is provided, as in point-light displays (PLDs). The aim of the current study was to assess the ability of functional near-infrared spectroscop...

  11. Geographic Information Systems in function of environmental protection

    International Nuclear Information System (INIS)

    Geographical information systems as a methodology is a relatively new technology in scientific research and finding practical solutions for geographical problems. One of those problems is the complex over categorical set [1] known as environment. It is a very actual and complex problematic, hard for organizing and optimization when it has to set about the needs of humanity.Therefore, this article deals with the application of geographic information systems as one of the latest scientific techniques and technologies through which one can analyze and define the most optimal solutions in terms of environmental protection and sustainable development. The aim is to highlight the quantitative and qualitative aspects of GIS technology in function of the environment on the one hand, and through concrete examples to point out to the power of these technologies in the process of finding optimal solutions. It is briefly pointed out to some general criteria that are inevitable in the process of creating databases in GIS necessary for adequate and suitable GIS analyses.(Author)

  12. Stochastic analysis of response functions in environmental modeling

    Energy Technology Data Exchange (ETDEWEB)

    Tumeo, M.A.

    1988-01-01

    Development of a new mathematical technique to include stochasticity in environmental models used of resource management and public health risk analysis is reported. The technique is based on the expansion of basic governing equations to include stochastic terms. The stochastic terms are then separated from the non-fluctuating terms, and the resulting set of equations solved simultaneously. The solutions of this set of equations are used to calculate the moments of the output variables. In addition, the moments are used in conjunction with the Fokker-Planck Equation to produce an analytical solution for the probability density functions of the dependent variables. The technique is applied in two examples. The first example is an application to the Streeter-Phelps BOD-OD Equations. Results of the analysis are compared to field data as well as to results of a Monte Carlo model and to moments derived using a Stochastic Differential Equations approach. The second application involves analysis of health risks associated with waterborne diseases. Results are compared to the results of a Monte Carlo simulation of a similar system of equations.

  13. Development of PVDF Membrane Nanocomposites via Various Functionalization Approaches for Environmental Applications

    Directory of Open Access Journals (Sweden)

    Douglas M. Davenport

    2016-01-01

    Full Text Available Membranes are finding wide applications in various fields spanning biological, water, and energy areas. Synthesis of membranes to provide tunable flux, metal sorption, and catalysis has been done through pore functionalization of microfiltration (MF type membranes with responsive behavior. This methodology provides an opportunity to improve synthetic membrane performance via polymer fabrication and surface modification. By optimizing the polymer coagulation conditions in phase inversion fabrication, spongy polyvinylidene fluoride (PVDF membranes with high porosity and large internal pore volume were created in lab and full scale. This robust membrane shows a promising mechanical strength as well as high capacity for loading of adsorptive and catalytic materials. By applying surface modification techniques, synthetic membranes with different functionality (carboxyl, amine, and nanoparticle-based were obtained. These functionalities provide an opportunity to fine-tune the membrane surface properties such as charge and reactivity. The incorporation of stimuli-responsive acrylic polymers (polyacrylic acid or sodium polyacrylate in membrane pores also results in tunable pore size and ion-exchange capacity. This provides the added benefits of adjustable membrane permeability and metal capture efficiency. The equilibrium and dynamic binding capacity of these functionalized spongy membranes were studied via calcium ion-exchange. Iron/palladium catalytic nanoparticles were immobilized in the polymer matrix in order to perform the challenging degradation of the environmental pollutant trichloroethylene (TCE.

  14. Diurnal rhythmicity in biological processes involved in bioavailability of functional food factors

    OpenAIRE

    Tsurusaki, Takashi; Sakakibara, Hiroyuki; Aoshima, Yoshiki; Yamazaki, Shunsuke; Sakono, Masanobu; Shimoi, Kayoko

    2013-01-01

    In the past few decades, many types of functional factors have been identified in dietary foods; for example, flavonoids are major groups widely distributed in the plant kingdom. However, the absorption rates of the functional food factors are usually low, and many of these are difficult to be absorbed in the intact forms because of metabolization by biological processes during absorption. To gain adequate beneficial effects, it is therefore mandatory to know whether functional food factors a...

  15. Exergames: neuroplastic hypothesis about cognitive improvement and biological effects on physical function of institutionalized older persons

    OpenAIRE

    Renato Sobral Monteiro; César Augusto Otero Vaghetti; Osvaldo José M. Nascimento; Jerson Laks; Andrea Camaz Deslandes

    2016-01-01

    Exergames can be considered a dual task because the games are performed by a man-videogame interface, requiring cognitive and motor functions simultaneously. Although the literature has shown improvements of cognitive and physical functions due to exergames, the intrinsic mechanisms involved in these functional changes have still not been elucidated. The aims of the present study were (1) to demonstrate the known biological mechanisms of physical exercise regarding muscle adaptation and estab...

  16. Application of femtosecond-pulsed lasers for direct optical manipulation of biological functions

    Energy Technology Data Exchange (ETDEWEB)

    Yoon, Jonghee; Park, Junseong; Jong Choi, Won [Department of Bio and Brain Engineering, KAIST, Daejeon (Korea, Republic of); Choi, Myunghwan [Graduate School of Nanoscience and Technology, KAIST, Daejeon (Korea, Republic of); Harvard Medical School and Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA (United States); Choi, Chulhee [Department of Bio and Brain Engineering, KAIST, Daejeon (Korea, Republic of); KAIST Institute for the BioCentury, KAIST, Daejeon (Korea, Republic of)

    2013-03-15

    Absorption of photon energy by cells or tissue can evoke photothermal, photomechanical, and photochemical effects, depending on the density of the deposited energy. Photochemical effects require a low energy density and can be used for reversible modulation of biological functions. Ultrashort-pulsed lasers have a high intensity due to the short pulse duration, despite its low average energy. Through nonlinear absorption, these lasers can deliver very high peak energy into the submicrometer focus area without causing collateral damage. Absorbed energy delivered by ultrashort-pulsed laser irradiation induces free electrons, which can be readily converted to reactive oxygen species (ROS) and related free radicals in the localized region. Free radicals are best known to induce irreversible biological effects via oxidative modification; however, they have also been proposed to modulate biological functions by releasing calcium ions from intracellular organelles. Calcium can evoke variable biological effects in both excitable and nonexcitable cell types. Controlled stimulation by ultrashort laser pulses generate intracellular calcium waves that can modulate many biological functions, such as cardiomyocyte beat rate, muscle contractility, and blood-brain barrier (BBB) permeability. This article presents optical methods that are useful therapeutic and research tools in the biomedical field and discuss the possible mechanisms responsible for biological modulation by ultrashort-pulsed lasers, especially femtosecond-pulsed lasers. (copyright 2012 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  17. Molecular Biology at the Quantum Level: Can Modern Density Functional Theory Forge the Path?

    CERN Document Server

    Kolb, Brian; 10.1142/S1793984412300063

    2012-01-01

    Recent years have seen vast improvements in the ability of rigorous quantum-mechanical methods to treat systems of interest to molecular biology. In this review article, we survey common computational methods used to study such large, weakly bound systems, starting from classical simulations and reaching to quantum chemistry and density functional theory. We sketch their underlying frameworks and investigate their strengths and weaknesses when applied to potentially large biomolecules. In particular, density functional theory---a framework that can treat thousands of atoms on firm theoretical ground---can now accurately describe systems dominated by weak van der Waals interactions. This newfound ability has rekindled interest in using this tried-and-true approach to investigate biological systems of real importance. In this review, we focus on some new methods within density functional theory that allow for accurate inclusion of the weak interactions that dominate binding in biological macromolecules. Recent ...

  18. Priority of TCM in Regulating Gene Function as a Whole Through Development of Modern Biology

    Institute of Scientific and Technical Information of China (English)

    Hu zuo-wei; zhou yan-ping; Shen zi-yin

    2004-01-01

    Molecular Biology based on the DNA Double-helix structure has made great progress in 20 century.After Human Genome Project (HGP) completed, Molecular Biology is faced upon more and more challenges, andtake changes from protion concept to integration concept, from linear thinking to complicated thinking. so post-genomics, including functional genomics, proteomics, is gradually established. Among them, System Biology is themost prominent. It is becoming to tend to integration, and infiltrate to each other for the two thinking of genomeand TCM in studying life science, which reflect the inevitablility and importance of integration of TCM and West-ern Medicine. The priority of TCM in treatment as a whole, and regulating functional gene and functional networkmay take greater achievement in post - genomic time.

  19. Supercritical Fluid Extraction and Ultra Performance Liquid Chromatography of Respiratory Quinones for Microbial Community Analysis in Environmental and Biological Samples

    OpenAIRE

    Koichi Fujie; Hiroyuki Daimon; Yoichi Atsuta; Muhammad Hanif

    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 analysi...

  20. Biologic

    CERN Document Server

    Kauffman, L H

    2002-01-01

    In this paper we explore the boundary between biology and the study of formal systems (logic). In the end, we arrive at a summary formalism, a chapter in "boundary mathematics" where there are not only containers but also extainers ><, entities open to interaction and distinguishing the space that they are not. The boundary algebra of containers and extainers is to biologic what boolean algebra is to classical logic. We show how this formalism encompasses significant parts of the logic of DNA replication, the Dirac formalism for quantum mechanics, formalisms for protein folding and the basic structure of the Temperley Lieb algebra at the foundations of topological invariants of knots and links.

  1. The Function of Remote Sensing in Support of Environmental Policy

    OpenAIRE

    Maarten Smies; Davaa Narantuya; Jelle Ferwerda; Yoshio Inoue; Alfred de Gier; Yola Georgiadou; Norman Kerle; Jan de Leeuw

    2010-01-01

    Limited awareness of environmental remote sensing’s potential ability to support environmental policy development constrains the technology’s utilization. This paper reviews the potential of earth observation from the perspective of environmental policy. A literature review of “remote sensing and policy” revealed that while the number of publications in this field increased almost twice as rapidly as that of remote sensing literature as a whole (15.3 versus 8.8% yr−1), there is apparently lit...

  2. INVESTIGATION OF THE BIOLOGY TEACHER CANDIDATES' ENVIRONMENTAL LITERACY IN TERMS OF DIFFERENT VARIABLES

    OpenAIRE

    GÜRBÜZ, HASAN; KIŞOĞLU, Mustafa; ALAŞ, Ali; SÜLÜN, Ali

    2011-01-01

    Problem and Purpose: One of the problems that waits to be solved in the world is environmental problems whose effect is increasingly felt. The most important reason for environmental problems is the lack of environmental consciousness in socıety.. Constructing the environmental consciousness among the people is possible through an effective environmental education. The first aim of the environmental education is to make people environmentally literate. At this point, teachers who instruct env...

  3. The Halogenated Metabolism of Brown Algae (Phaeophyta, Its Biological Importance and Its Environmental Significance

    Directory of Open Access Journals (Sweden)

    Stéphane La Barre

    2010-03-01

    Full Text Available Brown algae represent a major component of littoral and sublittoral zones in temperate and subtropical ecosystems. An essential adaptive feature of this independent eukaryotic lineage is the ability to couple oxidative reactions resulting from exposure to sunlight and air with the halogenations of various substrates, thereby addressing various biotic and abiotic stresses i.e., defense against predators, tissue repair, holdfast adhesion, and protection against reactive species generated by oxidative processes. Whereas marine organisms mainly make use of bromine to increase the biological activity of secondary metabolites, some orders of brown algae such as Laminariales have also developed a striking capability to accumulate and to use iodine in physiological adaptations to stress. We review selected aspects of the halogenated metabolism of macrophytic brown algae in the light of the most recent results, which point toward novel functions for iodide accumulation in kelps and the importance of bromination in cell wall modifications and adhesion properties of brown algal propagules. The importance of halogen speciation processes ranges from microbiology to biogeochemistry, through enzymology, cellular biology and ecotoxicology.

  4. Progress in Computational Physics (PiCP) Vol 2 Coupled Fluid Flow in Energy, Biology and Environmental Research

    CERN Document Server

    Ehrhardt, Matthias

    2012-01-01

    This second volume contains both, the mathematical analysis of the coupling between fluid flow and porous media flow and state-of-the art numerical techniques, like tailor-made finite element and finite volume methods. Readers will come across articles devoted to concrete applications of these models in the field of energy, biology and environmental research.

  5. Motion as a source of environmental information: a fresh view on biological motion computation by insect brains.

    Science.gov (United States)

    Egelhaaf, Martin; Kern, Roland; Lindemann, Jens Peter

    2014-01-01

    Despite their miniature brains insects, such as flies, bees and wasps, are able to navigate by highly erobatic flight maneuvers in cluttered environments. They rely on spatial information that is contained in the retinal motion patterns induced on the eyes while moving around ("optic flow") to accomplish their extraordinary performance. Thereby, they employ an active flight and gaze strategy that separates rapid saccade-like turns from translatory flight phases where the gaze direction is kept largely constant. This behavioral strategy facilitates the processing of environmental information, because information about the distance of the animal to objects in the environment is only contained in the optic flow generated by translatory motion. However, motion detectors as are widespread in biological systems do not represent veridically the velocity of the optic flow vectors, but also reflect textural information about the environment. This characteristic has often been regarded as a limitation of a biological motion detection mechanism. In contrast, we conclude from analyses challenging insect movement detectors with image flow as generated during translatory locomotion through cluttered natural environments that this mechanism represents the contours of nearby objects. Contrast borders are a main carrier of functionally relevant object information in artificial and natural sceneries. The motion detection system thus segregates in a computationally parsimonious way the environment into behaviorally relevant nearby objects and-in many behavioral contexts-less relevant distant structures. Hence, by making use of an active flight and gaze strategy, insects are capable of performing extraordinarily well even with a computationally simple motion detection mechanism. PMID:25389392

  6. Exergames: neuroplastic hypothesis about cognitive improvement and biological effects on physical function of institutionalized older persons

    Science.gov (United States)

    Monteiro-Junior, Renato Sobral; Vaghetti, César Augusto Otero; Nascimento, Osvaldo José M.; Laks, Jerson; Deslandes, Andrea Camaz

    2016-01-01

    Exergames can be considered a dual task because the games are performed by a man-videogame interface, requiring cognitive and motor functions simultaneously. Although the literature has shown improvements of cognitive and physical functions due to exergames, the intrinsic mechanisms involved in these functional changes have still not been elucidated. The aims of the present study were (1) to demonstrate the known biological mechanisms of physical exercise regarding muscle adaptation and establish a relationship with exergames; and (2) to present a neurobiological hypothesis about the neuroplastic effects of exergames on the cognitive function of institutionalized older persons. These hypotheses are discussed. PMID:27073355

  7. Exergames: neuroplastic hypothesis about cognitive improvement and biological effects on physical function of institutionalized older persons.

    Science.gov (United States)

    Monteiro-Junior, Renato Sobral; Vaghetti, César Augusto Otero; Nascimento, Osvaldo José M; Laks, Jerson; Deslandes, Andrea Camaz

    2016-02-01

    Exergames can be considered a dual task because the games are performed by a man-videogame interface, requiring cognitive and motor functions simultaneously. Although the literature has shown improvements of cognitive and physical functions due to exergames, the intrinsic mechanisms involved in these functional changes have still not been elucidated. The aims of the present study were (1) to demonstrate the known biological mechanisms of physical exercise regarding muscle adaptation and establish a relationship with exergames; and (2) to present a neurobiological hypothesis about the neuroplastic effects of exergames on the cognitive function of institutionalized older persons. These hypotheses are discussed. PMID:27073355

  8. [Distribution and environmental function of glomalin-related soil protein: A review].

    Science.gov (United States)

    Wang, Jian; Zhou, Zi-yan; Ling, Wan-ting

    2016-02-01

    Glomalin-related soil protein (GRSP), a glycoprotein secreted by arbuscular mycorrhizal fungi (AMF), is abundant in soil. GRSP can be fractionated into total glomalin-related soil protein (TG), easily extracted glomalin-related soil protein (EEG), immunoreactive total glomalin (IRTG) and immunoreactive easily extracted glomalin (IREEG). The content of GRSP in soil differed with different soil use type, fertilization condition, AMF and host plant species, and environmental conditions. GRSP significantly positively correlates to the aggregate water stability. GRSP may reduce the release of CO2 in agro-ecosystem, benefit the soil carbon fixation, and reduce the bioavailability and plant toxicity of heavy metals in soil. The extraction and characterization of GRSP are of great importance to understanding the basic behaviors of GRSP in soil environments. Further studies are needed to clarify the molecular biology function of GRSP in agro-ecosystem based on the knowledge of proteins and related genes, and impacts of GRSP on the environmental behavior of organic pollutants in soil. PMID:27396140

  9. [Distribution and environmental function of glomalin-related soil protein: A review].

    Science.gov (United States)

    Wang, Jian; Zhou, Zi-yan; Ling, Wan-ting

    2016-02-01

    Glomalin-related soil protein (GRSP), a glycoprotein secreted by arbuscular mycorrhizal fungi (AMF), is abundant in soil. GRSP can be fractionated into total glomalin-related soil protein (TG), easily extracted glomalin-related soil protein (EEG), immunoreactive total glomalin (IRTG) and immunoreactive easily extracted glomalin (IREEG). The content of GRSP in soil differed with different soil use type, fertilization condition, AMF and host plant species, and environmental conditions. GRSP significantly positively correlates to the aggregate water stability. GRSP may reduce the release of CO2 in agro-ecosystem, benefit the soil carbon fixation, and reduce the bioavailability and plant toxicity of heavy metals in soil. The extraction and characterization of GRSP are of great importance to understanding the basic behaviors of GRSP in soil environments. Further studies are needed to clarify the molecular biology function of GRSP in agro-ecosystem based on the knowledge of proteins and related genes, and impacts of GRSP on the environmental behavior of organic pollutants in soil.

  10. Women are underrepresented on the editorial boards of journals in environmental biology and natural resource management

    Directory of Open Access Journals (Sweden)

    Alyssa H. Cho

    2014-08-01

    Full Text Available Despite women earning similar numbers of graduate degrees as men in STEM disciplines, they are underrepresented in upper level positions in both academia and industry. Editorial board memberships are an important example of such positions; membership is both a professional honor in recognition of achievement and an opportunity for professional advancement. We surveyed 10 highly regarded journals in environmental biology, natural resource management, and plant sciences to quantify the number of women on their editorial boards and in positions of editorial leadership (i.e., Associate Editors and Editors-in-Chief from 1985 to 2013. We found that during this time period only 16% of subject editors were women, with more pronounced disparities in positions of editorial leadership. Although the trend was towards improvement over time, there was surprising variation between journals, including those with similar disciplinary foci. While demographic changes in academia may reduce these disparities over time, we argue journals should proactively strive for gender parity on their editorial boards. This will both increase the number of women afforded the opportunities and benefits that accompany board membership and increase the number of role models and potential mentors for early-career scientists and students.

  11. Women are underrepresented on the editorial boards of journals in environmental biology and natural resource management.

    Science.gov (United States)

    Cho, Alyssa H; Johnson, Shelly A; Schuman, Carrie E; Adler, Jennifer M; Gonzalez, Oscar; Graves, Sarah J; Huebner, Jana R; Marchant, D Blaine; Rifai, Sami W; Skinner, Irina; Bruna, Emilio M

    2014-01-01

    Despite women earning similar numbers of graduate degrees as men in STEM disciplines, they are underrepresented in upper level positions in both academia and industry. Editorial board memberships are an important example of such positions; membership is both a professional honor in recognition of achievement and an opportunity for professional advancement. We surveyed 10 highly regarded journals in environmental biology, natural resource management, and plant sciences to quantify the number of women on their editorial boards and in positions of editorial leadership (i.e., Associate Editors and Editors-in-Chief) from 1985 to 2013. We found that during this time period only 16% of subject editors were women, with more pronounced disparities in positions of editorial leadership. Although the trend was towards improvement over time, there was surprising variation between journals, including those with similar disciplinary foci. While demographic changes in academia may reduce these disparities over time, we argue journals should proactively strive for gender parity on their editorial boards. This will both increase the number of women afforded the opportunities and benefits that accompany board membership and increase the number of role models and potential mentors for early-career scientists and students.

  12. Biological and Environmental Research Program at Oak Ridge National Laboratory, FY 1992--1994

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    This report is the 1992--1994 Program Director's Overview Report for Oak Ridge National Laboratory's (ORNL's) Biological and Environmental Research (BER) Program, and as such it addresses KP-funded work at ORNL conducted during FY 1991 and in progress during FY 1992; it also serves as a planning document for the remainder of FY 1992 through FY 1994. Non-BER funded work at ORNL relevant to the mission of OHER is also discussed. The second section of the report describes ORNL facilities and resources used by the BER program. The third section addresses research management practices at ORNL. The fourth, fifth, and sixth sections address BER-funded research in progress, program accomplishments and research highlights, and program orientation for the remainder of FY 1992 through FY 1994, respectively. Work for non-BER sponsors is described in the seventh section, followed by a discussion of significant near and long-term issues facing BER work at ORNL in the eighth section. The last section provides a statistical summary of BER research at ORNL. Appendices supplement the above topics with additional detail.

  13. Large Scale Computing and Storage Requirements for Biological and Environmental Research

    Energy Technology Data Exchange (ETDEWEB)

    DOE Office of Science, Biological and Environmental Research Program Office (BER),

    2009-09-30

    In May 2009, NERSC, DOE's Office of Advanced Scientific Computing Research (ASCR), and DOE's Office of Biological and Environmental Research (BER) held a workshop to characterize HPC requirements for BER-funded research over the subsequent three to five years. The workshop revealed several key points, in addition to achieving its goal of collecting and characterizing computing requirements. Chief among them: scientific progress in BER-funded research is limited by current allocations of computational resources. Additionally, growth in mission-critical computing -- combined with new requirements for collaborative data manipulation and analysis -- will demand ever increasing computing, storage, network, visualization, reliability and service richness from NERSC. This report expands upon these key points and adds others. It also presents a number of"case studies" as significant representative samples of the needs of science teams within BER. Workshop participants were asked to codify their requirements in this"case study" format, summarizing their science goals, methods of solution, current and 3-5 year computing requirements, and special software and support needs. Participants were also asked to describe their strategy for computing in the highly parallel,"multi-core" environment that is expected to dominate HPC architectures over the next few years.

  14. Biological and Environmental Research Program at Oak Ridge National Laboratory, FY 1992--1994

    Energy Technology Data Exchange (ETDEWEB)

    1992-01-01

    This report is the 1992--1994 Program Director`s Overview Report for Oak Ridge National Laboratory`s (ORNL`s) Biological and Environmental Research (BER) Program, and as such it addresses KP-funded work at ORNL conducted during FY 1991 and in progress during FY 1992; it also serves as a planning document for the remainder of FY 1992 through FY 1994. Non-BER funded work at ORNL relevant to the mission of OHER is also discussed. The second section of the report describes ORNL facilities and resources used by the BER program. The third section addresses research management practices at ORNL. The fourth, fifth, and sixth sections address BER-funded research in progress, program accomplishments and research highlights, and program orientation for the remainder of FY 1992 through FY 1994, respectively. Work for non-BER sponsors is described in the seventh section, followed by a discussion of significant near and long-term issues facing BER work at ORNL in the eighth section. The last section provides a statistical summary of BER research at ORNL. Appendices supplement the above topics with additional detail.

  15. The impact of environmental stress on male reproductive development in plants: biological processes and molecular mechanisms.

    Science.gov (United States)

    De Storme, Nico; Geelen, Danny

    2014-01-01

    In plants, male reproductive development is extremely sensitive to adverse climatic environments and (a)biotic stress. Upon exposure to stress, male gametophytic organs often show morphological, structural and metabolic alterations that typically lead to meiotic defects or premature spore abortion and male reproductive sterility. Depending on the type of stress involved (e.g. heat, cold, drought) and the duration of stress exposure, the underlying cellular defect is highly variable and either involves cytoskeletal alterations, tapetal irregularities, altered sugar utilization, aberrations in auxin metabolism, accumulation of reactive oxygen species (ROS; oxidative stress) or the ectopic induction of programmed cell death (PCD). In this review, we present the critically stress-sensitive stages of male sporogenesis (meiosis) and male gametogenesis (microspore development), and discuss the corresponding biological processes involved and the resulting alterations in male reproduction. In addition, this review also provides insights into the molecular and/or hormonal regulation of the environmental stress sensitivity of male reproduction and outlines putative interaction(s) between the different processes involved.

  16. Liquid membrane extraction techniques for trace metal analysis and speciation in environmental and biological matrices

    Energy Technology Data Exchange (ETDEWEB)

    Ndungu, Kuria

    1999-04-01

    In this thesis, liquid-membrane-based methods for the analysis of trace metal species in samples of environmental and biological origin were developed. By incorporating extracting reagents in the membrane liquid, trace metal ions were selectively separated from humic-rich natural waters and urine samples, prior to their determination using various instrumental techniques. The extractions were performed in closed flow systems thus allowing easy automation of both the sample clean-up and enrichment. An acidic organophosphorus reagent (DEHPA) and a basic tetraalkylammonium reagent (Aliquat-336) were used as extractants in the membrane liquid to selectively extract and enrich cationic and anionic metal species respectively. A speciation method for chromium species was developed that allowed the determination of cationic Cr(III) species and anionic CR(VI) species in natural water samples without the need of a chromatographic separation step prior to their detection. SLM was also coupled on-line to potentiometric stripping analysis providing a fast and sensitive method for analysis of Pb in urine samples. A microporous membrane liquid-liquid extraction (MMLLE) method was developed for the determination of organotin compounds in natural waters that reduced the number of manual steps involved in the LLE of organotin compounds prior to their CC separation. Clean extracts obtained after running unfiltered humic-rich river water samples through the MMLLE flow system allowed selective determination of all the organotin compounds in a single run using GC-MS in the selected ion monitoring mode (SIM) 171 refs, 9 figs, 4 tabs

  17. Biological and Environmental Research Program at Oak Ridge National Laboratory, FY 1992--1994

    International Nuclear Information System (INIS)

    This report is the 1992--1994 Program Director's Overview Report for Oak Ridge National Laboratory's (ORNL's) Biological and Environmental Research (BER) Program, and as such it addresses KP-funded work at ORNL conducted during FY 1991 and in progress during FY 1992; it also serves as a planning document for the remainder of FY 1992 through FY 1994. Non-BER funded work at ORNL relevant to the mission of OHER is also discussed. The second section of the report describes ORNL facilities and resources used by the BER program. The third section addresses research management practices at ORNL. The fourth, fifth, and sixth sections address BER-funded research in progress, program accomplishments and research highlights, and program orientation for the remainder of FY 1992 through FY 1994, respectively. Work for non-BER sponsors is described in the seventh section, followed by a discussion of significant near and long-term issues facing BER work at ORNL in the eighth section. The last section provides a statistical summary of BER research at ORNL. Appendices supplement the above topics with additional detail

  18. Women are underrepresented on the editorial boards of journals in environmental biology and natural resource management.

    Science.gov (United States)

    Cho, Alyssa H; Johnson, Shelly A; Schuman, Carrie E; Adler, Jennifer M; Gonzalez, Oscar; Graves, Sarah J; Huebner, Jana R; Marchant, D Blaine; Rifai, Sami W; Skinner, Irina; Bruna, Emilio M

    2014-01-01

    Despite women earning similar numbers of graduate degrees as men in STEM disciplines, they are underrepresented in upper level positions in both academia and industry. Editorial board memberships are an important example of such positions; membership is both a professional honor in recognition of achievement and an opportunity for professional advancement. We surveyed 10 highly regarded journals in environmental biology, natural resource management, and plant sciences to quantify the number of women on their editorial boards and in positions of editorial leadership (i.e., Associate Editors and Editors-in-Chief) from 1985 to 2013. We found that during this time period only 16% of subject editors were women, with more pronounced disparities in positions of editorial leadership. Although the trend was towards improvement over time, there was surprising variation between journals, including those with similar disciplinary foci. While demographic changes in academia may reduce these disparities over time, we argue journals should proactively strive for gender parity on their editorial boards. This will both increase the number of women afforded the opportunities and benefits that accompany board membership and increase the number of role models and potential mentors for early-career scientists and students. PMID:25177537

  19. Role of Biological Sex in Normal Cardiac Function and in its Disease Outcome – A Review

    OpenAIRE

    Prabhavathi, K.; Selvi, K.Tamarai; Poornima, K.N.; Sarvanan, A.

    2014-01-01

    Biological sex plays an important role in normal cardiac physiology as well as in the heart‘s response to cardiac disease. Women generally have better cardiac function and survival than do men in the face of cardiac disease; however, this is progressively lost when comparing postmenopausal women with age matched men. Animal model of cardiac disease mirror what is seen in humans. Sex hormones contribute significantly to sex based difference in cardiac functioning and in its disease outcome. Es...

  20. The Impact of Environmental Fluctuations on Evolutionary Fitness Functions.

    Science.gov (United States)

    Melbinger, Anna; Vergassola, Massimo

    2015-10-19

    The concept of fitness as a measure for a species' success in natural selection is central to the theory of evolution. We here investigate how reproduction rates which are not constant but vary in response to environmental fluctuations, influence a species' prosperity and thereby its fitness. Interestingly, we find that not only larger growth rates but also reduced sensitivities to environmental changes substantially increase the fitness. Thereby, depending on the noise level of the environment, it might be an evolutionary successful strategy to minimize this sensitivity rather than to optimize the reproduction speed. Also for neutral evolution, where species with exactly the same properties compete, variability in the growth rates plays a crucial role. The time for one species to fixate is strongly reduced in the presence of environmental noise. Hence, environmental fluctuations constitute a possible explanation for effective population sizes inferred from genetic data that often are much smaller than the census population size.

  1. Determining the impacts of trawling on benthic function in European waters : a biological traits approach

    DEFF Research Database (Denmark)

    Bolam, Stefan; Kenny, Andrew; Garcia, Clement;

    on benthic ecosystem functioning over much larger spatial scales than previously undertaken. Biological traits information from 887 stations across European waters (Norwegian, UK, Belgian, Dutch, Danish waters, the Mediterranean and Black Sea) were analysed to: i) quantify the relationships between infaunal...

  2. PreproVIP-derived peptides in the human female genital tract: expression and biological function

    DEFF Research Database (Denmark)

    Bredkjoer, H E; Palle, C; Ekblad, E;

    1997-01-01

    The aim of the study was to elucidate the localization, distribution, colocalization and biological effect of preproVIP-derived peptides in the human female genital tract. Radioimmunoassays applying antisera against the five functional domains of the VIP precursor in combination with immunohistoc...

  3. Late-stage diversification of biologically active pyridazinones via a direct C-H functionalization strategy.

    Science.gov (United States)

    Li, Wei; Fan, Zhoulong; Geng, Kaijun; Xu, Youjun; Zhang, Ao

    2015-01-14

    Divergent C-H functionalization reactions (arylation, carboxylation, olefination, thiolation, acetoxylation, halogenation, naphthylation) using a pyridazinone moiety as an internal directing group were successfully established. This approach offers a late-stage, ortho-selective diversification of a biologically active pyridazinone scaffold. Seven series of novel pyridazinone analogues were synthesized conveniently as the synthetic precursors of potential sortase A (SrtA) inhibitors.

  4. Functional annotation of the vlinc class of non-coding RNAs using systems biology approach.

    Science.gov (United States)

    St Laurent, Georges; Vyatkin, Yuri; Antonets, Denis; Ri, Maxim; Qi, Yao; Saik, Olga; Shtokalo, Dmitry; de Hoon, Michiel J L; Kawaji, Hideya; Itoh, Masayoshi; Lassmann, Timo; Arner, Erik; Forrest, Alistair R R; Nicolas, Estelle; McCaffrey, Timothy A; Carninci, Piero; Hayashizaki, Yoshihide; Wahlestedt, Claes; Kapranov, Philipp

    2016-04-20

    Functionality of the non-coding transcripts encoded by the human genome is the coveted goal of the modern genomics research. While commonly relied on the classical methods of forward genetics, integration of different genomics datasets in a global Systems Biology fashion presents a more productive avenue of achieving this very complex aim. Here we report application of a Systems Biology-based approach to dissect functionality of a newly identified vast class of very long intergenic non-coding (vlinc) RNAs. Using highly quantitative FANTOM5 CAGE dataset, we show that these RNAs could be grouped into 1542 novel human genes based on analysis of insulators that we show here indeed function as genomic barrier elements. We show that vlinc RNAs genes likely function in cisto activate nearby genes. This effect while most pronounced in closely spaced vlinc RNA-gene pairs can be detected over relatively large genomic distances. Furthermore, we identified 101 vlinc RNA genes likely involved in early embryogenesis based on patterns of their expression and regulation. We also found another 109 such genes potentially involved in cellular functions also happening at early stages of development such as proliferation, migration and apoptosis. Overall, we show that Systems Biology-based methods have great promise for functional annotation of non-coding RNAs.

  5. Functional Genomics Assistant (FUGA: a toolbox for the analysis of complex biological networks

    Directory of Open Access Journals (Sweden)

    Ouzounis Christos A

    2011-10-01

    Full Text Available Abstract Background Cellular constituents such as proteins, DNA, and RNA form a complex web of interactions that regulate biochemical homeostasis and determine the dynamic cellular response to external stimuli. It follows that detailed understanding of these patterns is critical for the assessment of fundamental processes in cell biology and pathology. Representation and analysis of cellular constituents through network principles is a promising and popular analytical avenue towards a deeper understanding of molecular mechanisms in a system-wide context. Findings We present Functional Genomics Assistant (FUGA - an extensible and portable MATLAB toolbox for the inference of biological relationships, graph topology analysis, random network simulation, network clustering, and functional enrichment statistics. In contrast to conventional differential expression analysis of individual genes, FUGA offers a framework for the study of system-wide properties of biological networks and highlights putative molecular targets using concepts of systems biology. Conclusion FUGA offers a simple and customizable framework for network analysis in a variety of systems biology applications. It is freely available for individual or academic use at http://code.google.com/p/fuga.

  6. To be well - to function well. Health biology at Copenhagen University

    DEFF Research Database (Denmark)

    Rosenkilde, Per

    1995-01-01

    Human Fysiologi, Health biology, Public health, Biology Curriculum, University curriculum, Health promotion.......Human Fysiologi, Health biology, Public health, Biology Curriculum, University curriculum, Health promotion....

  7. Environmental quality evaluation. Indexing tools to evaluate environmental quality from biological data, floristic and vegetational data in Ponte Galeria (Rome, Italy)

    International Nuclear Information System (INIS)

    In the present work the study of indexing tools to evaluate environmental quality from biological data has been performed using a certain number of floristic and vegetational indices near Macchia Grande of Ponte Galeria (Rome, Italy). The indices have been applied on the basis of the data coming from a phyto sociological study of the area. Multivariate statistics methodologies have been utilized to obtain a synthetic evaluation of the indices

  8. A biologically inspired psychometric function for accuracy of visual identification as a function of exposure duration

    DEFF Research Database (Denmark)

    Petersen, Anders; Andersen, Tobias

    rising from zero, then peaking, and finally decaying to a somewhat sustained plateau, mimicking closely observed instantaneous firing rates of monkey visual cortex neurons. The new psychometric function fits well to experimental data in both the present study and in a previous study of single......-letter identification accuracy (Bundesen & Harms, 1999). Also, we conducted a follow-up experiment to test the ability of the psychometric functions to fit single-letter identification data, at different stimulus contrast levels; also in this experiment the new psychometric function prevailed. Further, after insertion...... into Bundesen’s Theory of Visual Attention (Bundesen, 1990), the new psychometric function enables closer fits to data from a previous whole and partial report experiment....

  9. Interconnection of reactive oxygen species chemistry across the interfaces of atmospheric, environmental, and biological processes.

    Science.gov (United States)

    Anglada, Josep M; Martins-Costa, Marilia; Francisco, Joseph S; Ruiz-López, Manuel F

    2015-03-17

    Oxidation reactions are ubiquitous and play key roles in the chemistry of the atmosphere, in water treatment processes, and in aerobic organisms. Ozone (O3), hydrogen peroxide (H2O2), hydrogen polyoxides (H2Ox, x > 2), associated hydroxyl and hydroperoxyl radicals (HOx = OH and HO2), and superoxide and ozonide anions (O2(-) and O3(-), respectively) are the primary oxidants in these systems. They are commonly classified as reactive oxygen species (ROS). Atmospheric chemistry is driven by a complex system of chain reactions of species, including nitrogen oxides, hydroxyl and hydroperoxide radicals, alkoxy and peroxy radicals, and ozone. HOx radicals contribute to keeping air clean, but in polluted areas, the ozone concentration increases and creates a negative impact on plants and animals. Indeed, ozone concentration is used to assess air quality worldwide. Clouds have a direct effect on the chemical composition of the atmosphere. On one hand, cloud droplets absorb many trace atmospheric gases, which can be scavenged by rain and fog. On the other hand, ionic species can form in this medium, which makes the chemistry of the atmosphere richer and more complex. Furthermore, recent studies have suggested that air-cloud interfaces might have a significant impact on the overall chemistry of the troposphere. Despite the large differences in molecular composition, concentration, and thermodynamic conditions among atmospheric, environmental, and biological systems, the underlying chemistry involving ROS has many similarities. In this Account, we examine ROS and discuss the chemical characteristics common to all of these systems. In water treatment, ROS are key components of an important subset of advanced oxidation processes. Ozonation, peroxone chemistry, and Fenton reactions play important roles in generating sufficient amounts of hydroxyl radicals to purify wastewater. Biochemical processes within living organisms also involve ROS. These species can come from pollutants in

  10. Interconnection of reactive oxygen species chemistry across the interfaces of atmospheric, environmental, and biological processes.

    Science.gov (United States)

    Anglada, Josep M; Martins-Costa, Marilia; Francisco, Joseph S; Ruiz-López, Manuel F

    2015-03-17

    Oxidation reactions are ubiquitous and play key roles in the chemistry of the atmosphere, in water treatment processes, and in aerobic organisms. Ozone (O3), hydrogen peroxide (H2O2), hydrogen polyoxides (H2Ox, x > 2), associated hydroxyl and hydroperoxyl radicals (HOx = OH and HO2), and superoxide and ozonide anions (O2(-) and O3(-), respectively) are the primary oxidants in these systems. They are commonly classified as reactive oxygen species (ROS). Atmospheric chemistry is driven by a complex system of chain reactions of species, including nitrogen oxides, hydroxyl and hydroperoxide radicals, alkoxy and peroxy radicals, and ozone. HOx radicals contribute to keeping air clean, but in polluted areas, the ozone concentration increases and creates a negative impact on plants and animals. Indeed, ozone concentration is used to assess air quality worldwide. Clouds have a direct effect on the chemical composition of the atmosphere. On one hand, cloud droplets absorb many trace atmospheric gases, which can be scavenged by rain and fog. On the other hand, ionic species can form in this medium, which makes the chemistry of the atmosphere richer and more complex. Furthermore, recent studies have suggested that air-cloud interfaces might have a significant impact on the overall chemistry of the troposphere. Despite the large differences in molecular composition, concentration, and thermodynamic conditions among atmospheric, environmental, and biological systems, the underlying chemistry involving ROS has many similarities. In this Account, we examine ROS and discuss the chemical characteristics common to all of these systems. In water treatment, ROS are key components of an important subset of advanced oxidation processes. Ozonation, peroxone chemistry, and Fenton reactions play important roles in generating sufficient amounts of hydroxyl radicals to purify wastewater. Biochemical processes within living organisms also involve ROS. These species can come from pollutants in

  11. The functional biology and trophic role of krill (Thysanoessa raschii) in a Greenlandic fjord

    DEFF Research Database (Denmark)

    Agersted, Mette Dalgaard; Nielsen, Torkel Gissel; Munk, Peter;

    2011-01-01

    Despite being a key zooplankton group, knowledge on krill biology from the Arctic is inadequate. The present study examine the functional biology and evaluate the trophic role of krill in the GodthAyenbsfjord (64 degrees N, 51 degrees W) SW Greenland, through a combination of fieldwork and...... ration of 1% body C d(-1). Furthermore, T. raschii was capable of exploiting plankton cells from 5 to 400 mu m, covering several trophic levels of the pelagic food web. The calculated grazing impact by T. raschii on the fjord plankton community was negligible. However, the schooling and migratory...

  12. Multi-functionalized single-walled carbon nanotubes as tumor cell targeting biological transporters

    International Nuclear Information System (INIS)

    Multi-functionalized single walled carbon nanotubes (SWNTs) were prepared and applied as tumor cell targeting biological transporters. A positive charge was introduced on SWNTs to get high loading efficiency of fluorescein (FAM) labeled short double strands DNA (20 base pairs). The SWNTs were encapsulated with the folic acid modified phospholipids for active targeting into tumor cell. The tumor cell-targeting properties of these multi-functionalized SWNTs were investigated by active targeting into mouse ovarian surface epithelial cells. The experimental results show that these multi-functionalized SWNTs have good tumor cell targeting property

  13. The Structure of a Gene Co-Expression Network Reveals Biological Functions Underlying eQTLs

    Science.gov (United States)

    Villa-Vialaneix, Nathalie; Liaubet, Laurence; Laurent, Thibault; Cherel, Pierre; Gamot, Adrien; SanCristobal, Magali

    2013-01-01

    What are the commonalities between genes, whose expression level is partially controlled by eQTL, especially with regard to biological functions? Moreover, how are these genes related to a phenotype of interest? These issues are particularly difficult to address when the genome annotation is incomplete, as is the case for mammalian species. Moreover, the direct link between gene expression and a phenotype of interest may be weak, and thus difficult to handle. In this framework, the use of a co-expression network has proven useful: it is a robust approach for modeling a complex system of genetic regulations, and to infer knowledge for yet unknown genes. In this article, a case study was conducted with a mammalian species. It showed that the use of a co-expression network based on partial correlation, combined with a relevant clustering of nodes, leads to an enrichment of biological functions of around 83%. Moreover, the use of a spatial statistics approach allowed us to superimpose additional information related to a phenotype; this lead to highlighting specific genes or gene clusters that are related to the network structure and the phenotype. Three main results are worth noting: first, key genes were highlighted as a potential focus for forthcoming biological experiments; second, a set of biological functions, which support a list of genes under partial eQTL control, was set up by an overview of the global structure of the gene expression network; third, pH was found correlated with gene clusters, and then with related biological functions, as a result of a spatial analysis of the network topology. PMID:23577081

  14. Graphical methods and Cold War scientific practice: the Stommel Diagram's intriguing journey from the physical to the biological environmental sciences.

    Science.gov (United States)

    Vance, Tiffany C; Doel, Ronald E

    2010-01-01

    In the last quarter of the twentieth century, an innovative three-dimensional graphical technique was introduced into biological oceanography and ecology, where it spread rapidly. Used to improve scientists' understanding of the importance of scale within oceanic ecosystems, this influential diagram addressed biological scales from phytoplankton to fish, physical scales from diurnal tides to ocean currents, and temporal scales from hours to ice ages. Yet the Stommel Diagram (named for physical oceanographer Henry Stommel, who created it in 1963) had not been devised to aid ecological investigations. Rather, Stommel intended it to help plan large-scale research programs in physical oceanography, particularly as Cold War research funding enabled a dramatic expansion of physical oceanography in the 1960s. Marine ecologists utilized the Stommel Diagram to enhance research on biological production in ocean environments, a key concern by the 1970s amid growing alarm about overfishing and ocean pollution. Before the end of the twentieth century, the diagram had become a significant tool within the discipline of ecology. Tracing the path that Stommel's graphical techniques traveled from the physical to the biological environmental sciences reveals a great deal about practices in these distinct research communities and their relative professional and institutional standings in the Cold War era. Crucial to appreciating the course of that path is an understanding of the divergent intellectual and social contexts of the physical versus the biological environmental sciences.

  15. Variation of Phenolic Content in Globe Artichoke in Relation to Biological, Technical and Environmental Factors

    Directory of Open Access Journals (Sweden)

    Giovanni Mauromicale

    2011-02-01

    Full Text Available In Italy, globe artichoke production is prevailingly concentrated in the South and islands, where it provides an important contribution to the agricultural economy. In recent years, there has been a renewed interest in this crop as a promising source of polyphenols, a heterogeneous class of secondary metabolites characterized by various healthy properties well-documented in literature. The phenolic fraction, present in the different artichoke plant parts, varies widely in relation to biotic and abiotic factors. Therefore, the present study aimed at evaluating the variation of phenolic content in globe artichoke in relation to biological, technical and environmental factors. Two field-experiments were carried out in Sicily (South Italy in two representative cultivation areas, in order to examine the effects of genotype, head fraction, season conditions, planting density and arrangement on the globe artichoke phenolic concentration. Both the total polyphenols and the individual phenolic compounds detected were notably genotype- dependent. Particularly, the high level of caffeoylquinic acids (chlorogenic acid, among others and apigenin 7- O-glucuronide, reported respectively by “Violetto di Sicilia” and “Romanesco clone C3”, could be used to encourage globe artichoke fresh consumption. Total polyphenols content also resulted more abundant in specific accumulation sites within the inflorescence, such as the floral stem and receptacle, and for most of genotypes it decreased during the second year in response to the different meteorological conditions. Additionally, total polyphenols content significantly and linearly increased as plant density increased from 1.0 to 1.8 plant m-2 and it significantly increased by 13% passing from single to twin rows plant arrangement.

  16. Phytoplankton biomass dynamics and environmental variables around the Rocas Atoll Biological Reserve, South Atlantic

    Directory of Open Access Journals (Sweden)

    Marina Cavalcanti Jales

    2015-12-01

    Full Text Available Abstract The Rocas Atoll Biological Reserve is located in the Atlantic Ocean, at 3º 51' S and 33º 49' W. It lies 143 nautical miles from the City of Natal, Rio Grande do Norte (Brazil. The purpose of this study was to analyze the hydrology, water masses, currents and chlorophyll a content to determine the dynamics of phytoplankton biomass around the Rocas Atoll. Samples were collected in July 2010 in the area around the Atoll, using the Research Vessel Cruzeiro do Sul of the Brazilian Navy. Two transects were established according to the surface currents, one of which at the southeast of the Atoll (SE and the other at norwest (NW. Three collection points were determined on each of these transects. Samples were collected at different depths (surface and DCM - Deep Chlorophyll Maximum and different times (day and night. According to PCA (Principal Component Analysis, the nutrients analyzed, DIN (dissolved inorganic nitrogen, DIP (dissolved inorganic phosphorus and silicate, were inversely correlated with temperature and dissolved oxygen. Most environmental variables showed a significant increase due to the turbulence on the Northwest transect. There was an increase in the concentration of chlorophyll a and nutrients when the temperature and oxygen in the mixed layer was reduced due to the influence of the SACW (South Atlantic Central Water. Despite the increase observed in some variables such as nutrient salts and chlorophyll a, the temperature in the mixed layer attained a mean value of 23.23 ºC due to the predominance of Tropical Water. The increase of the phytoplankton biomass on the NW transect was, therefore, caused by the "island effect" and not by upwelling.

  17. Autofluorescence of atmospheric bioaerosols - Biological standard particles and the influence of environmental conditions

    Science.gov (United States)

    Pöhlker, Christopher; Huffman, J. Alex; Förster, Jan-David; Pöschl, Ulrich

    2013-04-01

    Primary biological aerosol particles (PBAP) such as pollen, fungal spores, bacteria, biogenic polymers and debris from larger organisms are known to influence atmospheric chemistry and physics, the biosphere and public health. PBAP can account for up to ~30% of fine and up to ~70% of coarse particulate matter in urban, rural and pristine environment and are released with estimated emission rates of up to ~1000 Tg/a [1]. Continuous measurements of the abundance, variability and diversity of PBAP have been difficult until recently, however. The application of on-line instruments able to detect autofluorescence from biological particles in real-time has been a promising development for the measurement of PBAP concentrations and fluxes in different environments [2,3]. The detected fluorescent biological aerosol particles (FBAP) can be regarded as a subset of PBAP, although the exact relationship between PBAP and FBAP is still being investigated. Autofluorescence of FBAP is usually a superposition of fluorescence from a mixture of individual fluorescent molecules (fluorophores). Numerous biogenic fluorophores such as amino acids (e.g., tryptophan, tyrosine), coenzymes (e.g., NAD(P)H, riboflavin) and biopolymers (e.g., cellulose) emit fluorescent light due to heterocyclic aromatic rings or conjugated double bonds within their molecular structures. The tryptophan emission peak is a common feature of most bioparticles because the amino acid is a constituent of many proteins and peptides. The influence of the coenzymes NAD(P)H and riboflavin on the autofluorescence of bacteria can be regarded as an indicator for bacterial metabolism and has been utilized to discriminate between viable and non-viable organisms [4]. However, very little information is available about other essential biofluorophores in fungal spores and pollen. In order to better understand the autofluorescence behavior of FBAP, we have used fluorescence spectroscopy and fluorescence microscopy to analyze

  18. Random regression models for the estimation of genetic and environmental covariance functions for growth traits in Santa Ines sheep.

    Science.gov (United States)

    Sarmento, J L R; Torres, R A; Sousa, W H; Lôbo, R N B; Albuquerque, L G; Lopes, P S; Santos, N P S; Bignard, A B

    2016-01-01

    Polynomial functions of different orders were used to model random effects associated with weight of Santa Ines sheep from birth to 196 days. Fixed effects included in the models were contemporary groups, age of ewe at lambing, and fourth-order Legendre polynomials for age to represent the average growth curve. In the random part, functions of different orders were included to model variances associated with direct additive and maternal genetic effects and with permanent environmental effects of the animal and mother. Residual variance was fitted by a sixth-order ordinary polynomial for age. The higher the order of the functions, the better the model fit the data. According to the Akaike information criterion and likelihood ratio test, a continuous function of order, five, five, seven, and three for direct additive genetic, maternal genetic, animal permanent environmental, and maternal permanent environmental effects (k = 5573), respectively, was sufficient to model changes in (co)variances with age. However, a more parsimonious model of order three, three, five, and three (k = 3353) was suggested based on Schwarz's Bayesian information criterion for the same effects. Since it was a more flexible model, model k = 5573 provided inconsistent genetic parameter estimates when compared to the biologically expected result. Predicted breeding values obtained with models k = 3353 and k = 5573 differed, especially at young ages. Model k = 3353 adequately fit changes in variances and covariances with time, and may be used to describe changes in variances with age in the Santa Ines sheep studied.

  19. Random regression models for the estimation of genetic and environmental covariance functions for growth traits in Santa Ines sheep.

    Science.gov (United States)

    Sarmento, J L R; Torres, R A; Sousa, W H; Lôbo, R N B; Albuquerque, L G; Lopes, P S; Santos, N P S; Bignard, A B

    2016-01-01

    Polynomial functions of different orders were used to model random effects associated with weight of Santa Ines sheep from birth to 196 days. Fixed effects included in the models were contemporary groups, age of ewe at lambing, and fourth-order Legendre polynomials for age to represent the average growth curve. In the random part, functions of different orders were included to model variances associated with direct additive and maternal genetic effects and with permanent environmental effects of the animal and mother. Residual variance was fitted by a sixth-order ordinary polynomial for age. The higher the order of the functions, the better the model fit the data. According to the Akaike information criterion and likelihood ratio test, a continuous function of order, five, five, seven, and three for direct additive genetic, maternal genetic, animal permanent environmental, and maternal permanent environmental effects (k = 5573), respectively, was sufficient to model changes in (co)variances with age. However, a more parsimonious model of order three, three, five, and three (k = 3353) was suggested based on Schwarz's Bayesian information criterion for the same effects. Since it was a more flexible model, model k = 5573 provided inconsistent genetic parameter estimates when compared to the biologically expected result. Predicted breeding values obtained with models k = 3353 and k = 5573 differed, especially at young ages. Model k = 3353 adequately fit changes in variances and covariances with time, and may be used to describe changes in variances with age in the Santa Ines sheep studied. PMID:27323203

  20. The bottom-up approach to defining life : deciphering the functional organization of biological cells via multi-objective representation of biological complexity from molecules to cells

    Directory of Open Access Journals (Sweden)

    Sathish ePeriyasamy

    2013-12-01

    Full Text Available In silico representation of cellular systems needs to represent the adaptive dynamics of biological cells, recognizing a cell’s multi-objective topology formed by spatially and temporally cohesive intracellular structures. The design of these models needs to address the hierarchical and concurrent nature of cellular functions and incorporate the ability to self-organise in response to transitions between healthy and pathological phases, and adapt accordingly. The functions of biological systems are constantly evolving, due to the ever changing demands of their environment. Biological systems meet these demands by pursuing objectives, aided by their constituents, giving rise to biological functions. A biological cell is organised into an objective/task hierarchy. These objective hierarchy corresponds to the nested nature of temporally cohesive structures and representing them will facilitate in studying pleiotropy and polygeny by modeling causalities propagating across multiple interconnected intracellular processes. Although biological adaptations occur in physiological, developmental and reproductive timescales, the paper is focused on adaptations that occur within physiological timescales, where the biomolecular activities contributing to functional organisation, play a key role in cellular physiology. The paper proposes a multi-scale and multi-objective modelling approach from the bottom-up by representing temporally cohesive structures for multi-tasking of intracellular processes. Further the paper characterises the properties and constraints that are consequential to the organisational and adaptive dynamics in biological cells.

  1. Fundamental and functional aspects of mesoscopic architectures with examples in physics, cell biology, and chemistry.

    Science.gov (United States)

    Kalay, Ziya

    2011-08-01

    How small can a macroscopic object be made without losing its intended function? Obviously, the smallest possible size is determined by the size of an atom, but it is not so obvious how many atoms are required to assemble an object so small, and yet that performs the same function as its macroscopic counterpart. In this review, we are concerned with objects of intermediate nature, lying between the microscopic and the macroscopic world. In physics and chemistry literature, this regime in-between is often called mesoscopic, and is known to bear interesting and counterintuitive features. After a brief introduction to the concept of mesoscopic systems from the perspective of physics, we discuss the functional aspects of mesoscopic architectures in cell biology, and supramolecular chemistry through many examples from the literature. We argue that the biochemistry of the cell is largely regulated by mesoscopic functional architectures; however, the significance of mesoscopic phenomena seems to be quite underappreciated in biological sciences. With this motivation, one of our main purposes here is to emphasize the critical role that mesoscopic structures play in cell biology and biochemistry.

  2. The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

    Science.gov (United States)

    McDougall, Carmel; Woodcroft, Ben J; Degnan, Bernard M

    2016-01-01

    In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs) identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the construction of

  3. The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials.

    Directory of Open Access Journals (Sweden)

    Carmel McDougall

    Full Text Available In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the

  4. The Widespread Prevalence and Functional Significance of Silk-Like Structural Proteins in Metazoan Biological Materials

    Science.gov (United States)

    McDougall, Carmel; Woodcroft, Ben J.

    2016-01-01

    In nature, numerous mechanisms have evolved by which organisms fabricate biological structures with an impressive array of physical characteristics. Some examples of metazoan biological materials include the highly elastic byssal threads by which bivalves attach themselves to rocks, biomineralized structures that form the skeletons of various animals, and spider silks that are renowned for their exceptional strength and elasticity. The remarkable properties of silks, which are perhaps the best studied biological materials, are the result of the highly repetitive, modular, and biased amino acid composition of the proteins that compose them. Interestingly, similar levels of modularity/repetitiveness and similar bias in amino acid compositions have been reported in proteins that are components of structural materials in other organisms, however the exact nature and extent of this similarity, and its functional and evolutionary relevance, is unknown. Here, we investigate this similarity and use sequence features common to silks and other known structural proteins to develop a bioinformatics-based method to identify similar proteins from large-scale transcriptome and whole-genome datasets. We show that a large number of proteins identified using this method have roles in biological material formation throughout the animal kingdom. Despite the similarity in sequence characteristics, most of the silk-like structural proteins (SLSPs) identified in this study appear to have evolved independently and are restricted to a particular animal lineage. Although the exact function of many of these SLSPs is unknown, the apparent independent evolution of proteins with similar sequence characteristics in divergent lineages suggests that these features are important for the assembly of biological materials. The identification of these characteristics enable the generation of testable hypotheses regarding the mechanisms by which these proteins assemble and direct the construction of

  5. Teleology then and now: the question of Kant's relevance for contemporary controversies over function in biology.

    Science.gov (United States)

    Zammito, John

    2006-12-01

    'Naturalism' is the aspiration of contemporary philosophy of biology, and Kant simply cannot be refashioned into a naturalist. Instead, epistemological 'deflation' was the decisive feature of Kant's treatment of the 'biomedical' science in his day, so it is not surprising that this might attract some philosophers of science to him today. A certain sense of impasse in the contemporary 'function talk' seems to motivate renewed interest in Kant. Kant--drawing on his eighteenth-century predecessors-provided a discerning and powerful characterization of what biologists had to explain in organic form. His difference from the rest is that he opined that it was impossible to explain it. Its 'inscrutability' was intrinsic. The third Critique essentially proposed the reduction of biology to a kind of pre-scientific descriptivism, doomed never to attain authentic scientificity, to have its 'Newton of the blade of grass'. By contrast, for Locke, and a fortiori for Buffon and his followers, 'intrinsic purposiveness' was a fact of the matter about concrete biological phenomena; the features of internal self-regulation were hypotheses arising out of actual research practice. The difference comes most vividly to light once we recognize Kant's distinction of the concept of organism from the concept of life. If biology must conceptualize self-organization as actual in the world, Kant's regulative/constitutive distinction is pointless in practice and the (naturalist) philosophy of biology has urgent work to undertake for which Kant turns out not to be very helpful. PMID:17157770

  6. Environmental assessment of nutrient recycling from biological pig slurry treatment--impact of fertilizer substitution and field emissions.

    Science.gov (United States)

    Brockmann, Doris; Hanhoun, Mary; Négri, Ophélie; Hélias, Arnaud

    2014-07-01

    Pig slurry treatment is an important means in reducing nitrogen loads applied to farmland. Solid phase separation prior to biological treatment further allows for recovering phosphorus with the solid phase. The organic residues from the pig slurry treatment can be applied as organic fertilizers to farmland replacing mineral fertilizers. The environmental impacts of nutrient recycling from aerobic, biological pig slurry treatment were evaluated applying the life cycle assessment (LCA) methodology. LCA results revealed that direct field emissions from organic fertilizer application and the amount of avoided mineral fertilizers dominated the environmental impacts. A modified plant available nitrogen calculation (PAN) was introduced taking into account calculated nitrogen emissions from organic fertilizer application. Additionally, an equation for calculating the quantity of avoided mineral fertilizers based on the modified PAN calculation was proposed, which accounted for nitrogen emissions from mineral fertilizer application.

  7. Profile of social, environmental and biological correlates in intellectual disability in a resource-poor setting in India

    Directory of Open Access Journals (Sweden)

    Ram Lakhan

    2015-01-01

    Full Text Available Background: Intellectual disability (ID is a major public health issue in India. Social, environmental and biological factors all contribute to the nation′s high rate of ID. Objective: We aimed to investigate the distribution, differences and the association of social, environmental and biological factors with different types of ID in a mixed (tribal and non-tribal population in India. Materials and Methods: Secondary data was collected during a community-based rehabilitation project and analyzed with descriptive statistics: Frequency, percentage and χ2 . Results: Poverty, low levels of parental education and a family history of epilepsy and ID were all associated in both tribal and non-tribal populations (P < 0.05. Conclusion: The outcome of this study may be helpful in planning public health initiatives that aim to reduce the burden of ID in mixed populations.

  8. Form and function: Perspectives on structural biology and resources for the future

    International Nuclear Information System (INIS)

    The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs

  9. Mediating objects: scientific and public functions of models in nineteenth-century biology.

    Science.gov (United States)

    Ludwig, David

    2013-01-01

    The aim of this article is to examine the scientific and public functions of two- and three-dimensional models in the context of three episodes from nineteenth-century biology. I argue that these models incorporate both data and theory by presenting theoretical assumptions in the light of concrete data or organizing data through theoretical assumptions. Despite their diverse roles in scientific practice, they all can be characterized as mediators between data and theory. Furthermore, I argue that these different mediating functions often reflect their different audiences that included specialized scientists, students, and the general public. In this sense, models in nineteenth-century biology can be understood as mediators between theory, data, and their diverse audiences.

  10. Form and function: Perspectives on structural biology and resources for the future

    Energy Technology Data Exchange (ETDEWEB)

    Vaughan, D. (ed.)

    1990-12-01

    The purpose of this study is largely to explore and expand on the thesis that biological structures and their functions are suited to. Form indeed follows function and if we are to understand the workings of a living system, with all that such an understanding promises, we must first seek to describe the structure of its parts. Descriptions of a few achievements of structural biology lay the groundwork, but the substance of this booklet is a discussion of important questions yet unanswered and opportunities just beyond our grasp. The concluding pages then outline a course of action in which the Department of Energy would exercise its responsibility to develop the major resources needed to extend our reach and to answer some of those unanswered questions. 22 figs.

  11. Correlation Between Toluene Environmental Monitoring and Biological Index of Urinary Hippuric Acid of Workers in the Coke Industry

    OpenAIRE

    MM Amin; Kalantari, A.; N BASHARDOOST; AR Bahrami; M. Rismanchian; Gh Mirsatari; Mansouri, F.

    2007-01-01

    Introduction: Toluene is an organic solvent that it is one of the byproducts in the coke industry. Exposure to toluene causes central nervous system dysfunction and others disorders. Many workers are exposed to toluene due to leakage from tracks. Therefore the aim of this study was to determine the levels of exposure through environmental and biological monitoring of toluene Methods: Air toluene sampling of air inhaled by 36 coke oven workers was done by using activated charcoal tubes and per...

  12. Modeling Genetic and Environmental Factors in Biological Systems Using Structural Equation Modeling: An Application to Energy Balance

    OpenAIRE

    Nock, Nora L.; Li, Li; Elston, Robert C.

    2009-01-01

    To improve our understanding of the role(s) that genes and environmental factors play in a complex disease, we need statistical approaches that model multiple factors simultaneously in a hierarchical manner that aims to reflect the underlying biological system(s). We present an approach that models genes as latent constructs, defined by multiple variants (single nucleotide polymorphisms, SNPs) within each gene, using the multivariate statistical framework of structural equation modeling (SEM)...

  13. Influence of Lipid Oxidization on Structures and Functions of Biological Membranes

    OpenAIRE

    Korytowski, Agatha Anna

    2016-01-01

    The primary aim of this thesis is to clarify how the structures and functions of biological membranes are influenced by the oxidative damage mediated by free radicals. As a precisely defined model systems, artificially reconstituted lipid membranes (Langmuir monolayers, vesicles, supported membranes, multilamellar membranes) incorporating two oxidized phospholipids bearing aldehyde or carboxyl groups at the end of truncated sn-2 acyl chains were fabricated. By the combination of various exper...

  14. The SYK tyrosine kinase: a crucial player in diverse biological functions

    OpenAIRE

    Mócsai, Attila; Ruland, Jürgen; Tybulewicz, Victor L.J.

    2010-01-01

    Spleen tyrosine kinase (SYK) has been known to relay adaptive immune receptor signalling. However, recent reports indicate that SYK also mediates other, unexpectedly diverse biological functions including cellular adhesion, innate immune recognition, osteoclast maturation, platelet activation and vascular development. SYK is activated by C-type lectins and integrins, and activates novel targets including the CARD9/CARMA1–BCL10–MALT1 pathway and the NLRP3 inflammasome. Drosophila studies indic...

  15. Integrating biological knowledge based on functional annotations for biclustering of gene expression data.

    Science.gov (United States)

    Nepomuceno, Juan A; Troncoso, Alicia; Nepomuceno-Chamorro, Isabel A; Aguilar-Ruiz, Jesús S

    2015-05-01

    Gene expression data analysis is based on the assumption that co-expressed genes imply co-regulated genes. This assumption is being reformulated because the co-expression of a group of genes may be the result of an independent activation with respect to the same experimental condition and not due to the same regulatory regime. For this reason, traditional techniques are recently being improved with the use of prior biological knowledge from open-access repositories together with gene expression data. Biclustering is an unsupervised machine learning technique that searches patterns in gene expression data matrices. A scatter search-based biclustering algorithm that integrates biological information is proposed in this paper. In addition to the gene expression data matrix, the input of the algorithm is only a direct annotation file that relates each gene to a set of terms from a biological repository where genes are annotated. Two different biological measures, FracGO and SimNTO, are proposed to integrate this information by means of its addition to-be-optimized fitness function in the scatter search scheme. The measure FracGO is based on the biological enrichment and SimNTO is based on the overlapping among GO annotations of pairs of genes. Experimental results evaluate the proposed algorithm for two datasets and show the algorithm performs better when biological knowledge is integrated. Moreover, the analysis and comparison between the two different biological measures is presented and it is concluded that the differences depend on both the data source and how the annotation file has been built in the case GO is used. It is also shown that the proposed algorithm obtains a greater number of enriched biclusters than other classical biclustering algorithms typically used as benchmark and an analysis of the overlapping among biclusters reveals that the biclusters obtained present a low overlapping. The proposed methodology is a general-purpose algorithm which allows

  16. Emerging Molecular and Biological Functions of MBD2, a Reader of DNA Methylation

    Directory of Open Access Journals (Sweden)

    Kathleen H Wood

    2016-05-01

    Full Text Available DNA methylation is an epigenetic mark that is essential for many biological processes and is linked to diseases such as cancer. Methylation is usually associated with transcriptional silencing, but new research has challenged this model. Both transcriptional activation and repression have recently been found to be associated with DNA methylation in a context-specific manner. How DNA methylation patterns are interpreted into different functional output remains poorly understood. One mechanism involves the protein ‘readers’ of methylation, which includes the methyl-CpG binding domain (MBD family of proteins. This review examines the molecular and biological functions of MBD2, which binds to CpG methylation and is an integral part of the nucleosome remodeling and histone deacetylation (NuRD complex. MBD2 has been linked to immune system function and tumorigenesis, yet little is known about its functions in vivo. Recent studies have found the MBD2 protein is ubiquitously expressed, with relatively high levels in the lung, liver and colon. Mbd2 null mice surprisingly show relatively mild phenotypes compared to mice with loss of function of other MBD proteins. This evidence has previously been interpreted as functional redundancy between the MBD proteins. Here we examine and contextualize research that suggests MBD2 has unique properties and functions among the MBD proteins. These functions translate to recently described roles in the development and differentiation of multiple cell lineages, including pluripotent stem cells and various cell types of the immune system, as well as in tumorigenesis. We also consider possible models for the dynamic interactions between MBD2 and NuRD in different tissues in vivo. The functions of MBD2 may have direct therapeutic implications for several areas of human disease, including autoimmune conditions and cancer, in addition to providing insights into the actions of NuRD and chromatin regulation.

  17. Applications of synchrotron μ-XRF to study the distribution of biologically important elements in different environmental matrices: a review.

    Science.gov (United States)

    Majumdar, Sanghamitra; Peralta-Videa, Jose R; Castillo-Michel, Hiram; Hong, Jie; Rico, Cyren M; Gardea-Torresdey, Jorge L

    2012-11-28

    Environmental matrices including soils, sediments, and living organisms are reservoirs of several essential as well as non-essential elements. Accurate qualitative and quantitative information on the distribution and interaction of biologically significant elements is vital to understand the role of these elements in environmental and biological samples. Synchrotron micro-X-ray fluorescence (μ-SXRF) allows in situ mapping of biologically important elements at nanometer to sub-micrometer scale with high sensitivity, negligible sample damage and enable tuning of the incident energy as desired. Beamlines in the synchrotron facilities are rapidly increasing their analytical versatility in terms of focusing optics, detector technologies, incident energy, and sample environment. Although extremely competitive, it is now feasible to find stations offering complimentary techniques like micro-X-ray diffraction (μ-XRD) and micro-X-ray absorption spectroscopy (μ-XAS) that will allow a more complete characterization of complex matrices. This review includes the most recent literature on the emerging applications and challenges of μ-SXRF in studying the distribution of biologically important elements and manufactured nanoparticles in soils, sediments, plants, and microbes. The advantages of using μ-SXRF and complimentary techniques in contrast to conventional techniques used for the respective studies are discussed. PMID:23146389

  18. Coronary flow and left ventricular function during environmental stress.

    Science.gov (United States)

    Erickson, H. H.; Adams, J. D.; Stone, H. L.; Sandler, H.

    1972-01-01

    A canine model was used to study the effects of different environmental stresses on the heart and coronary circulation. The heart was surgically instrumented to measure coronary blood flow, left ventricular pressure, and other cardiovascular variables. Coronary flow was recorded by telemetry. Physiologic data were processed and analyzed by analog and digital computers. By these methods the physiologic response to altitude hypoxia, carbon monoxide, hypercapnia, acceleration, exercise, and the interaction of altitude hypoxia and carbon monoxide were described. The effects of some of these stresses on the heart and coronary circulation are discussed.

  19. Tuning of nanoparticle biological functionality through controlled surface chemistry and characterisation at the bioconjugated nanoparticle surface

    Science.gov (United States)

    Hristov, Delyan R.; Rocks, Louise; Kelly, Philip M.; Thomas, Steffi S.; Pitek, Andrzej S.; Verderio, Paolo; Mahon, Eugene; Dawson, Kenneth A.

    2015-12-01

    We have used a silica - PEG based bionanoconjugate synthetic scheme to study the subtle connection between cell receptor specific recognition and architecture of surface functionalization chemistry. Extensive physicochemical characterization of the grafted architecture is capable of capturing significant levels of detail of both the linker and grafted organization, allowing for improved reproducibility and ultimately insight into biological functionality. Our data suggest that scaffold details, propagating PEG layer architecture effects, determine not only the rate of uptake of conjugated nanoparticles into cells but also, more significantly, the specificity of pathways via which uptake occurs.

  20. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth.

    Directory of Open Access Journals (Sweden)

    Timothy G Bromage

    Full Text Available The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the

  1. The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth.

    Science.gov (United States)

    Bromage, Timothy G; Idaghdour, Youssef; Lacruz, Rodrigo S; Crenshaw, Thomas D; Ovsiy, Olexandra; Rotter, Björn; Hoffmeier, Klaus; Schrenk, Friedemann

    2016-01-01

    The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien) chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA) drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the biological bases that

  2. Strategies for quantifying C60 fullerenes in environmental and biological samples and implications for studies in environmental health and ecotoxicology

    OpenAIRE

    Pycke, Benny F. G.; Benn, Troy M.; Herckes, Pierre; Westerhoff, Paul; Halden, Rolf U.

    2011-01-01

    Fullerenes are sphere-like molecules with unique physico-chemical properties, which render them of particular interest in biomedical research, consumer products and industrial applications. Human and environmental exposure to fullerenes is not a new phenomenon, due to a long history of hydrocarbon-combustion sources, and will only increase in the future, as incorporation of fullerenes into consumer products becomes more widespread for use as anti-aging, anti-bacterial or anti-apoptotic agents.

  3. Symptoms, ventilatory function, and environmental exposures in Portland cement workers.

    OpenAIRE

    Abrons, H L; Petersen, M R; Sanderson, W T; Engelberg, A L; Harber, P

    1988-01-01

    Data on respiratory symptoms and pulmonary function were obtained for 2736 Portland cement plant workers and 755 controls. Personal dust samples contained a geometric mean concentration of 0.57 mg/m3 for respirable dust and 2.90 mg/m3 for total dust. Cement workers and controls had similar prevalences of symptoms, except that 5.4% of the cement workers had dyspnoea compared with 2.7% of the controls. The mean pulmonary function indices were similar for the two groups. Among cement plant worke...

  4. Danish consumers' attitudes to the functional and environmental characteristics of food packaging

    OpenAIRE

    Bech-Larsen, Tino

    1996-01-01

    Executive summary The purpose of the studies presented in the paper is to research different aspects of Danish consumers' views about the functional and environmental consequences of packaging, as well as to study cognitive barriers that can prevent consumer attitudes to environmental consequences of food packaging to influence the buying of food products. The results of these studies will be employed to consider whether and how to influence Danish consumers to buy products with environmental...

  5. Effects of wastewater effluent discharge and treatment facility upgrades on environmental and biological conditions of Indian Creek, Johnson County, Kansas, June 2004 through June 2013

    Science.gov (United States)

    Graham, Jennifer L.; Stone, Mandy L.; Rasmussen, Teresa J.; Foster, Guy M.; Poulton, Barry C.; Paxson, Chelsea R.; Harris, Theodore D.

    2014-01-01

    Indian Creek is one of the most urban drainage basins in Johnson County, Kansas, and environmental and biological conditions of the creek are affected by contaminants from point and other urban sources. The Johnson County Douglas L. Smith Middle Basin (hereafter referred to as the “Middle Basin”) and Tomahawk Creek Wastewater Treatment Facilities (WWTFs) discharge to Indian Creek. In summer 2010, upgrades were completed to increase capacity and include biological nutrient removal at the Middle Basin facility. There have been no recent infrastructure changes at the Tomahawk Creek facility; however, during 2009, chemically enhanced primary treatment was added to the treatment process for better process settling before disinfection and discharge with the added effect of enhanced phosphorus removal. The U.S. Geological Survey, in cooperation with Johnson County Wastewater, assessed the effects of wastewater effluent on environmental and biological conditions of Indian Creek by comparing two upstream sites to four sites located downstream from the WWTFs using data collected during June 2004 through June 2013. Environmental conditions were evaluated using previously and newly collected discrete and continuous data and were compared with an assessment of biological community composition and ecosystem function along the upstream-downstream gradient. This study improves the understanding of the effects of wastewater effluent on stream-water and streambed sediment quality, biological community composition, and ecosystem function in urban areas. After the addition of biological nutrient removal to the Middle Basin WWTF in 2010, annual mean total nitrogen concentrations in effluent decreased by 46 percent, but still exceeded the National Pollutant Discharge Elimination System (NPDES) wastewater effluent permit concentration goal of 8.0 milligrams per liter (mg/L); however, the NPDES wastewater effluent permit total phosphorus concentration goal of 1.5 mg/L or less was

  6. Distribution of functional traits in subtropical trees across environmental and forest use gradients

    Science.gov (United States)

    Blundo, Cecilia; Malizia, Lucio R.; González-Espinosa, Mario

    2015-11-01

    The relationship between functional traits and environmental factors contribute to understanding community structure and predicting which species will be able to elude environmental filters in different habitats. We selected 10 functional traits related to morphology, demography and regeneration niche in 54 subtropical premontane tree species to describe their main axes of functional differentiation. We derived species traits, environmental variables and species abundance data from 20 1-ha permanent plots established in a seasonal subtropical premontane forest in northwestern Argentina. We analyzed the relationship between species functional traits and environmental factors through RLQ and fourth-corner analyzes. We found an axis of structural differentiation that segregates understory from canopy species, and an axis of functional differentiation that segregates species that maximize resource acquisition from those that promote resource conservation. Environmental and forest use gradients operate hierarchically over subtropical premontane tree species influencing the distribution of demographic and morphological traits. The interaction between climatic and topographic factors influences the distribution of species functional traits at the regional scale. In addition, the history of forest use seems to operate at the landscape scale and explains the distribution of species traits reflecting a trade-off between resource acquisition and resource conservation strategies in secondary forests across different successional stages. Our results support the idea that functional traits may be used to analyze community structure and dynamics through niche differentiation and environmental filtering processes.

  7. 75 FR 69396 - Availability of an Environmental Assessment for a Biological Control Agent for Arundo donax

    Science.gov (United States)

    2010-11-12

    ... the control of Arundo donax (giant reed, Carrizo cane). The environmental assessment considers the..., prescribed fires, biomass removal, and other methods. However, these management measures are...

  8. Hubs of knowledge: using the functional link structure in Biozon to mine for biologically significant entities

    Directory of Open Access Journals (Sweden)

    Isganitis Timothy

    2006-02-01

    Full Text Available Abstract Background Existing biological databases support a variety of queries such as keyword or definition search. However, they do not provide any measure of relevance for the instances reported, and result sets are usually sorted arbitrarily. Results We describe a system that builds upon the complex infrastructure of the Biozon database and applies methods similar to those of Google to rank documents that match queries. We explore different prominence models and study the spectral properties of the corresponding data graphs. We evaluate the information content of principal and non-principal eigenspaces, and test various scoring functions which combine contributions from multiple eigenspaces. We also test the effect of similarity data and other variations which are unique to the biological knowledge domain on the quality of the results. Query result sets are assessed using a probabilistic approach that measures the significance of coherence between directly connected nodes in the data graph. This model allows us, for the first time, to compare different prominence models quantitatively and effectively and to observe unique trends. Conclusion Our tests show that the ranked query results outperform unsorted results with respect to our significance measure and the top ranked entities are typically linked to many other biological entities. Our study resulted in a working ranking system of biological entities that was integrated into Biozon at http://biozon.org.

  9. 2012 best practices for repositories collection, storage, retrieval, and distribution of biological materials for research international society for biological and environmental repositories.

    Science.gov (United States)

    2012-04-01

    Third Edition [Formula: see text] [Box: see text] Printed with permission from the International Society for Biological and Environmental Repositories (ISBER) © 2011 ISBER All Rights Reserved Editor-in-Chief Lori D. Campbell, PhD Associate Editors Fay Betsou, PhD Debra Leiolani Garcia, MPA Judith G. Giri, PhD Karen E. Pitt, PhD Rebecca S. Pugh, MS Katherine C. Sexton, MBA Amy P.N. Skubitz, PhD Stella B. Somiari, PhD Individual Contributors to the Third Edition Jonas Astrin, Susan Baker, Thomas J. Barr, Erica Benson, Mark Cada, Lori Campbell, Antonio Hugo Jose Froes Marques Campos, David Carpentieri, Omoshile Clement, Domenico Coppola, Yvonne De Souza, Paul Fearn, Kelly Feil, Debra Garcia, Judith Giri, William E. Grizzle, Kathleen Groover, Keith Harding, Edward Kaercher, Joseph Kessler, Sarah Loud, Hannah Maynor, Kevin McCluskey, Kevin Meagher, Cheryl Michels, Lisa Miranda, Judy Muller-Cohn, Rolf Muller, James O'Sullivan, Karen Pitt, Rebecca Pugh, Rivka Ravid, Katherine Sexton, Ricardo Luis A. Silva, Frank Simione, Amy Skubitz, Stella Somiari, Frans van der Horst, Gavin Welch, Andy Zaayenga 2012 Best Practices for Repositories: Collection, Storage, Retrieval and Distribution of Biological Materials for Research INTERNATIONAL SOCIETY FOR BIOLOGICAL AND ENVIRONMENTAL REPOSITORIES (ISBER) INTRODUCTION T he availability of high quality biological and environmental specimens for research purposes requires the development of standardized methods for collection, long-term storage, retrieval and distribution of specimens that will enable their future use. Sharing successful strategies for accomplishing this goal is one of the driving forces for the International Society for Biological and Environmental Repositories (ISBER). For more information about ISBER see www.isber.org . ISBER's Best Practices for Repositories (Best Practices) reflect the collective experience of its members and has received broad input from other repository professionals. Throughout this document

  10. Applications of post-translational modifications of FoxO family proteins in biological functions

    Institute of Scientific and Technical Information of China (English)

    Ying Zhao; Yachen Wang; Wei-Guo Zhu

    2011-01-01

    The functions of the FoxO family proteins, in particular their transcriptional activities, are modulated by post-translational modifications (PTMs), including phosphorylation, acetylation, ubiquitination, methylation and glycosylation. These PTMs occur in response to different cellular stresses, which in turn regulate the subcellular localization of FoxO family proteins, as well as their half-life, DNA binding, transcriptional activity and ability to interact with other cellular proteins. In this review, we summarize the role of PTMs of FoxO family proteins in linking their biological and functional relevance with various diseases.%The functions of the FoxO family proteins,in particular their transcriptional activities,are modulated by post-translational modifications (PTMs),including phosphorylation,acetylation,ubiquitination,methylation and glycosylation.These PTMs occur in response to different cellular stresses,which in turn regulate the subceilular localization of FoxO family proteins,as well as their half-life,DNA binding,transcriptional activity and ability to interact with other cellular proteins.In this review,we summarize the role of PTMs of FoxO family proteins in linking their biological and functional relevance with various diseases.

  11. Recent advances in alveolar biology: Evolution and function of alveolar proteins☆

    OpenAIRE

    Orgeig, Sandra; Hiemstra, Pieter S.; Edwin J A Veldhuizen; Casals, Cristina; Clark, Howard W.; Haczku, Angela; Knudsen, Lars; Possmayer, Fred

    2010-01-01

    This review is focused on the evolution and function of alveolar proteins. The lung faces physical and environmental challenges, due to changing pressures/volumes and foreign pathogens, respectively. The pulmonary surfactant system is integral in protecting the lung from these challenges via two groups of surfactant proteins – the small molecular weight hydrophobic SPs, SP-B and -C, that regulate interfacial adsorption of the lipids, and the large hydrophilic SPs, SP-A and -D, which are surfa...

  12. Applications of NMR-based metabolomics in biological and environmental research

    Science.gov (United States)

    As a complimentary tool to other omics platforms, metabolomics is increasingly being used by biologists to study the dynamic response of biological systems (cells, tissues, or whole organisms) under diverse physiological or pathological conditions. Metabolomics deals with the qu...

  13. Environmental Contaminants Monitoring in Selected Wetlands of Wyoming: Biologically Active Elements Study

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — Sediment, water and biota were collected from selected wetlands in Wyoming for the Biologically Active Elements (BAE) Study in 1988, 1989 and 1990 to identify...

  14. Subjective Theories of Indonesian Agronomy and Biology Teacher Students on Environmental Commons Dilemmas

    Science.gov (United States)

    Koch, Sebastian; Barkmann, Jan; Sundawati, Leti; Bogeholz, Susanne

    2013-01-01

    Fostering the cognitive skills to analyse environmental "commons dilemmas" is an urgent task of environmental education globally. Commons dilemmas are characterised by structural incentives to overexploit a natural resource; their solution is particularly pressing in threatened biodiversity "hotspot" areas. Solutions to these dilemmas require…

  15. An integrated approach to the preventive conservation of cultural heritage: indoor biological environmental monitoring

    OpenAIRE

    Cesira Pasquarella; Giovanna Pasquariello; Carla Balocco; Elisa Saccani; Manuela Ugolotti; Oriana Maggi; Roberto Albertini

    2013-01-01

    In recent times has emerged a particular focus on the study of methods and techniques of investigation and prevention of biological risk in the area of cultural properties. The importance of preventing biological risk in cultural heritage has been laid out by the Italian Ministry of Cultural Heritage in the Atto di indirizzo sui criteri tecnico-scientifici e sugli standard di funzionamento e sviluppo dei musei (Guidelines on technical and scientific criteria, and operating and development sta...

  16. Applications of synchrotron {mu}-XRF to study the distribution of biologically important elements in different environmental matrices: A review

    Energy Technology Data Exchange (ETDEWEB)

    Majumdar, Sanghamitra; Peralta-Videa, Jose R. [Chemistry Department, University of Texas at El Paso, 500 West University Ave. El Paso, TX 79968 (United States); Castillo-Michel, Hiram [European Synchrotron Radiation Facility, B.P. 220, 38043 Grenoble, Cedex (France); Hong Jie [Environmental Science and Engineering PhD Program, University of Texas at El Paso, 500 West University Ave. El Paso, TX 79968 (United States); Rico, Cyren M. [Chemistry Department, University of Texas at El Paso, 500 West University Ave. El Paso, TX 79968 (United States); Gardea-Torresdey, Jorge L., E-mail: jgardea@utep.edu [Chemistry Department, University of Texas at El Paso, 500 West University Ave. El Paso, TX 79968 (United States); Environmental Science and Engineering PhD Program, University of Texas at El Paso, 500 West University Ave. El Paso, TX 79968 (United States)

    2012-11-28

    Highlights: Black-Right-Pointing-Pointer {mu}-SXRF is a state-of-the-art technique to map biologically important elements. Black-Right-Pointing-Pointer {mu}-SXRF allows in situ mapping of the elements at nanometer to sub-micrometer scale. Black-Right-Pointing-Pointer {mu}-SXRF can be used in plant, soil, microbe and particulate matter samples. Black-Right-Pointing-Pointer {mu}-SXRF is coupled with other synchrotron techniques to study chemical speciation. - Abstract: Environmental matrices including soils, sediments, and living organisms are reservoirs of several essential as well as non-essential elements. Accurate qualitative and quantitative information on the distribution and interaction of biologically significant elements is vital to understand the role of these elements in environmental and biological samples. Synchrotron micro-X-ray fluorescence ({mu}-SXRF) allows in situ mapping of biologically important elements at nanometer to sub-micrometer scale with high sensitivity, negligible sample damage and enable tuning of the incident energy as desired. Beamlines in the synchrotron facilities are rapidly increasing their analytical versatility in terms of focusing optics, detector technologies, incident energy, and sample environment. Although extremely competitive, it is now feasible to find stations offering complimentary techniques like micro-X-ray diffraction ({mu}-XRD) and micro-X-ray absorption spectroscopy ({mu}-XAS) that will allow a more complete characterization of complex matrices. This review includes the most recent literature on the emerging applications and challenges of {mu}-SXRF in studying the distribution of biologically important elements and manufactured nanoparticles in soils, sediments, plants, and microbes. The advantages of using {mu}-SXRF and complimentary techniques in contrast to conventional techniques used for the respective studies are discussed.

  17. Potential environmental functions of widespread, abundant, uncultured marine archaea

    Science.gov (United States)

    Lloyd, K. G.; Schreiber, L.; Petersen, D. G.; Schramm, A.; Jorgensen, B.

    2012-12-01

    The vast majority of marine subsurface microorganisms are uncultivated, and therefore have unknown metabolisms. Much of the prokaryotes present in the marine subsurface are archaea, and, in turn, much of the archaea fall into the Miscellaneous Crenarchaeotal Group. These organisms are widely distributed globally and are phylogenetically diverse, comprising 17 distinct subgroups, defined by 16S rRNA genes (Kubo et al. 2012). The subgroups do not seem to have any well-defined environmental distribution (i.e., they are all present in different types of marine and terrestrial environments). However, the abundance of sequences from a certain environment type differs among subgroups, and may provide clues to their role in these environments. We sequenced the genome of a single cell of MCG extracted directly from marine sediments. Although coverage was low (~30%), the data quality was high. Conserved genes show that MCG is deeply branching within the newly named "Thaumarchaeota", and contains a complete pathway for the degradation or extracellular proteins. A further search through metagenomic data shows that this process may be widespread in marine sediments. We hypothesize that MCG archaea may be important in anaerobic protein decomposition in marine sediments. Reference Kubo et al., 2012. Archaea of the Miscellaneous Crenarchaeotal Group (MCG) are abundant, diverse, and widespread in marine sediments. ISME Journal, in press, doi:10.1038/ismej.2012.37.

  18. Functional results after repair of large hiatal hernia by use of a biologic mesh

    Directory of Open Access Journals (Sweden)

    Filimon eAntonakis

    2016-03-01

    Full Text Available Background: The aim of this observational study is to analyze the results of patients with large hiatal hernia and upside-down stomach after surgical closure with a biologic mesh (Permacol®, Covidien, Neustadt an der Donau, Germany. Biologic mesh is used to prevent long-term detrimental effects of artificial meshes and to reduce recurrence rates. Methods: A total of 13 patients with a large hiatal hernia and endothoracic stomach, who underwent surgery between 2010 and 2014, were included. Interviews and upper endoscopy were conducted to determine recurrence, lifestyle restrictions and current complaints. Results: After a mean follow-up of 26+18 months (range 3-58 months 10 patients (three men, mean age 73+13, range 26-81 years were evaluated. A small recurrent axial hernia was found in one patient postoperatively. Dysphagia was the most common complaint (four cases, while in one case the problem was solved after endoscopic dilatation. In three cases bloat and postprandial pain were documented. In one case explantation of the mesh was necessary due to mesh migration and painful adhesions. In one further case with gastroparesis pyloroplasty was performed without success.Conclusion: Recurrence was rare after hernia repair with the biologic mesh Permacol®. Dysphagia, gas bloat and intraabdominal pain were frequent complaints. Despite the small number of patients it can be concluded that a biologic mesh may be an alternative to synthetic meshes to reduce recurrences. Long-term results should be studied in the future in order to assess the potential of biologic meshes to preserve esophageal function as well. This is important since artificial meshes are known to erode the esophagus after 5–10 years.

  19. A Gaussian mixture model based cost function for parameter estimation of chaotic biological systems

    Science.gov (United States)

    Shekofteh, Yasser; Jafari, Sajad; Sprott, Julien Clinton; Hashemi Golpayegani, S. Mohammad Reza; Almasganj, Farshad

    2015-02-01

    As we know, many biological systems such as neurons or the heart can exhibit chaotic behavior. Conventional methods for parameter estimation in models of these systems have some limitations caused by sensitivity to initial conditions. In this paper, a novel cost function is proposed to overcome those limitations by building a statistical model on the distribution of the real system attractor in state space. This cost function is defined by the use of a likelihood score in a Gaussian mixture model (GMM) which is fitted to the observed attractor generated by the real system. Using that learned GMM, a similarity score can be defined by the computed likelihood score of the model time series. We have applied the proposed method to the parameter estimation of two important biological systems, a neuron and a cardiac pacemaker, which show chaotic behavior. Some simulated experiments are given to verify the usefulness of the proposed approach in clean and noisy conditions. The results show the adequacy of the proposed cost function.

  20. Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions

    Directory of Open Access Journals (Sweden)

    Werner Mark

    2008-08-01

    Full Text Available Abstract Background Variations in the influenza Hemagglutinin protein contributes to antigenic drift resulting in decreased efficiency of seasonal influenza vaccines and escape from host immune response. We performed an in silico study to determine characteristics of novel variable and conserved motifs in the Hemagglutinin protein from previously reported H3N2 strains isolated from Hong Kong from 1968–1999 to predict viral motifs involved in significant biological functions. Results 14 MEME blocks were generated and comparative analysis of the MEME blocks identified blocks 1, 2, 3 and 7 to correlate with several biological functions. Analysis of the different Hemagglutinin sequences elucidated that the single block 7 has the highest frequency of amino acid substitution and the highest number of co-mutating pairs. MEME 2 showed intermediate variability and MEME 1 was the most conserved. Interestingly, MEME blocks 2 and 7 had the highest incidence of potential post-translational modifications sites including phosphorylation sites, ASN glycosylation motifs and N-myristylation sites. Similarly, these 2 blocks overlap with previously identified antigenic sites and receptor binding sites. Conclusion Our study identifies motifs in the Hemagglutinin protein with different amino acid substitution frequencies over a 31 years period, and derives relevant functional characteristics by correlation of these motifs with potential post-translational modifications sites, antigenic and receptor binding sites.

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

    Science.gov (United States)

    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

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

    Science.gov (United States)

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

    2012-03-05

    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).

  3. Supercritical Fluid Extraction and Ultra Performance Liquid Chromatography of Respiratory Quinones for Microbial Community Analysis in Environmental and Biological Samples

    Directory of Open Access Journals (Sweden)

    Koichi Fujie

    2012-03-01

    Full Text Available 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 (scCO2 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.

  4. State of the art of environmentally friendly sample preparation approaches for determination of PBDEs and metabolites in environmental and biological samples: A critical review.

    Science.gov (United States)

    Berton, Paula; Lana, Nerina B; Ríos, Juan M; García-Reyes, Juan F; Altamirano, Jorgelina C

    2016-01-28

    Green chemistry principles for developing methodologies have gained attention in analytical chemistry in recent decades. A growing number of analytical techniques have been proposed for determination of organic persistent pollutants in environmental and biological samples. In this light, the current review aims to present state-of-the-art sample preparation approaches based on green analytical principles proposed for the determination of polybrominated diphenyl ethers (PBDEs) and metabolites (OH-PBDEs and MeO-PBDEs) in environmental and biological samples. Approaches to lower the solvent consumption and accelerate the extraction, such as pressurized liquid extraction, microwave-assisted extraction, and ultrasound-assisted extraction, are discussed in this review. Special attention is paid to miniaturized sample preparation methodologies and strategies proposed to reduce organic solvent consumption. Additionally, extraction techniques based on alternative solvents (surfactants, supercritical fluids, or ionic liquids) are also commented in this work, even though these are scarcely used for determination of PBDEs. In addition to liquid-based extraction techniques, solid-based analytical techniques are also addressed. The development of greener, faster and simpler sample preparation approaches has increased in recent years (2003-2013). Among green extraction techniques, those based on the liquid phase predominate over those based on the solid phase (71% vs. 29%, respectively). For solid samples, solvent assisted extraction techniques are preferred for leaching of PBDEs, and liquid phase microextraction techniques are mostly used for liquid samples. Likewise, green characteristics of the instrumental analysis used after the extraction and clean-up steps are briefly discussed.

  5. Integration of multiscale dendritic spine structure and function data into systems biology models

    Directory of Open Access Journals (Sweden)

    James J Mancuso

    2014-11-01

    Full Text Available Comprising 1011 neurons with 1014 synaptic connections the human brain is the ultimate systems biology puzzle. An increasing body of evidence highlights the observation that changes in brain function, both normal and pathological, consistently correlate with dynamic changes in neuronal anatomy. Anatomical changes occur on a full range of scales from the trafficking of individual proteins, to alterations in synaptic morphology both individually and on a systems level, to reductions in long distance connectivity and brain volume. The major sites of contact for synapsing neurons are dendritic spines, which provide an excellent metric for the number and strength of signaling connections between elements of functional neuronal circuits. A comprehensive model of anatomical changes and their functional consequences would be a holy grail for the field of systems neuroscience but its realization appears far on the horizon. Various imaging technologies have advanced to allow for multi-scale visualization of brain plasticity and pathology, but computational analysis of the massive big data sets involved forms the bottleneck toward the creation of multiscale models of brain structure and function. While a full accounting of techniques and progress toward a comprehensive model of brain anatomy and function is beyond the scope of this or any other single paper, this review serves to highlight the opportunities for analysis of neuronal spine anatomy and function provided by new imaging technologies and the high-throughput application of older technologies while surveying the strengths and weaknesses of currently available computational analytical tools and room for future improvement.

  6. Functional Effects of Delivering Human Mesenchymal Stem Cell-Seeded Biological Sutures to an Infarcted Heart.

    Science.gov (United States)

    Hansen, Katrina J; Favreau, John T; Guyette, Jacques P; Tao, Ze-Wei; Coffin, Spencer T; Cunha-Gavidia, Anny; D'Amore, Brian; Perreault, Luke R; Fitzpatrick, John P; DeMartino, Angelica; Gaudette, Glenn R

    2016-01-01

    Stem cell therapy has the potential to improve cardiac function after myocardial infarction (MI); however, existing methods to deliver cells to the myocardium, including intramyocardial injection, suffer from low engraftment rates. In this study, we used a rat model of acute MI to assess the effects of human mesenchymal stem cell (hMSC)-seeded fibrin biological sutures on cardiac function at 1 week after implant. Biological sutures were seeded with quantum dot (Qdot)-loaded hMSCs for 24 h before implantation. At 1 week postinfarct, the heart was imaged to assess mechanical function in the infarct region. Regional parameters assessed were regional stroke work (RSW) and systolic area of contraction (SAC) and global parameters derived from the pressure waveform. MI (n = 6) significantly decreased RSW (0.026 ± 0.011) and SAC (0.022 ± 0.015) when compared with sham operation (RSW: 0.141 ± 0.009; SAC: 0.166 ± 0.005, n = 6) (p  0.05); however, there was a trend toward improved function with the addition of either unseeded or seeded biological suture. Histology demonstrated that Qdot-loaded hMSCs remained present in the infarcted myocardium after 1 week. Analysis of serial sections of Masson's trichrome staining revealed that the greatest infarct size was in the infarct group (7.0% ± 2.2%), where unseeded (3.8% ± 0.6%) and hMSC-seeded (3.7% ± 0.8%) suture groups maintained similar infarct sizes. Furthermore, the remaining suture area was significantly decreased in the unseeded group compared with that in the hMSC-seeded group (p < 0.05). This study demonstrated that hMSC-seeded biological sutures are a method to deliver cells to the infarcted myocardium and have treatment potential. PMID:27610271

  7. An expanded role for microbial physiology in metabolic engineering and functional genomics: moving towards systems biology

    DEFF Research Database (Denmark)

    Nielsen, Jens; Olsson, Lisbeth

    2002-01-01

    . With the progress in molecular biology it has become possible to optimize industrial fermentations through introduction of directed genetic modification - an approach referred to as metabolic engineering. Furthermore, as a consequence of large sequencing programs the complete genomic sequence has become available......Microbial physiology has traditionally played a very important role in both fundamental research and in industrial applications of microorganisms. The classical approach in microbial physiology has been to analyze the role of individual components (genes or proteins) in the overall cell function...

  8. Late-stage functionalization of biologically active heterocycles through photoredox catalysis.

    Science.gov (United States)

    Dirocco, Daniel A; Dykstra, Kevin; Krska, Shane; Vachal, Petr; Conway, Donald V; Tudge, Matthew

    2014-05-01

    The direct CH functionalization of heterocycles has become an increasingly valuable tool in modern drug discovery. However, the introduction of small alkyl groups, such as methyl, by this method has not been realized in the context of complex molecule synthesis since existing methods rely on the use of strong oxidants and elevated temperatures to generate the requisite radical species. Herein, we report the use of stable organic peroxides activated by visible-light photoredox catalysis to achieve the direct methyl-, ethyl-, and cyclopropylation of a variety of biologically active heterocycles. The simple protocol, mild reaction conditions, and unique tolerability of this method make it an important tool for drug discovery.

  9. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid

    Science.gov (United States)

    Ruder, Warren C.; Hsu, Chia-Pei D.; Edelman, Brent D.; Schwartz, Russell; LeDuc, Philip R.

    2012-08-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe3O4) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zero-field. The engineered self-assembly process we describe here provides an approach for the creation of ordered magnetic structures that could impact fields ranging from micro-electro-mechanical systems development to magnetic imaging of biological structures.

  10. Functional knowledge transfer for high-accuracy prediction of under-studied biological processes.

    Directory of Open Access Journals (Sweden)

    Christopher Y Park

    Full Text Available A key challenge in genetics is identifying the functional roles of genes in pathways. Numerous functional genomics techniques (e.g. machine learning that predict protein function have been developed to address this question. These methods generally build from existing annotations of genes to pathways and thus are often unable to identify additional genes participating in processes that are not already well studied. Many of these processes are well studied in some organism, but not necessarily in an investigator's organism of interest. Sequence-based search methods (e.g. BLAST have been used to transfer such annotation information between organisms. We demonstrate that functional genomics can complement traditional sequence similarity to improve the transfer of gene annotations between organisms. Our method transfers annotations only when functionally appropriate as determined by genomic data and can be used with any prediction algorithm to combine transferred gene function knowledge with organism-specific high-throughput data to enable accurate function prediction. We show that diverse state-of-art machine learning algorithms leveraging functional knowledge transfer (FKT dramatically improve their accuracy in predicting gene-pathway membership, particularly for processes with little experimental knowledge in an organism. We also show that our method compares favorably to annotation transfer by sequence similarity. Next, we deploy FKT with state-of-the-art SVM classifier to predict novel genes to 11,000 biological processes across six diverse organisms and expand the coverage of accurate function predictions to processes that are often ignored because of a dearth of annotated genes in an organism. Finally, we perform in vivo experimental investigation in Danio rerio and confirm the regulatory role of our top predicted novel gene, wnt5b, in leftward cell migration during heart development. FKT is immediately applicable to many bioinformatics

  11. Biological methylation of inorganic mercury by Saccharomyces cerevisiae - a possible environmental process

    Energy Technology Data Exchange (ETDEWEB)

    Reisinger, K.; Stoeppler, M.; Nuernberg, H.W.

    1983-11-01

    The biological methylation of inorganic mercury by S-adenosylmethione (SAM) was investigated by incubation experiments with Saccharomyces cerevisae (''bakers' yeast''). The methyl donor (methionine) and the acceptor (Hg/sup 2 +/ as HgCl/sub 2/) were also applied in their labelled form (double labelling). Methylmercury as a result of a possibly biological methyl group transfer could not be detected. As reaction product only small amounts (0.01per mille yield) of elemental mercury (Hg/sup 0/) were found, while the overwhelming amount of HgCl/sub 2/ had not reacted.

  12. The origin of neutron biological effectiveness as a function of energy

    Science.gov (United States)

    Baiocco, G.; Barbieri, S.; Babini, G.; Morini, J.; Alloni, D.; Friedland, W.; Kundrát, P.; Schmitt, E.; Puchalska, M.; Sihver, L.; Ottolenghi, A.

    2016-01-01

    The understanding of the impact of radiation quality in early and late responses of biological targets to ionizing radiation exposure necessarily grounds on the results of mechanistic studies starting from physical interactions. This is particularly true when, already at the physical stage, the radiation field is mixed, as it is the case for neutron exposure. Neutron Relative Biological Effectiveness (RBE) is energy dependent, maximal for energies ~1 MeV, varying significantly among different experiments. The aim of this work is to shed light on neutron biological effectiveness as a function of field characteristics, with a comprehensive modeling approach: this brings together transport calculations of neutrons through matter (with the code PHITS) and the predictive power of the biophysical track structure code PARTRAC in terms of DNA damage evaluation. Two different energy dependent neutron RBE models are proposed: the first is phenomenological and based only on the characterization of linear energy transfer on a microscopic scale; the second is purely ab-initio and based on the induction of complex DNA damage. Results for the two models are compared and found in good qualitative agreement with current standards for radiation protection factors, which are agreed upon on the basis of RBE data. PMID:27654349

  13. Prediction of glass durability as a function of environmental conditions

    International Nuclear Information System (INIS)

    The author reports on thermodynamic model of glass durability applied to natural, ancient, and nuclear waste glasses. The durabilities of over 150 different natural and man-made glasses, including actual ancient Roman and Islamic glasses (Jalame ca. 350 A. D., Nishapur 10-11th century A. D., and Gorgon 9-11th century A.D.), have been compared. Glass durability had been shown to be a function of the thermodynamic hydration free energy. Δ Ghyd, which can be calculated from glass composition and solution pH. Using this approach, the durability of the most durable nuclear waste glasses examined was ≅106 years by comparison with the durability of the natural basalts of ≅106 years. The least durable waste glass formulations were comparable in durability to the most durable simulated medieval window glasses of ≅103 years. In this manner, the durability of nuclear waste glasses has been interpolated to be ≅106 years and no less than 103 years. Hydration thermodynamics are shown to be applicable to the dissolution of glass in various natural environments. Groundwater-glass interactions relative to geologic disposal of nuclear waste, hydration rind dating of obsidians, and/or other archeological studies can be modeled, e.g. the relative durabilities of six simulated medieval window glasses have been correctly predicted for both laboratory (one month) and burial (5 year) experiments

  14. Desenvolvimento motor e funcional em crianças nascidas pré-termo e a termo: influência de fatores de risco biológico e ambiental Desarrollo motor y funcional en niños nacidos pretérmino y a término: influencia de factores de riesgo biológico y ambiental Motor and functional development in infants born preterm and full term: influence of biological and environmental risk factors

    Directory of Open Access Journals (Sweden)

    Edifrance Sá de Souza

    2012-12-01

    adquisición de la marcha en el grupo pretérmino (p=0,005, aunque no se haya encontrado diferencia significativa entre los grupos en la AIMS a los 12 (p=0,187 y a los 15 meses (p=0,80. A los 18 meses se encontraron diferencias significativas en el desarrollo motor grueso (pOBJECTIVE: To compare motor development in preterm and full term infants from 12 to 18 months and to investigate the relationship between functional performance and quantity and quality of environmental stimulation. METHODS: Quantitative, exploratory and longitudinal study, which included 30 preterm (gestational age: 30.0±2.3 weeks and birth weight: 1178±193g and 30 full term infants (39±1.3 weeks and 3270±400g. Motor development was evaluated by the Alberta Infant Motor Scale and the Peabody Developmental Motor Scales. Home environment was assessed by the Home Observation Measurement of the Environment. The Pediatric Evaluation of Disability Inventory was used to examine functional abilities. RESULTS: The preterm group presented slower gait acquisition (p=0.005, although no significant differences between groups were found in the Alberta Infant Motor Scale at 12 (p=0.187 and 15 months (p=0.80. At 18 months, significant differences were found in gross (p<0.001 and fine (p=0.001 motor development and in functional abilities, with a better performance of the full term group. There were differences between groups in the Home Observation Measurement of the Environment inventory (p=0.008. CONCLUSIONS: Performance differences between groups increased from 12 to 18 months, and environmental factors might have enhanced the effects of biological risks. Developmental follow-up programs should focus on aspects of the environment where the child lives.

  15. Current role of NAA in biological and health-related environmental studies as exemplified by programs of the IAEA

    International Nuclear Information System (INIS)

    The International Atomic Energy Agency (IAEA) has many projects and activities supporting the utilization of nuclear research reactors for neutron activation analysis (NAA). Globally the number of operating nuclear research reactors has been in decline since about 1975. This contrasts with the situation in developing countries where the numbers show a modest increase over the same period. This paper reviews the current status of NAA as seen from the particular perspective of IAEA programs involving studies of biological and environmental specimens. Some of the areas in which NAA is maintaining its role as a competitive technique are briefly reviewed. (author)

  16. [Plasma antioxidant activity--a test for impaired biological functions of endoecology, exotrophy, and inflammation reactions].

    Science.gov (United States)

    Titov, V N; Krylin, V V; Dmitriev, V A; Iashin, Ia I

    2010-07-01

    The authors discuss the diagnostic value of a test for total serum antioxidant activity determined by an electrochemistry method on a liquid chromatograph (without a column), by using an amperometric detector, as well as the composition of the endogenously synthesized hydrophilic and hydrophobic acceptors of reactive oxygen species (ROS). Uric acid is a major hydrophilic acceptor of ROS; monoenic oleic fatty acid acts as its major lipophilic acceptor. The constant determined by the authors for of 03 oleic acid oxidation during automatic titration in the organic medium is an order of magnitude higher than that for alpha-tocopherol, beta-carotene and linoleic fatty acid; its concentration is also an order of magnitude higher. In oxidative stress, the adrenal steroid hormone dehydroepiandrosterone initiates oleic acid synthesis via expression of palmitoyl elongase and steatoryl desaturase. In early steps of phylogenesis in primates, spontaneous mutation resulted in ascorbic acid synthesis gene knockout; phylogenetically, further other mutation knocked out the gene encoding the synthesis of uricase and the conversion of uric acid to alantoin. In primates, uric acid became not only a catabolite of purine bases in vivo, but also the major endogenous hydrophilic acceptor of ROS. This philogenetic order makes it clear why the epithelium in the proximal nephron tubule entirely reabsorbs uric acid (a catabolite?) from primary urine and then secretes it again to urine depending on the impairment of biological functions of endoecology (the intercellular medium being contaminated with biological rubbish), the activation of a biological inflammatory reaction, the cellular production of ROS, and the reduction in serum total antioxidant activity. With each biological reaction, there was an increase in the blood content of uric acid as a hydrophilic acceptor of ROS, by actively lowering its secretion into urine. Uric acid is a diagnostic test of inflammation, or rather compensatory

  17. Environmental Learning Workshop: Lichen as Biological Indicator of Air Quality and Impact on Secondary Students' Performance

    Science.gov (United States)

    Samsudin, Mohd Wahid; Daik, Rusli; Abas, Azlan; Meerah, T. Subahan Mohd; Halim, Lilia

    2013-01-01

    In this study, the learning of science outside the classroom is believe to be an added value to science learning as well as it offers students to interact with the environment. This study presents data obtained from two days' workshop on Lichen as Biological Indicator for Air Quality. The aim of the workshop is for the students to gain an…

  18. The use of remote sensors to relate biological and physical indicators to environmental and public health problems

    Science.gov (United States)

    1972-01-01

    Relationships between biological, ecological and botanical structures, and disease organisms and their vectors which might be detected and measured by remote sensing are determined. In addition to the use of trees as indicators of disease or potential disease, an attempt is made to identify environmental factors such as soil moisture and soil and water temperatures as they relate to disease or health problems and may be detected by remote sensing. The following three diseases and one major health problem are examined: Malaria, Rocky Mountain spotted fever, Encephalitis and Red Tide. It is shown that no single species of vascular plant nor any one environmental factor can be used as the indicator of disease or health problems. Entire vegetation types, successional stages and combinations of factors must be used.

  19. Clustering of DNA words and biological function: a proof of principle.

    Science.gov (United States)

    Hackenberg, Michael; Rueda, Antonio; Carpena, Pedro; Bernaola-Galván, Pedro; Barturen, Guillermo; Oliver, José L

    2012-03-21

    Relevant words in literary texts (key words) are known to be clustered, while common words are randomly distributed. Given the clustered distribution of many functional genome elements, we hypothesize that the biological text per excellence, the DNA sequence, might behave in the same way: k-length words (k-mers) with a clear function may be spatially clustered along the one-dimensional chromosome sequence, while less-important, non-functional words may be randomly distributed. To explore this linguistic analogy, we calculate a clustering coefficient for each k-mer (k=2-9bp) in human and mouse chromosome sequences, then checking if clustered words are enriched in the functional part of the genome. First, we found a positive general trend relating clustering level and word enrichment within exons and Transcription Factor Binding Sites (TFBSs), while a much weaker relation exists for repeats, and no relation at all exists for introns. Second, we found that 38.45% of the 200 top-clustered 8-mers, but only 7.70% of the non-clustered words, are represented in known motif databases. Third, enrichment/depletion experiments show that highly clustered words are significantly enriched in exons and TFBSs, while they are depleted in introns and repetitive DNA. Considering exons and TFBSs together, 1417 (or 72.26%) in human and 1385 (or 72.97%) in mouse of the top-clustered 8-mers showed a statistically significant association to either exons or TFBSs, thus strongly supporting the link between word clustering and biological function. Lastly, we identified a subset of clustered, diagnostic words that are enriched in exons but depleted in introns, and therefore might help to discriminate between these two gene regions. The clustering of DNA words thus appears as a novel principle to detect functionality in genome sequences. As evolutionary conservation is not a prerequisite, the proof of principle described here may open new ways to detect species-specific functional DNA sequences

  20. Enzymes for ecdysteroid biosynthesis: their biological functions in insects and beyond.

    Science.gov (United States)

    Niwa, Ryusuke; Niwa, Yuko S

    2014-01-01

    Steroid hormones are responsible for the coordinated regulation of many aspects of biological processes in multicellular organisms. Since the last century, many studies have identified and characterized steroidogenic enzymes in vertebrates, including mammals. However, much less is known about invertebrate steroidogenic enzymes. In the last 15 years, a number of steroidogenic enzymes and their functions have been characterized in ecdysozoan animals, especially in the fruit fly Drosophila melanogaster. In this review, we summarize the latest knowledge of enzymes crucial for synthesizing ecdysteroids, the principal insect steroid hormones. We also discuss the functional conservation and diversity of ecdysteroidogenic enzymes in other insects and even non-insect species, such as nematodes, vertebrates, and lower eukaryotes.

  1. Automated methods of predicting the function of biological sequences using GO and BLAST

    Directory of Open Access Journals (Sweden)

    Baumann Ute

    2005-11-01

    Full Text Available Abstract Background With the exponential increase in genomic sequence data there is a need to develop automated approaches to deducing the biological functions of novel sequences with high accuracy. Our aim is to demonstrate how accuracy benchmarking can be used in a decision-making process evaluating competing designs of biological function predictors. We utilise the Gene Ontology, GO, a directed acyclic graph of functional terms, to annotate sequences with functional information describing their biological context. Initially we examine the effect on accuracy scores of increasing the allowed distance between predicted and a test set of curator assigned terms. Next we evaluate several annotator methods using accuracy benchmarking. Given an unannotated sequence we use the Basic Local Alignment Search Tool, BLAST, to find similar sequences that have already been assigned GO terms by curators. A number of methods were developed that utilise terms associated with the best five matching sequences. These methods were compared against a benchmark method of simply using terms associated with the best BLAST-matched sequence (best BLAST approach. Results The precision and recall of estimates increases rapidly as the amount of distance permitted between a predicted term and a correct term assignment increases. Accuracy benchmarking allows a comparison of annotation methods. A covering graph approach performs poorly, except where the term assignment rate is high. A term distance concordance approach has a similar accuracy to the best BLAST approach, demonstrating lower precision but higher recall. However, a discriminant function method has higher precision and recall than the best BLAST approach and other methods shown here. Conclusion Allowing term predictions to be counted correct if closely related to a correct term decreases the reliability of the accuracy score. As such we recommend using accuracy measures that require exact matching of predicted

  2. Differential Function of Lip Residues in the Mechanism and Biology of an Anthrax Hemophore

    Energy Technology Data Exchange (ETDEWEB)

    Ekworomadu, MarCia T.; Poor, Catherine B.; Owens, Cedric P.; Balderas, Miriam A.; Fabian, Marian; Olson, John S.; Murphy, Frank; Balkabasi, Erol; Honsa, Erin S.; He, Chuan; Goulding, Celia W.; Maresso, Anthony W. (Baylor); (UCI); (Cornell); (Rice); (UC)

    2014-10-02

    To replicate in mammalian hosts, bacterial pathogens must acquire iron. The majority of iron is coordinated to the protoporphyrin ring of heme, which is further bound to hemoglobin. Pathogenic bacteria utilize secreted hemophores to acquire heme from heme sources such as hemoglobin. Bacillus anthracis, the causative agent of anthrax disease, secretes two hemophores, IsdX1 and IsdX2, to acquire heme from host hemoglobin and enhance bacterial replication in iron-starved environments. Both proteins contain NEAr-iron Transporter (NEAT) domains, a conserved protein module that functions in heme acquisition in Gram-positive pathogens. Here, we report the structure of IsdX1, the first of a Gram-positive hemophore, with and without bound heme. Overall, IsdX1 forms an immunoglobin-like fold that contains, similar to other NEAT proteins, a 3{sub 10}-helix near the heme-binding site. Because the mechanistic function of this helix in NEAT proteins is not yet defined, we focused on the contribution of this region to hemophore and NEAT protein activity, both biochemically and biologically in cultured cells. Site-directed mutagenesis of amino acids in and adjacent to the helix identified residues important for heme and hemoglobin association, with some mutations affecting both properties and other mutations affecting only heme stabilization. IsdX1 with mutations that reduced the ability to associate with hemoglobin and bind heme failed to restore the growth of a hemophore-deficient strain of B. anthracis on hemoglobin as the sole iron source. These data indicate that not only is the 3{sub 10}-helix important for NEAT protein biology, but also that the processes of hemoglobin and heme binding can be both separate as well as coupled, the latter function being necessary for maximal heme-scavenging activity. These studies enhance our understanding of NEAT domain and hemophore function and set the stage for structure-based inhibitor design to block NEAT domain interaction with

  3. Substrate chemistry influences the morphology and biological function of adsorbed extracellular matrix assemblies.

    Science.gov (United States)

    Sherratt, Michael J; Bax, Daniel V; Chaudhry, Shazia S; Hodson, Nigel; Lu, Jian R; Saravanapavan, Priya; Kielty, Cay M

    2005-12-01

    In addition to mediating cell signalling events, native extracellular matrix (ECM) assemblies interact with other ECM components, act as reservoirs for soluble signalling molecules and perform structural roles. The potential of native ECM assemblies in the manufacture of biomimetic materials has not been fully exploited due, in part, to the effects of substrate interactions on their morphology. We have previously demonstrated that the ECM components, fibrillin and type VI collagen microfibrils, exhibit substrate dependent morphologies on chemically and topographically variable heterogeneous surfaces. Using both cleaning and coating approaches on silicon wafers and glass coverslips we have produced chemically homogeneous, topographically similar substrates which cover a large amphiphilic range. Extremes of substrate amphiphilicity induced morphological changes in periodicity, curvature and lateral spreading which may mask binding sites or disrupt domain structure. Biological functionality, as assayed by the ability to support cell spreading, was significantly reduced for fibrillin microfibrils adsorbed on highly hydrophilic substrates (contact angle 20.7 degrees) compared with less hydrophilic (contact angle 38.3 degrees) and hydrophobic (contact angle 92.8 degrees) substrates. With an appropriate choice of surface chemistry, multifunctional ECM assemblies retain their native morphology and biological functionality.

  4. Structural characteristics and biological functions of the HIV-1 gp120 V3 region

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Recent studies demonstrate that the V3 loop of HIV-1 gp120 plays an important role in the attachment of HIV-1 to the target cells. Several amino acids in this domain are involved in the interaction of gp120 with the co-receptors. The V3 loop elicits one of the earliest antiviral antibody responses in HIV-1 infection and has been identified as the principal neutralizing determinant (PND). A subset of antibodies to V3 loop show a broad range of neutralizing activity. Unfortunately, this loop undergoes broad mutation and is one of the hypervariable regions. Mutations of some amino acids in this PND could affect syncytium formation, virus infectivity and neutralization. Knowing the structural characteristics and biological functions of the V3 region could help us to understand mechanism of HIV infection and to develop new strategy against HIV-1. In this review, the structural characteristics, variation and biological functions of the V3 loop as well as immunological responses to the V3 loop are discussed.

  5. Functional and molecular characterization of the role of CTCF in human embryonic stem cell biology.

    Directory of Open Access Journals (Sweden)

    Sri Kripa Balakrishnan

    Full Text Available The CCCTC-binding factor CTCF is the only known vertebrate insulator protein and has been shown to regulate important developmental processes such as imprinting, X-chromosome inactivation and genomic architecture. In this study, we examined the role of CTCF in human embryonic stem cell (hESC biology. We demonstrate that CTCF associates with several important pluripotency genes, including NANOG, SOX2, cMYC and LIN28 and is critical for hESC proliferation. CTCF depletion impacts expression of pluripotency genes and accelerates loss of pluripotency upon BMP4 induced differentiation, but does not result in spontaneous differentiation. We find that CTCF associates with the distal ends and internal sites of the co-regulated 160 kb NANOG-DPPA3-GDF3 locus. Each of these sites can function as a CTCF-dependent enhancer-blocking insulator in heterologous assays. In hESCs, CTCF exists in multisubunit protein complexes and can be poly(ADPribosylated. Known CTCF cofactors, such as Cohesin, differentially co-localize in the vicinity of specific CTCF binding sites within the NANOG locus. Importantly, the association of some cofactors and protein PARlation selectively changes upon differentiation although CTCF binding remains constant. Understanding how unique cofactors may impart specialized functions to CTCF at specific genomic locations will further illuminate its role in stem cell biology.

  6. Biology of bone and how it orchestrates the form and function of the skeleton

    Science.gov (United States)

    Sommerfeldt, D. W.; Rubin, C. T.

    2001-01-01

    The principal role of the skeleton is to provide structural support for the body. While the skeleton also serves as the body's mineral reservoir, the mineralized structure is the very basis of posture, opposes muscular contraction resulting in motion, withstands functional load bearing, and protects internal organs. Although the mass and morphology of the skeleton is defined, to some extent, by genetic determinants, it is the tissue's ability to remodel--the local resorption and formation of bone--which is responsible for achieving this intricate balance between competing responsibilities. The aim of this review is to address bone's form-function relationship, beginning with extensive research in the musculoskeletal disciplines, and focusing on several recent cellular and molecular discoveries which help understand the complex interdependence of bone cells, growth factors, physical stimuli, metabolic demands, and structural responsibilities. With a clinical and spine-oriented audience in mind, the principles of bone cell and molecular biology and physiology are presented, and an attempt has been made to incorporate epidemiologic data and therapeutic implications. Bone research remains interdisciplinary by nature, and a deeper understanding of bone biology will ultimately lead to advances in the treatment of diseases and injuries to bone itself.

  7. The biology of cancer testis antigens: putative function, regulation and therapeutic potential.

    Science.gov (United States)

    Fratta, Elisabetta; Coral, Sandra; Covre, Alessia; Parisi, Giulia; Colizzi, Francesca; Danielli, Riccardo; Nicolay, Hugues Jean Marie; Sigalotti, Luca; Maio, Michele

    2011-04-01

    Cancer testis antigens (CTA) are a large family of tumor-associated antigens expressed in human tumors of different histological origin, but not in normal tissues except for testis and placenta. This tumor-restricted pattern of expression, together with their strong in vivo immunogenicity, identified CTA as ideal targets for tumor-specific immunotherapeutic approaches, and prompted the development of several clinical trials of CTA-based vaccine therapy. Driven by this practical clinical interest, a more detailed characterization of CTA biology has been recently undertaken. So far, at least 70 families of CTA, globally accounting for about 140 members, have been identified. Most of these CTA are expressed during spermatogenesis, but their function is still largely unknown. Epigenetic events, particularly DNA methylation, appear to be the primary mechanism regulating CTA expression in both normal and transformed cells, as well as in cancer stem cells. In view of the growing interest in CTA biology, the aim of this review is to provide the most recent information on their expression, regulation and function, together with a brief summary of the major clinical trials involving CTA as therapeutic agents. The pharmacologic modulation of CTA expression profiles on neoplastic cells by DNA hypomethylating drugs will also be discussed as a feasible approach to design new combination therapies potentially able to improve the clinical efficacy of currently adopted CTA-based immunotherapeutic regimens in cancer patients.

  8. Biological performance of functionalized biomedical polymers for potential applications as intraocular lens.

    Science.gov (United States)

    Zheng, Zhiwen; Wang, Yingjun; Jiao, Yan; Zhai, Zhichen

    2016-08-01

    To study the biological performance of surface-modified biomedical polymer materials, a model of the functional mechanism of nonspecific adsorption resistance was constructed. Cell behavior on the surface and in vivo transplantation features of intraocular lens (IOL) materials, such as hydrophobic acrylic ester and polymethyl methacrylate (PMMA), were investigated. The results of cell adhesion and proliferation studies showed that the addition of hirudin can significantly resist epithelial cell adhesion, better than the pure amination process, and thereby inhibit excessive proliferation on the surface. Experiments on the eyes of rabbits indicated that the IOL surfaces with hirudin modification reduced the incidence of cell aggregation and inflammation. Combined with a study of protein-resistant layer construction with recombinant hirudin on the material surface, the mechanism of surface functionalization was determined. The biological performance indicated that nonspecific adsorption is greatly decreased due to the existence of amphiphilic ions or hydration layers, which lead to stability and long-term resistance to nonspecific adsorption. These results offer a theoretical basis for the use of traditional biomedical polymer materials in long-term clinical applications. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1961-1967, 2016.

  9. A bottom-up characterization of transfer functions for synthetic biology designs: lessons from enzymology.

    Science.gov (United States)

    Carbonell-Ballestero, Max; Duran-Nebreda, Salva; Montañez, Raúl; Solé, Ricard; Macía, Javier; Rodríguez-Caso, Carlos

    2014-12-16

    Within the field of synthetic biology, a rational design of genetic parts should include a causal understanding of their input-output responses-the so-called transfer function-and how to tune them. However, a commonly adopted strategy is to fit data to Hill-shaped curves without considering the underlying molecular mechanisms. Here we provide a novel mathematical formalization that allows prediction of the global behavior of a synthetic device by considering the actual information from the involved biological parts. This is achieved by adopting an enzymology-like framework, where transfer functions are described in terms of their input affinity constant and maximal response. As a proof of concept, we characterize a set of Lux homoserine-lactone-inducible genetic devices with different levels of Lux receptor and signal molecule. Our model fits the experimental results and predicts the impact of the receptor's ribosome-binding site strength, as a tunable parameter that affects gene expression. The evolutionary implications are outlined. PMID:25404136

  10. Environmental gradient favours functionally diverse macrobenthic community in a placer rich tropical bay

    Digital Repository Service at National Institute of Oceanography (India)

    Sivadas, S.K.; Ingole, B.S.; Fernandes, C.E.G.

    Corporation The Scientific World Journal Volume 2013, Article ID 750580, 12 pages http://dx.doi.org/10.1155/2013/750580 Research Article Environmental Gradient Favours Functionally Diverse Macrobenthic Community in a Placer Rich Tropical Bay S. K. Sivadas, B... to disturbance compared to impoverished ones. Further, a species with particular functional trait will exist in a region based on the environment which helps 2 The Scientific World Journal it to coexist in a community [8]. Therefore, functional diversity...

  11. Danish consumers' attitudes to the functional and environmental characteristics of food packaging

    DEFF Research Database (Denmark)

    Bech-Larsen, Tino

    1996-01-01

    decisions of consumers. Although this is not true for the environmental aspects of packaging. Between 16 and 37% (for the four different products) of the respondents mentioned functional packaging among other product attributes, when given a sequence of open questions as to why they h chosen the specific......Executive summary The purpose of the studies presented in the paper is to research different aspects of Danish consumers' views about the functional and environmental consequences of packaging, as well as to study cognitive barriers that can prevent consumer attitudes to environmental consequences...... and on the more specific levels, because of the social sensibility of environmental issues, and owing to the fact that it is difficult to establish any aim for the external validity of the studies, it is chosen to use four different methods of data collection. The point of purchase study is based on personal...

  12. Systems Biology Approach for Understanding MOA, Dose-Response and Susceptibility to Environmental Chemicals

    Science.gov (United States)

    There is an increasing need for assays for the rapid and efficient assessment of toxicities of large numbers of environmental chemicals. To meet this need, we have developed a battery of cell-based reporter assays that measure the activation of key cellular stress pathways. These...

  13. 76 FR 3076 - Availability of an Environmental Assessment for a Biological Control Agent for Air Potato

    Science.gov (United States)

    2011-01-19

    ... Control Agent for Air Potato AGENCY: Animal and Plant Health Inspection Service, USDA. ACTION: Notice of... Inspection Service has prepared an environmental assessment (EA) relative to the control of air potato... severity of air potato infestations. We are making the EA available to the public for review and...

  14. Experiences performed at the C:R: Saluggia of ENEA in low-level determination of plutonium in biological and environmental samples

    International Nuclear Information System (INIS)

    This report describes some experiences performed at the Research Center Saluggia of ENEA concerning low-level determination of plutonium in biological and environmental samples, with discussions of practical analytical problems. The main characteristics and properties of plutonium with emphasis to aqueous solutions chemistry and environmental behaviour are also reported

  15. How biological soil crusts became recognized as a functional unit: a selective history

    Science.gov (United States)

    Lange, Otto L.; Belnap, Jayne

    2016-01-01

    It is surprising that despite the world-wide distribution and general importance of biological soil crusts (biocrusts), scientific recognition and functional analysis of these communities is a relatively young field of science. In this chapter, we sketch the historical lines that led to the recognition of biocrusts as a community with important ecosystem functions. The idea of biocrusts as a functional ecological community has come from two main scientific branches: botany and soil science. For centuries, botanists have long recognized that multiple organisms colonize the soil surface in the open and often dry areas occurring between vascular plants. Much later, after the initial taxonomic and phyto-sociological descriptions were made, soil scientists and agronomists observed that these surface organisms interacted with soils in ways that changed the soil structure. In the 1970’s, research on these communities as ecological units that played an important functional role in drylands began in earnest, and these studies have continued to this day. Here, we trace the history of these studies from the distant past until 1990, when biocrusts became well-known to scientists and the public.

  16. Social representations and directing to the environmental education in the Perobas Biological Reserve, State of Paraná, Brazil

    Directory of Open Access Journals (Sweden)

    Carlos Alberto de Oliveira Magalhães Júnior

    2012-05-01

    Full Text Available The Perobas Biological Reserve is situated in the Brazilian municipalities of Tuneiras do Oeste and Cianorte, State of Paraná. Prior to the foundation, the local and state communities’ representatives manifested different standpoints, favorable and unfavorable, concerning the establishment of this environmental protection area. Considering the importance of comprehending social representations that students from the City of Tuneiras do Oeste have concerning the Perobas Biological Reserve, the present study aimed at investigating Basic Education students, as well as indicating ways for an environmental education development. We used the Free Evocation of Words technique and the analysis of composition contents. We identified that representations of the analyzed group are based on the Nature components present in the Reserve and on the role of the local inhabitants for their conservation, however such knowledge is not well-founded. We understand that educative actions must be initiated in order to proportionate the construction of knowledge concerning the Reserve´s Nature components and the mutual interactions involved. This knowledge can, subsequently, lead students to comprehend that a role is ascribed to them in the protection and the co-responsibility for the preservation of the protected area.

  17. Assessment of biological effects of environmental pollution along the NW Mediterranean Sea using mussels as sentinel organisms

    Energy Technology Data Exchange (ETDEWEB)

    Zorita, Izaskun [Biologia Zelularra eta Histologia Laborategia, Zoologia eta Biologia Zelularra Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea/Univ. del Pais Vasco, 644 P.K., E-48080 Bilbao, Basque Country (Spain); Apraiz, Itxaso [Biologia Zelularra eta Histologia Laborategia, Zoologia eta Biologia Zelularra Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea/Univ. del Pais Vasco, 644 P.K., E-48080 Bilbao, Basque Country (Spain); Ortiz-Zarragoitia, Maren [Biologia Zelularra eta Histologia Laborategia, Zoologia eta Biologia Zelularra Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea/Univ. del Pais Vasco, 644 P.K., E-48080 Bilbao, Basque Country (Spain); Orbea, Amaia [Biologia Zelularra eta Histologia Laborategia, Zoologia eta Biologia Zelularra Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea/Univ. del Pais Vasco, 644 P.K., E-48080 Bilbao, Basque Country (Spain); Cancio, Ibon [Biologia Zelularra eta Histologia Laborategia, Zoologia eta Biologia Zelularra Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea/Univ. del Pais Vasco, 644 P.K., E-48080 Bilbao, Basque Country (Spain); Soto, Manu [Biologia Zelularra eta Histologia Laborategia, Zoologia eta Biologia Zelularra Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea/Univ. del Pais Vasco, 644 P.K., E-48080 Bilbao, Basque Country (Spain); Marigomez, Ionan [Biologia Zelularra eta Histologia Laborategia, Zoologia eta Biologia Zelularra Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea/Univ. del Pais Vasco, 644 P.K., E-48080 Bilbao, Basque Country (Spain); Cajaraville, Miren P. [Biologia Zelularra eta Histologia Laborategia, Zoologia eta Biologia Zelularra Saila, Zientzia eta Teknologia Fakultatea, Euskal Herriko Unibertsitatea/Univ. del Pais Vasco, 644 P.K., E-48080 Bilbao, Basque Country (Spain)]. E-mail: mirenp.cajaraville@ehu.es

    2007-07-15

    With the aim of assessing the biological effects of pollution along three gradients of pollution in the NW Mediterranean Sea, a biomonitoring survey was implemented using a battery of biomarkers (lysosomal membrane stability, lysosomal structural changes, metallothionein (MT) induction and peroxisome proliferation) in mussels over a period of two years as part of the EU-funded BEEP project. Mussels from the most impacted zones (Fos, Genova and Barcelona harbours) showed enlarged lysosomes accompanied by reduced labilisation period of lysosomal membranes, indicating disturbed health. MT levels did not reveal significant differences between stations and were significantly correlated with gonad index, suggesting that they were influenced by gamete development. Peroxisomal acyl-CoA oxidase (AOX) activity was significantly inhibited in polluted stations possibly due to interactions among mixtures of pollutants. In conclusion, the application of a battery of effect and exposure biomarkers provided relevant data for the assessment of biological effects of environmental pollution along the NW Mediterranean Sea. - The biomarker approach is suitable for assessment of environmental pollution in the NW Mediterranean Sea.

  18. Functional group based Ligand binding affinity scoring function at atomic environmental level

    OpenAIRE

    Varadwaj, Pritish Kumar; Lahiri, Tapobrata

    2009-01-01

    Use of knowledge based scoring function (KBSF) for virtual screening and molecular docking has become an established method for drug discovery. Lack of a precise and reliable free energy function that describes several interactions including water-mediated atomic interaction between amino-acid residues and ligand makes distance based statistical measure as the only alternative. Till now all the distance based scoring functions in KBSF arena use atom singularity concept, which neglects the env...

  19. Biogeosystem technique as a method to overcome the Biological and Environmental Hazards of modern Agricultural, Irrigational and Technological Activities

    Science.gov (United States)

    Kalinitchenko, Valery; Batukaev, Abdulmalik; Zinchenko, Vladimir; Zarmaev, Ali; Magomadov, Ali; Chernenko, Vladimir; Startsev, Viktor; Bakoev, Serojdin; Dikaev, Zaurbek

    2014-05-01

    Modern challenge for humanity is to replace the paradigm of nature use and overcome environmental hazards of agronomy, irrigation, industry, and other human activities in biosphere. It is utterly reasonable to stop dividing biosphere on shares - the human habitat and the environment. In the 21st century it is an outdated anthropocentrism. Contradicting himself to biosphere Humankind has the problems. The new paradigm of biosphere control by methods of Biogeosystem technique is on agenda of Humankind. Key directions of Biogeosystem technique. Tillage. Single rotary milling 20…30-50…60 sm soil layer optimizes the evolution and environment of soil, creates a favorable conditions for the rhizosphere, increases the biological productivity of biosphere by 30-50% compared to the standard agricultural practices for the period up to 40 years. Recycle material. Recycling of mineral and organic substances in soil layer of 20…30-50…60 sm in rotary milling soil processing provides wastes clean return to biosphere. Direct intrasoil substances synthesis. Environmentally friendly robot wasteless nanotechnology provides direct substances synthesis, including fertilizers, inside the soil. It eliminates the prerequisites of the wastes formation under standard industrial technologies. Selective substance's extraction from soil. Electrochemical robotic nanotechnology provides selective substances extraction from soil. The technology provides recovery, collection and subsequent safe industrial use of extracted substances out of landscape. Saving fresh water. An important task is to save fresh water in biosphere. Irrigation spends water 4-5 times more of biological requirements of plants, leads to degradation of soil and landscape. The intrasoil pulse continuous-discrete paradigm of irrigation is proposed. It provides the soil and landscape conservation, increases the biological productivity, save the fresh water up to 10-20 times. The subsurface soil rotary processing and

  20. State of the art of environmentally friendly sample preparation approaches for determination of PBDEs and metabolites in environmental and biological samples: A critical review.

    Science.gov (United States)

    Berton, Paula; Lana, Nerina B; Ríos, Juan M; García-Reyes, Juan F; Altamirano, Jorgelina C

    2016-01-28

    Green chemistry principles for developing methodologies have gained attention in analytical chemistry in recent decades. A growing number of analytical techniques have been proposed for determination of organic persistent pollutants in environmental and biological samples. In this light, the current review aims to present state-of-the-art sample preparation approaches based on green analytical principles proposed for the determination of polybrominated diphenyl ethers (PBDEs) and metabolites (OH-PBDEs and MeO-PBDEs) in environmental and biological samples. Approaches to lower the solvent consumption and accelerate the extraction, such as pressurized liquid extraction, microwave-assisted extraction, and ultrasound-assisted extraction, are discussed in this review. Special attention is paid to miniaturized sample preparation methodologies and strategies proposed to reduce organic solvent consumption. Additionally, extraction techniques based on alternative solvents (surfactants, supercritical fluids, or ionic liquids) are also commented in this work, even though these are scarcely used for determination of PBDEs. In addition to liquid-based extraction techniques, solid-based analytical techniques are also addressed. The development of greener, faster and simpler sample preparation approaches has increased in recent years (2003-2013). Among green extraction techniques, those based on the liquid phase predominate over those based on the solid phase (71% vs. 29%, respectively). For solid samples, solvent assisted extraction techniques are preferred for leaching of PBDEs, and liquid phase microextraction techniques are mostly used for liquid samples. Likewise, green characteristics of the instrumental analysis used after the extraction and clean-up steps are briefly discussed. PMID:26755134

  1. A note on environmental aspects of penaeid shrimp biology and dynamics

    OpenAIRE

    Garcia, Serge

    1984-01-01

    Shrimps are short-lived animals living in highly variable inshore areas during the juvenile phase and are therefore subject to particularly strong environmentally driven variability in recruitment and stock size. This paper examines the likely consequences of this fact on the surplus yield production and stock-recruitment modelling underlining the high risk of generating artefactual models when the data series are short. (Résumé d'auteur)

  2. The role of environmental variables on Aedes albopictus biology and chikungunya epidemiology

    OpenAIRE

    Waldock, Joanna; Chandra, Nastassya L.; Lelieveld, Jos; Proestos, Yiannis; Michael, Edwin; Christophides, George; Parham, Paul E

    2013-01-01

    Aedes albopictus is a vector of dengue and chikungunya viruses in the field, along with around 24 additional arboviruses under laboratory conditions. As an invasive mosquito species, Ae. albopictus has been expanding in geographical range over the past 20 years, although the poleward extent of mosquito populations is limited by winter temperatures. Nonetheless, population densities depend on environmental conditions and since global climate change projections indicate increasing temperatures ...

  3. Exploiting the Physicochemical Properties of Dendritic Polymers for Environmental and Biological Applications

    Energy Technology Data Exchange (ETDEWEB)

    Bhattacharya, Priyanka; Geitner, Nicholas K.; Sarupria, Sapna; Ke, Pu Chun

    2013-04-07

    In this Perspective we first examine the rich physicochemical properties of dendritic polymers for hosting cations, anions, and polyaromatic hydrocarbons. We then extrapolate these conceptual discussions to the use of dendritic polymers for humic acid antifouling, oil dispersion, copper sensing, and fullerenol remediation. In addition, we review the state-of-the-art of dendrimer research and elaborate on their 10 implications for water purification, environmental remediation, nanomedicine, and energy harvesting.

  4. Biological Tools to Study the Effects of Environmental Contaminants at the Feto–Maternal Interface

    OpenAIRE

    Mannelli, Chiara; Ietta, Francesca; Avanzati, Anna Maria; Skarzynski, Dariusz; Paulesu, Luana

    2015-01-01

    The identification of reproductive toxicants is a major scientific challenge for human health. Prenatal life is the most vulnerable and important time span of human development. For obvious ethical reasons, in vivo models cannot be used in human pregnancy, and animal models do not perfectly reflect human physiology. This review describes the in vitro test models representative of the human feto–maternal interface and the effects of environmental chemicals with estrogen-like activity, mainly b...

  5. Habitual Snoring in school-aged children: environmental and biological predictors

    Directory of Open Access Journals (Sweden)

    Wu Shenghu

    2010-10-01

    Full Text Available Abstract Background Habitual snoring, a prominent symptom of sleep-disordered breathing, is an important indicator for a number of health problems in children. Compared to adults, large epidemiological studies on childhood habitual snoring and associated predisposing factors are extremely scarce. The present study aimed to assess the prevalence and associated factors of habitual snoring among Chinese school-aged children. Methods A random sample of 20,152 children aged 5.08 to 11.99 years old participated in a cross-sectional survey, which was conducted in eight cities of China. Parent-administrated questionnaires were used to collect information on children's snoring frequency and the possible correlates. Results The prevalence of habitual snoring was 12.0% (14.5% for boys vs. 9.5% for girls in our sampled children. Following factors were associated with an increased risk for habitual snoring: lower family income (adjusted odds ratio [OR] = 1.46, lower father's education (OR = 1.38 and 1.14 for middle school or under and high school of educational level, respectively, breastfeeding duration Conclusion The prevalence of habitual snoring in Chinese children was similar to that observed in other countries. The potential predisposing factors covered socioeconomic characteristics, environmental exposures, chronic health problems, and family susceptibility. Compared to socioeconomic status and family susceptibility, environmental exposures and chronic health problems had greater impact, indicating childhood habitual snoring could be partly prevented by health promotion and environmental intervention.

  6. Seasonal Variation of δ13C of Four Tree Species: A Biological Integrator of Environmental Variables

    Institute of Scientific and Technical Information of China (English)

    Hai-Tao LI; Jun XIA; Le XIANG; Tao LIANG; Qi-Jing LIU

    2005-01-01

    Foliar δ13C values, an indicator of long-term intercellular carbon dioxide concentration and, thus,of long-term water use efficiency (WUE) in plants, were measured for Pinus massoniana Lamb., P. elliottii Engelm., Cunninghamia laceolata (Lamb.) Hook., and Schima superba Gardn. et Champ. in a restored forest ecosystem in the Jiazhu River Basin. Seasonal variation and the relationship between the foliar δ13Cvalues of the four species and environmental factors (monthly total precipitation, monthly average air temperature, relative humidity, atmospheric pressure, and monthly total solar radiation and evaporation)were investigated. The monthly δ13C values and WUE of the four species increased with increasing precipitation, air temperature, solar radiation, and evaporation, whereas δ13C values of the four species decreased with increasing relative humidity and atmospheric pressure. Despite significant differences in δ13C seasonal means for the four species, our results demonstrate a significant convergence in the responses of δ13C values and WUE to seasonal variations in environmental factors among the species investigated and that the δ13C signature for each species gives a strong indication of environmental variables.

  7. Humic substances biological activity at the plant-soil interface: from environmental aspects to molecular factors.

    Science.gov (United States)

    Trevisan, Sara; Francioso, Ornella; Quaggiotti, Silvia; Nardi, Serenella

    2010-06-01

    Humic substances (HS) represent the organic material mainly widespread in nature. HS have positive effects on plant physiology by improving soil structure and fertility and by influencing nutrient uptake and root architecture. The biochemical and molecular mechanisms underlying these events are only partially known. HS have been shown to contain auxin and an "auxin-like" activity of humic substances has been proposed, but support to this hypothesis is fragmentary. In this review article, we are giving an overview of available data concerning molecular structures and biological activities of humic substances, with special emphasis on their hormone-like activities. PMID:20495384

  8. Identification of distinct biological functions for four 3′-5′ RNA polymerases

    Science.gov (United States)

    Long, Yicheng; Abad, Maria G.; Olson, Erik D.; Carrillo, Elisabeth Y.; Jackman, Jane E.

    2016-01-01

    The superfamily of 3′-5′ polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNAHis guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties. DdiTLP2 catalyzes a mitochondria-specific tRNAHis maturation reaction, which is distinct from the tRNAHis maturation reaction typically catalyzed by Thg1 enzymes on cytosolic tRNA. DdiTLP3 catalyzes tRNA repair during mitochondrial tRNA 5′-editing in vivo and in vitro, establishing template-dependent 3′-5′ polymerase activity of TLPs as a bona fide biological activity for the first time since its unexpected discovery more than a decade ago. DdiTLP4 is cytosolic and, surprisingly, catalyzes robust 3′-5′ polymerase activity on non-tRNA substrates, strongly implying further roles for TLP 3′-5′ polymerases in eukaryotes. PMID:27484477

  9. Identification of distinct biological functions for four 3'-5' RNA polymerases.

    Science.gov (United States)

    Long, Yicheng; Abad, Maria G; Olson, Erik D; Carrillo, Elisabeth Y; Jackman, Jane E

    2016-09-30

    The superfamily of 3'-5' polymerases synthesize RNA in the opposite direction to all other DNA/RNA polymerases, and its members include eukaryotic tRNA(His) guanylyltransferase (Thg1), as well as Thg1-like proteins (TLPs) of unknown function that are broadly distributed, with family members in all three domains of life. Dictyostelium discoideum encodes one Thg1 and three TLPs (DdiTLP2, DdiTLP3 and DdiTLP4). Here, we demonstrate that depletion of each of the genes results in a significant growth defect, and that each protein catalyzes a unique biological reaction, taking advantage of specialized biochemical properties. DdiTLP2 catalyzes a mitochondria-specific tRNA(His) maturation reaction, which is distinct from the tRNA(His) maturation reaction typically catalyzed by Thg1 enzymes on cytosolic tRNA. DdiTLP3 catalyzes tRNA repair during mitochondrial tRNA 5'-editing in vivo and in vitro, establishing template-dependent 3'-5' polymerase activity of TLPs as a bona fide biological activity for the first time since its unexpected discovery more than a decade ago. DdiTLP4 is cytosolic and, surprisingly, catalyzes robust 3'-5' polymerase activity on non-tRNA substrates, strongly implying further roles for TLP 3'-5' polymerases in eukaryotes.

  10. Species composition,distribution patterns and ecological functions of biological soil crusts in the Gurbantunggut Desert

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    As one of the most important biological factors that maintain the stability of the largest fixed and semi-fixed desert in China,the Gurbantunggut Desert,the biological soil crusts (BSCs) develop well and play critical ecological roles in the desert ecosystem. In this paper,we briefly summarize our research findings since 2002 including species composition,distribution pattern and ecological functions of BSCs in the desert. Our results indicate abundant species diversity of BSCs in the Gurbantunggut Desert in comparison to other deserts in China. At the scales of sand dune or whole desert,the distribution patterns of BSCs are location-specific. The existence of BSCs in this desert could:(1) accelerate the formation of desert soil and the weathering of minerals; (2) accumulate organic matter in surface soil through related species in soil crusts; (3) enhance the abilities of sand surface to resist wind erosion; (4) influence seed germination of vascular plants; and (5) enhance the production of dew deposition on sandy soil surface.

  11. The relationship between the connecting peptide of recombined single chain insulin and its biological function

    Institute of Scientific and Technical Information of China (English)

    黄一丁; 梁镇和; 冯佑民

    2001-01-01

    To investigate the relationship between the biological activity of recombined single chain insulin and the length of the connecting peptide, we designed and prepared three single chain insulin molecules, namely, PIP, [A]5PIP and [A]10PIP, by site-directed mutagenesis, in which B30 and A1 were linked through dipeptide A-K, heptapeptide A-A-A-A-A-A-K, and dodecapeptide A-A-A-A-A-A-A-A-A-A-A-K, respectively. Their receptor binding capacities were 0.14%, 14.3% and 11.1% of that of insulin respectively and their in vivo biological activities were in consistence with their receptor binding capacity; whereas their growth promoting activities were 17%, 116.3% and 38% of that of insulin. These results suggested the following conclusions. (i) The recombined single chain insulin could also possess the same metabolic and mitogenic function as insulin. (ii) The receptor binding capacity of recombined single chain insulin to insulin receptor was closely related to the length and amino acid composition of the connecting peptide and could change from 0 to 100% of insulin depending on the different connecting peptides. This result further illustrated the necessity of B chain C-terminus swaying away from A chain N-terminus when insulin binds to its receptor. (iii) The mitogenic activity of recombined single chain insulin also depended on the length and the amino acid composition of the connecting peptide and was higher than its metabolic activity.

  12. Exploring new biological functions of amyloids: bacteria cell agglutination mediated by host protein aggregation.

    Directory of Open Access Journals (Sweden)

    Marc Torrent

    Full Text Available Antimicrobial proteins and peptides (AMPs are important effectors of the innate immune system that play a vital role in the prevention of infections. Recent advances have highlighted the similarity between AMPs and amyloid proteins. Using the Eosinophil Cationic Protein as a model, we have rationalized the structure-activity relationships between amyloid aggregation and antimicrobial activity. Our results show how protein aggregation can induce bacteria agglutination and cell death. Using confocal and total internal reflection fluorescence microscopy we have tracked the formation in situ of protein amyloid-like aggregates at the bacteria surface and on membrane models. In both cases, fibrillar aggregates able to bind to amyloid diagnostic dyes were detected. Additionally, a single point mutation (Ile13 to Ala can suppress the protein amyloid behavior, abolishing the agglutinating activity and impairing the antimicrobial action. The mutant is also defective in triggering both leakage and lipid vesicle aggregation. We conclude that ECP aggregation at the bacterial surface is essential for its cytotoxicity. Hence, we propose here a new prospective biological function for amyloid-like aggregates with potential biological relevance.

  13. The role of ontologies in biological and biomedical research: a functional perspective

    KAUST Repository

    Hoehndorf, Robert

    2015-04-10

    Ontologies are widely used in biological and biomedical research. Their success lies in their combination of four main features present in almost all ontologies: provision of standard identifiers for classes and relations that represent the phenomena within a domain; provision of a vocabulary for a domain; provision of metadata that describes the intended meaning of the classes and relations in ontologies; and the provision of machine-readable axioms and definitions that enable computational access to some aspects of the meaning of classes and relations. While each of these features enables applications that facilitate data integration, data access and analysis, a great potential lies in the possibility of combining these four features to support integrative analysis and interpretation of multimodal data. Here, we provide a functional perspective on ontologies in biology and biomedicine, focusing on what ontologies can do and describing how they can be used in support of integrative research. We also outline perspectives for using ontologies in data-driven science, in particular their application in structured data mining and machine learning applications.

  14. Enhanced surface functionality via plasma modification and plasma deposition techniques to create more biologically relevant materials

    Science.gov (United States)

    Shearer, Jeffrey C.

    Functionalizing nanoparticles and other unusually shaped substrates to create more biologically relevant materials has become central to a wide range of research programs. One of the primary challenges in this field is creating highly functionalized surfaces without modifying the underlying bulk material. Traditional wet chemistry techniques utilize thin film depositions to functionalize nanomaterials with oxygen and nitrogen containing functional groups, such as --OH and --NHx. These functional groups can serve to create surfaces that are amenable to cell adhesion or can act as reactive groups for further attachment of larger structures, such as macromolecules or antiviral agents. Additional layers, such as SiO2, are often added between the nanomaterial and the functionalized coating to act as a barrier films, adhesion layers, and to increase overall hydrophilicity. However, some wet chemistry techniques can damage the bulk material during processing. This dissertation examines the use of plasma processing as an alternative method for producing these highly functionalized surfaces on nanoparticles and polymeric scaffolds through the use of plasma modification and plasma enhanced chemical vapor deposition techniques. Specifically, this dissertation will focus on (1) plasma deposition of SiO2 barrier films on nanoparticle substrates; (2) surface functionalization of amine and alcohol groups through (a) plasma co-polymerization and (b) plasma modification; and (3) the design and construction of plasma hardware to facilitate plasma processing of nanoparticles and polymeric scaffolds. The body of work presented herein first examines the fabrication of composite nanoparticles by plasma processing. SiOxC y and hexylamine films were coated onto TiO2 nanoparticles to demonstrate enhanced water dispersion properties. Continuous wave and pulsed allyl alcohol plasmas were used to produce highly functionalized Fe2 O3 supported nanoparticles. Specifically, film composition was

  15. Restoration of voice function by using biological feedback in laryngeal and hypopharyngeal carcinoma patients

    Science.gov (United States)

    Choinzonov, E. L.; Balatskaya, L. N.; Chizhevskaya, S. Yu.; Meshcheryakov, R. V.; Kostyuchenko, E. Yu.; Ivanova, T. A.

    2016-08-01

    The aim of the research is to develop and introduce a new technique of post-laryngectomy voice rehabilitation of laryngeal and hypopharyngeal carcinoma patients. The study involves comparing and analyzing 82 cases of voice function restoration by using biological feedback based on mathematical modeling of voice production. The advantage of the modern technology-based method in comparison with the conventional one is proved. Restoration of voice function using biofeedback allows taking into account patient's abilities, adjusting parameters of voice trainings, and controlling their efficiency in real-time mode. The data obtained indicate that the new method contributes to the rapid inclusion of self-regulation mechanisms of the body and results in the overall success rate of voice rehabilitation in totally laryngectomized patients reaching 92%, which reduces the rehabilitation period to 18 days, compared to 86% and 38 days in the control group, respectively. Restoration of disturbed functions after successful treatment is an important task of rehabilitation and is crucial in terms of the quality of cancer patients' lives. To assess life quality of laryngeal cancer patients, the EORTC Quality of Life Core Questionnaire (QLQ-C30), and head and neck module (QLQ-H&N35) were used. The analyzed results proved that the technique of biofeedback voice restoration significantly improves the quality of life of laryngectomized patients. It allows reducing the number of disabled people, restoring patients' ability to work-related activities, and significantly improving social adaptation of these patients.

  16. FUSE: a profit maximization approach for functional summarization of biological networks

    Directory of Open Access Journals (Sweden)

    Seah Boon-Siew

    2012-03-01

    Full Text Available Abstract Background The availability of large-scale curated protein interaction datasets has given rise to the opportunity to investigate higher level organization and modularity within the protein interaction network (PPI using graph theoretic analysis. Despite the recent progress, systems level analysis of PPIS remains a daunting task as it is challenging to make sense out of the deluge of high-dimensional interaction data. Specifically, techniques that automatically abstract and summarize PPIS at multiple resolutions to provide high level views of its functional landscape are still lacking. We present a novel data-driven and generic algorithm called FUSE (Functional Summary Generator that generates functional maps of a PPI at different levels of organization, from broad process-process level interactions to in-depth complex-complex level interactions, through a pro t maximization approach that exploits Minimum Description Length (MDL principle to maximize information gain of the summary graph while satisfying the level of detail constraint. Results We evaluate the performance of FUSE on several real-world PPIS. We also compare FUSE to state-of-the-art graph clustering methods with GO term enrichment by constructing the biological process landscape of the PPIS. Using AD network as our case study, we further demonstrate the ability of FUSE to quickly summarize the network and identify many different processes and complexes that regulate it. Finally, we study the higher-order connectivity of the human PPI. Conclusion By simultaneously evaluating interaction and annotation data, FUSE abstracts higher-order interaction maps by reducing the details of the underlying PPI to form a functional summary graph of interconnected functional clusters. Our results demonstrate its effectiveness and superiority over state-of-the-art graph clustering methods with GO term enrichment.

  17. The universality and biological significance of signal molecules with intracellular-extracellular compatible functions

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Generally,cell signal molecules are classified into the extracellular signal molecules (the first messengers) and the intracellular signal ones (the second messengers).Cyclic adenosine monophosphate (cAMP),calcium ions and calmodulin (CaM) are the traditional intracellular messengers,but they are also present in extracellular matrix (ECM).Some of them have been discovered to act as the first messengers through cell surface receptors.Other second messengers,such as cyclic guanosine monophosphate (cGMP),cyclic adenosine diphosphate ribose (cADPR) and annexin,are also found existing outside animal and plant cells.The existence of these messengers with intracellular-extracellular compatible functions in cells may be a regular biological phenomenon.These compatible messengers might be the communication factors between intracellular and extracellular regions or among the cell populations,and are also important in regulating cell development procedure.

  18. Distinguishing Pattern Formation Phenotypes: Applying Minkowski Functionals to Cell Biology Systems

    Science.gov (United States)

    Rericha, Erin; Guven, Can; Parent, Carole; Losert, Wolfgang

    2011-03-01

    Spatial Clustering of proteins within cells or cells themselves frequently occur in cell biology systems. However quantifying the underlying order and determining the regulators of these cluster patterns have proved difficult due to the inherent high noise levels in the systems. For instance the patterns formed by wild type and cyclic-AMP regulatory mutant Dictyostelium cells are visually distinctive, yet the large error bars in measurements of the fractal number, area, Euler number, eccentricity, and wavelength making it difficult to quantitatively distinguish between the patterns. We apply a spatial analysis technique based on Minkowski functionals and develop metrics which clearly separate wild type and mutant cell lines into distinct categories. Having such a metric facilitated the development of a computational model for cellular aggregation and its regulators. Supported by NIH-NGHS Nanotechnology (R01GM085574) and the Burroughs Wellcome Fund.

  19. Function of parotid gland following irradiation and its relation to biological parameters

    Energy Technology Data Exchange (ETDEWEB)

    Sasaki, T. (Tohoku Univ., Sendai, Japan); Yamamoto, M.; Takeda, M.

    1980-09-01

    The function of the parotid gland in the mouse (synthesis and secretion of ..cap alpha..-amylase) following X irradiation was analyzed in relation to the parameters of surviving acinar cell fraction, DNA or protein content, and wet weight of the gland. Both synthesis and secretion of amylase in parotid were essentially unchanged when mice were irradiated with a dose of up to 3000 rad. When mice were irradiated and then given a proliferative stimulus of isoproterenol, latent lethal damage in the acinar cell population was expressed and resulted in cell degeneration in a dose-dependent manner. The mean value of amylase activity per gland in similarly treated parotids was, however, totally unaffected. The relationship between amylase activity per gland and the other biological parameters was analyzed by regression analysis. The results indicate that amylase activity per surviving acinar cell increased proportionately to compensate for the loss of acinar cells.

  20. Biological colloid engineering: Self-assembly of dipolar ferromagnetic chains in a functionalized biogenic ferrofluid.

    Science.gov (United States)

    Ruder, Warren C; Hsu, Chia-Pei D; Edelman, Brent D; Schwartz, Russell; Leduc, Philip R

    2012-08-01

    We have studied the dynamic behavior of nanoparticles in ferrofluids consisting of single-domain, biogenic magnetite (Fe(3)O(4)) isolated from Magnetospirillum magnetotacticum (MS-1). Although dipolar chains form in magnetic colloids in zero applied field, when dried upon substrates, the solvent front disorders nanoparticle aggregation. Using avidin-biotin functionalization of the particles and substrate, we generated self-assembled, linear chain motifs that resist solvent front disruption in zero-field. The engineered self-assembly process we describe here provides an approach for the creation of ordered magnetic structures that could impact fields ranging from micro-electro-mechanical systems development to magnetic imaging of biological structures. PMID:22952408

  1. Spatial, Phylogenetic, Environmental and Biological Components of Variation in Extinction Risk: A Case Study Using Banksia.

    Science.gov (United States)

    Cardillo, Marcel; Skeels, Alexander

    2016-01-01

    Comparative analyses of extinction risk routinely apply methods that account for phylogenetic non-independence, but few analyses of extinction risk have addressed the possibility of spatial non-independence. We explored patterns of extinction risk in Banksia, a plant genus largely endemic to Australia's southwest biodiversity hotspot, using methods to partition the variance in two response variables (threat status and range size) into phylogenetic, spatial, and independent components. We then estimated the effects of a number of biological and external predictors on extinction risk independently of phylogeny and space. The models explained up to 34.2% of the variation in range size and up to 9.7% of the variation in threat status, nearly all of which was accounted for by the predictors, not by phylogeny or space. In the case of Banksia, therefore, high extinction risk can be clearly linked with biological syndromes (such as a brief flowering period) or geographic indicators of human impact (such as extensive habitat loss), but cannot be predicted from phylogenetic relatedness or geographic proximity. PMID:27148745

  2. Synthetic biology: insights into biological computation.

    Science.gov (United States)

    Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

    2016-04-18

    Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

  3. Synthetic biology: insights into biological computation.

    Science.gov (United States)

    Manzoni, Romilde; Urrios, Arturo; Velazquez-Garcia, Silvia; de Nadal, Eulàlia; Posas, Francesc

    2016-04-18

    Organisms have evolved a broad array of complex signaling mechanisms that allow them to survive in a wide range of environmental conditions. They are able to sense external inputs and produce an output response by computing the information. Synthetic biology attempts to rationally engineer biological systems in order to perform desired functions. Our increasing understanding of biological systems guides this rational design, while the huge background in electronics for building circuits defines the methodology. In this context, biocomputation is the branch of synthetic biology aimed at implementing artificial computational devices using engineered biological motifs as building blocks. Biocomputational devices are defined as biological systems that are able to integrate inputs and return outputs following pre-determined rules. Over the last decade the number of available synthetic engineered devices has increased exponentially; simple and complex circuits have been built in bacteria, yeast and mammalian cells. These devices can manage and store information, take decisions based on past and present inputs, and even convert a transient signal into a sustained response. The field is experiencing a fast growth and every day it is easier to implement more complex biological functions. This is mainly due to advances in in vitro DNA synthesis, new genome editing tools, novel molecular cloning techniques, continuously growing part libraries as well as other technological advances. This allows that digital computation can now be engineered and implemented in biological systems. Simple logic gates can be implemented and connected to perform novel desired functions or to better understand and redesign biological processes. Synthetic biological digital circuits could lead to new therapeutic approaches, as well as new and efficient ways to produce complex molecules such as antibiotics, bioplastics or biofuels. Biological computation not only provides possible biomedical and

  4. [Historic and functional biology: the inadequacy of a system theory of evolution].

    Science.gov (United States)

    Regelmann, J P

    1982-01-01

    In the first half of the 20th century neo-Kantianism in a broad sense proved itself the main conceptual and methodological background of the central European biology. As such it contributed much to the victory on the typological, idealistic-morphological and psycho-vitalistic interpretations of life. On the other hand it could not give tools to the biologists for working out a strictly darwinian evolution theory. Kant's theory of organism was conceived without evolution as a theory of the internal functionality of the organism. There was only some 'play' with the evolutionary differentiation of the species. Since then the disputes around the work of August Weismann, a synthetical evolution theory which is now behind time, arose. This theory developed from coinciding claims, elaborated by geneticists, mathematicians, and by biologists studying development, natural history and systematics. This was done under a strong influence of marxist ideas. Through the interweaving of such different approaches it was possible for this evolutionary synthesis to influence successfully the development of evolution research during more than 40 years. Philosophically speaking modern evolution theory means therefore an aversion, even a positive abolition of Kantian positions. A number of biologists however--as L. von Bertalanffy--refused to adhere to a misinterpreted Kantian methodology and oriented themselves to an approach via system theory, which obtained a place in evolution research. In fact this is a Kantian approach as well. They only repeated the Kantian dilemma of the evolution which can also be found in Lamarck and Hegel. The system theory of the functionality of the organism never reaches to the level of the evolving species, but remains always on the level of epigenetic thinking, because of its philosophical origin. This paper points out the consequences of this still current dilemma. At the same time an all-enclosing reflection on the methodological, epistemological and

  5. Mapping the functional properties of soft biological tissues under shear loading

    Science.gov (United States)

    Buckley, Mark Raymond

    The structure and composition of articular cartilage and other load-bearing biological tissues are highly complex and heterogeneous. As a result, their functional mechanical properties exhibit clear spatial variations. Unlocking the structure-function relationship in these materials is critical for devising strategies to restore tissue impaired by injury or disease and can provide a template for successful implant design. Here, we describe a tissue deformation imaging stage (TDIS) allowing for simultaneous force measurement and visualization of microscale deformation in soft biological tissues under controlled shear strain. In combination with a fast confocal microscope, the TDIS is used to test the microscale response of articular cartilage to shear loading. To obtain the location-specific shear modulus of this tissue, we employ a high-resolution technique that involves tracking the deformation of a line photobleached into a fluorescently stained sample loaded in the TDIS. We find that the quasi-static and dynamic shear moduli are lowest roughly 100 mum below the articular surface. Here, articular cartilage is highly nonlinear, stiffening under increased shear strain and becoming more compliant under increased compressive strain. Using a simple thought model, we relate these results to structural features of the collagen network in articular cartilage. Furthermore, we demonstrate that the region of maximum compliance is also the primary site of shear energy dissipation in articular cartilage. Our findings suggest that damage to or surgical removal of the surface of this tissue will increase the joint's susceptibility to shear-induced damage. Finally, similar experiments are performed on intervertebral disc and growth plate, demonstrating the versatility of our in-situ strain mapping techniques.

  6. Virtual Agonist-antagonist Mechanisms Produce Biological Muscle-like Functions: An Application for Robot Joint Control

    DEFF Research Database (Denmark)

    Xiong, Xiaofeng; Wörgötter, Florentin; Manoonpong, Poramate

    2014-01-01

    Purpose – Biological muscles of animals have a surprising variety of functions, i.e., struts, springs, and brakes. According to this, the purpose of this paper is to apply virtual agonist-antagonist mechanisms to robot joint control allowing for muscle-like functions and variably compliant joint...

  7. Clinical, Functional, and Biological Correlates of Cognitive Dimensions in Major Depressive Disorder - Rationale, Design, and Characteristics of the Cognitive Function and Mood Study (CoFaM-Study).

    Science.gov (United States)

    Baune, Bernhard T; Air, Tracy

    2016-01-01

    Cross-sectional and longitudinal studies exploring clinical, functional, and biological correlates of major depressive disorder are frequent. In this type of research, depression is most commonly defined as a categorical diagnosis based on studies using diagnostic instruments. Given the phenotypic and biological heterogeneity of depression, we chose to focus the phenotypic assessments on three cognitive dimensions of depression including (a) cognitive performance, (b) emotion processing, and (c) social cognitive functioning. Hence, the overall aim of the study is to investigate the long-term clinical course of these cognitive dimensions in depression and its functional (psychosocial) correlates. We also aim to identify biological "genomic" correlates of these three cognitive dimensions of depression. To address the above overall aim, we created the Cognition and Mood Study (CoFaMS) with the key objective to investigate the clinical, functional, and biological correlates of cognitive dimensions of depression by employing a prospective study design and including a healthy control group. The study commenced in April 2015, including patients with a primary diagnosis of a major depressive episode of major depressive disorder or bipolar disorder according to DSM-IV-TR criteria. The assessments cover the three cognitive dimensions of depression (cognitive performance, emotion processing, and social cognition), cognitive function screening instrument, plus functional scales to assess general, work place, and psychosocial function, depression symptom scales, and clinical course of illness. Blood is collected for comprehensive genomic discovery analyses of biological correlates of cognitive dimensions of depression. The CoFaM-Study represents an innovative approach focusing on cognitive dimensions of depression and its functional and biological "genomic" correlates. The CoFaMS team welcomes collaborations with both national and international researchers. PMID:27616997

  8. A review on speciation of iodine-129 in the environmental and biological samples

    DEFF Research Database (Denmark)

    Hou, Xiaolin; Hansen, Violeta; Aldahan, Ala;

    2009-01-01

    As a long-lived beta-emitting radioisotope of iodine, I-129 is produced both naturally and as a result of human nuclear activities. At present time, the main part of I-129 in the environment originates from the human nuclear activity, especially the releases from the spent nuclear fuel reprocessing...... in the environment. Measurement techniques for the determination of I-129 are presented and compared. An overview of applications of I-129 speciation in various scientific disciplines such as radiation protection, waste depository, and environmental sciences is given. In addition, the bioavailability and radiation...

  9. Environmental and Biological Controls of Tidal Banding in the Common Mussel Mytilus californianus

    Science.gov (United States)

    Ford, H. L.; Schellenberg, S. A.

    2005-12-01

    Mytilus californianus, a common intertidal mussel of the North Pacific, is often used to monitor coastal water quality via tissue incorporation of heavy metals and biotoxins, and is increasingly used to reconstruct environmental conditions (i.e. temperature, salinity, and seasonality) archived within shell carbonate. However, little is known about what governs the banded shell growth of M. californianus and accordingly, the completeness of the environmental record contained within the shell. Presumably, the most important factor determining growth is submergence (required for biomineralization and feeding), but other factors such as temperature variability, subaerial exposure, and respiration stress may also influence growth patterns. Observations from thin sections oriented along the maximum growth axis reveal light and dark banding with diffuse purple coloration throughout the prismatic layer of the shell. Thickness of the banding oscillates from broadly to narrowly (~0.4-1.0μm) spaced light colored bands (periods of crystalline growth) separated by thin dark bands (emergence and respiration). We relate these band oscillations to 1) tidal regime and 2) mussel location within the intertidal zone. Both of these factors dictate the amount of submergence a mussel experiences and thus directly influences the growth and tidal banding. Providing submergence primarily governs the banding oscillations found in M. californianus, we predict that 1) specimens from a low intertidal height have maximum growth during the neap tide (nearly continual submergence and feeding) and diffuse growth increments with no obvious tidal banding and 2) specimens from a high intertidal height have maximum growth during the spring tide (longest duration of submergence), with broadly spaced banding during the spring tides and narrowly spaced bands during the neap tides. On going investigation on thin sections and acetate peels will test these growth predictions to produce a model of M

  10. Differential function of lip residues in the mechanism and biology of an anthrax hemophore.

    Directory of Open Access Journals (Sweden)

    MarCia T Ekworomadu

    Full Text Available To replicate in mammalian hosts, bacterial pathogens must acquire iron. The majority of iron is coordinated to the protoporphyrin ring of heme, which is further bound to hemoglobin. Pathogenic bacteria utilize secreted hemophores to acquire heme from heme sources such as hemoglobin. Bacillus anthracis, the causative agent of anthrax disease, secretes two hemophores, IsdX1 and IsdX2, to acquire heme from host hemoglobin and enhance bacterial replication in iron-starved environments. Both proteins contain NEAr-iron Transporter (NEAT domains, a conserved protein module that functions in heme acquisition in Gram-positive pathogens. Here, we report the structure of IsdX1, the first of a Gram-positive hemophore, with and without bound heme. Overall, IsdX1 forms an immunoglobin-like fold that contains, similar to other NEAT proteins, a 3(10-helix near the heme-binding site. Because the mechanistic function of this helix in NEAT proteins is not yet defined, we focused on the contribution of this region to hemophore and NEAT protein activity, both biochemically and biologically in cultured cells. Site-directed mutagenesis of amino acids in and adjacent to the helix identified residues important for heme and hemoglobin association, with some mutations affecting both properties and other mutations affecting only heme stabilization. IsdX1 with mutations that reduced the ability to associate with hemoglobin and bind heme failed to restore the growth of a hemophore-deficient strain of B. anthracis on hemoglobin as the sole iron source. These data indicate that not only is the 3(10-helix important for NEAT protein biology, but also that the processes of hemoglobin and heme binding can be both separate as well as coupled, the latter function being necessary for maximal heme-scavenging activity. These studies enhance our understanding of NEAT domain and hemophore function and set the stage for structure-based inhibitor design to block NEAT domain interaction

  11. Organic Composition and Morphology of Sea Spray Aerosols as a Function of Biological Life during IMPACTS

    Science.gov (United States)

    Pham, D.; Moffet, R.; Fraund, M. W.; O'Brien, R.; Laskina, O.; Prather, K. A.; Grassian, V. H.; Beall, C.; Wang, X.; Forestieri, S.; Cappa, C. D.

    2015-12-01

    Aerosols influence climate by directly reflecting or absorbing sunlight, or indirectly by affecting clouds. A major source of aerosols is from oceanic wave breaking. Due to their complexity, the effects of marine aerosol on climate are uncertain. To provide more detailed measurements of the chemical composition of marine aerosols, Scanning Transmission X-Ray Microscopy coupled with Near Edge X-Ray Absorption Fine Structure (SXTM-NEXAFS) was used to give spatially resolved molecular information for carbon and oxygen. Application of STXM/NEXAFS to particles collected during a mesocosm study using a unique wave channel facility to generate aerosols shows that the organic volume fraction of aerosols at the aerodynamic diameter size range of 0.18-0.32 μm are a direct function of the biological activity in the sea water. Aerosol organic volume fraction increased from 0.32 for particles generated from seawater containing low biolife to 0.49 and 0.40 for particles produced during phytoplankton blooms. However, the organic volume fraction of aerosols at the aerodynamic diameter size range of 0.56-1 μm did not change with biological activity. Measurements also show that different types of organics can concentrate into aerosols depending on the enzyme activity expressed at the time. Enhanced spectral signatures for aliphatic hydrocarbons were observed during the first phytoplankton bloom compared to a second phytoplankton bloom occurring directly thereafter. The decreased signature of aliphatic organics in the second phytoplankton bloom was correlated with increased lipase activity from heterobacteria. Organic aggregates having similar morphology also differ in composition from their carbon spectra from the two blooms. For July 17, organic aggregates were much richer in hydrocarbons, which showed a remarkably intense C-H absorbance and a broad C-C absorbance. Organic aggregates observed for July 26-27, did not have the C-H and C-C signatures, but contained more polar

  12. Environmental conditions influence the plant functional diversity effect on potential denitrification.

    Directory of Open Access Journals (Sweden)

    Ariana E Sutton-Grier

    Full Text Available Global biodiversity loss has prompted research on the relationship between species diversity and ecosystem functioning. Few studies have examined how plant diversity impacts belowground processes; even fewer have examined how varying resource levels can influence the effect of plant diversity on microbial activity. In a field experiment in a restored wetland, we examined the role of plant trait diversity (or functional diversity, (FD and its interactions with natural levels of variability of soil properties, on a microbial process, denitrification potential (DNP. We demonstrated that FD significantly affected microbial DNP through its interactions with soil conditions; increasing FD led to increased DNP but mainly at higher levels of soil resources. Our results suggest that the effect of species diversity on ecosystem functioning may depend on environmental factors such as resource availability. Future biodiversity experiments should examine how natural levels of environmental variability impact the importance of biodiversity to ecosystem functioning.

  13. Analytical quality assurance in laboratories using tracers for biological and environmental studies

    International Nuclear Information System (INIS)

    This work describe the way we are organizing a quality assurance system to apply in the analytical measurements of the relation 14N/15N in biological and soil material. The relation 14/15 is measured with a optic emission spectrometer (NOI6PC), which distinguish the differences in wave length of electromagnetic radiation emitted by N-28, N-29 and N-30. The major problem is the 'cross contamination' of samples with different enrichments. The elements that are been considered to reach satisfactory analytical results are: 1) A proper working area; 2) The samples must be homogeneous and the samples must represent the whole sampled system; 3) The use of reference materials. In each digestion, a known reference sample must be added; 4) Adequate equipment operation; 5) Standard operating procedures; 6) Control charts, laboratory and equipment books. All operations using the equipment is registered in a book; 7) Training of the operators. (author)

  14. Development and validation of evolutionary algorithm software as an optimization tool for biological and environmental applications.

    Science.gov (United States)

    Sys, K; Boon, N; Verstraete, W

    2004-06-01

    A flexible, extendable tool for the optimization of (micro)biological processes and protocols using evolutionary algorithms was developed. It has been tested using three different theoretical optimization problems: 2 two-dimensional problems, one with three maxima and one with five maxima and a river autopurification optimization problem with boundary conditions. For each problem, different evolutionary parameter settings were used for the optimization. For each combination of evolutionary parameters, 15 generations were run 20 times. It has been shown that in all cases, the evolutionary algorithm gave rise to valuable results. Generally, the algorithms were able to detect the more stable sub-maximum even if there existed less stable maxima. The latter is, from a practical point of view, generally more desired. The most important factors influencing the convergence process were the parameter value randomization rate and distribution. The developed software, described in this work, is available for free.

  15. Phanerozoic size history of the foraminifera: Implications for environmental and biological controls on macroevolutionary trends

    Science.gov (United States)

    Payne, J.; Jost, A. B.; Cummins, R.; Tachiki, N.; Ingram, K.

    2009-12-01

    Size is among the most important ecological characteristics of any organism, correlating with a wide variety of traits from metabolic rate to generation time. Although there have been numerous studies of body size evolution in the fossil record, few have spanned multiple geological eras. Thus, the effect of environmental changes occurring on Wilson-cycle timescales (hundreds of millions of years) on the evolution of size remains poorly understood. We compiled a comprehensive genus-level size database for benthic foraminifers through Phanerozoic time. We find that the average size of calcareous benthic foraminifers increased gradually through the Late Paleozoic, reaching local maxima in mean and maximum size during the Early Permian. Sizes decreased to a relative minimum during the Early Triassic before increasing gradually to a second local maximum in the Late Cretaceous (for maximum size) and early Paleogene (for mean size). Close resemblance of trends in mean size to trends in atmospheric oxygen concentrations suggest either oxygen has been an important driver of size evolution or the two variables share a common control. Superimposed on these long-term trends are signatures of the major extinction events. Four of the five largest drops in mean size occur in association with the Middle Permian (Guadalupian), end-Permian, end-Triassic, and end-Cretaceous mass extinctions. Thus, the Phanerozoic size history of benthic foraminifera appears to have been driven primarily by long-term and short-term environmental change.

  16. Image diagnosis of plant function under environmental pollution. Shokubutsu de kankyo osen wo shindansuru

    Energy Technology Data Exchange (ETDEWEB)

    Omasa, K. (National Inst. for Environmental studies, Tsukuba (Japan))

    1993-12-20

    Various physiological reaction of plants would be obstructed and troubles of their growth would be met under environmental pollution. There are also cases that the polluted materials as nutritious components are absorbed by plants. Consequently, if plant's reaction on this environmental pollution would be used, indexes of environmental pollution and environment can be improved. For examples, Ipomoea Nil and Petunia having high reaction on photochemical oxidate are widely used as index plant of air pollution. Zelkova trees and poplars planted as street trees can also greatly absorbed the polluted gas and have a function to clear air. In this paper, a diagnosis method by visualizing plant's reaction on environmental pollution by using technique of image measurement was explained. As devices of usable image measurement, a thermal camera, a solid measuring cameras, an ultrasonic camera, a multi-spectral camera and an X-ray TV camera were given. 6 refs., 4 figs., 1 tab.

  17. Home and Community Environmental Features, Activity Performance, and Community Participation among Older Adults with Functional Limitations

    Directory of Open Access Journals (Sweden)

    Hsiang-Yu Yang

    2012-01-01

    Full Text Available This paper describes relationships among home and community environmental features, activity performance in the home, and community participation potential to support aging in place. A subset of data on older adults with functional limitations (=122, sixty three (63 with mobility and 59 with other limitations, were utilized in this study from a larger project's subject pool. Results showed significant and positive correlations between environmental barriers, activity dependence and difficulty at home, and less community participation in the mobility limitation group. While kitchen and bathroom features were most limiting to home performance, bathtub or shower was the only home feature, and destination social environment was the only community feature, that explained community participation. Compared to environmental features, home performance explained much more community participation. Study results provide detailed information about environmental features as well as types of home activities that can be prioritized as interventions for aging in place.

  18. The biological mechanisms and behavioral functions of opsin-based light detection by the skin

    Directory of Open Access Journals (Sweden)

    Jennifer L Kelley

    2016-08-01

    Full Text Available Light detection not only forms the basis of vision (via visual retinal photoreceptors, but can also occur in other parts of the body, including many non-rod/non-cone ocular cells, the pineal complex, the deep brain, and the skin. Indeed, many of the photopigments (an opsin linked to a light-sensitive 11-cis retinal chromophore that mediate color vision in the eyes of vertebrates are also present in the skin of animals such as reptiles, amphibians, crustaceans and fishes (with related photoreceptive molecules present in cephalopods, providing a localized mechanism for light detection across the surface of the body. This form of non-visual photosensitivity may be particularly important for animals that can change their coloration by altering the dispersion of pigments within the chromatophores (pigment containing cells of the skin. Thus, skin coloration may be directly color matched or tuned to both the luminance and spectral properties of the local background environment, thereby facilitating behavioral functions such as camouflage, thermoregulation, and social signaling. This review examines the diversity and sensitivity of opsin-based photopigments present in the skin and considers their putative functional roles in mediating animal behavior. Furthermore, it discusses the potential underlying biochemical and molecular pathways that link shifts in environmental light to both photopigment expression and chromatophore photoresponses. Although photoreception that occurs independently of image formation remains poorly understood, this review highlights the important role of non-visual light detection in facilitating the multiple functions of animal coloration.

  19. Production of sorption functional media (SFM) from clinoptilolite tailings and its performance investigation in a biological aerated filter (BAF) reactor

    International Nuclear Information System (INIS)

    Highlights: ► Sorption functional media (SFM) were prepared using zeolite tailings. ► Two upflow BAFs were applied to treat municipal wastewater. ► SFM BAF brought a relative superiority to haydite reactor. ► SFM BAF has a stronger adaptability to low temperature (6–11°C) for NH3-N removal. ► The application provided a promising way in zeolite tailings utilization. -- Abstract: The few reuse and large stockpile of zeolite tailings led to a series of social and environmental problems. This study investigated the possibility of using the zeolite tailings as one of principal raw materials to prepare sorption functional media (SFM) by a high temperature sintering process. The SFM was used to serve as a biomedium in a biological aerated filter (BAF) reactor for domestic wastewater treatment, and its purification performance was examined. The physical, chemical and sorption properties of SFM were also determined. The microstructure of the SFM was analyzed by scanning electron microscopy (SEM). Results revealed that: (1) zeolite tailings could be used to produce the SFM under the optimal sintering parameters; (2) the sorption and desorption isotherm of ammonia nitrogen on SFM could be well described by the Langmuir formula; (3) in terms of removing organic matter, ammonia nitrogen, turbidity and colourity, the performance of the biofilter with SFM was superior to that with haydite; and (4) SFM BAF has a stronger adaptability to low temperature (6–11 °C) for NH3-N removal compared to haydite BAF. Therefore, the SFM produced from the zeolite tailings was suitable to serve as the biomedium in the domestic wastewater treatment

  20. Production of sorption functional media (SFM) from clinoptilolite tailings and its performance investigation in a biological aerated filter (BAF) reactor

    Energy Technology Data Exchange (ETDEWEB)

    Feng, Yan [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); School of Civil Engineering and Architecture, University of Jinan, Jinan 250022 (China); Qi, Jingyao, E-mail: qjy_hit@yahoo.cn [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Chi, Liying [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China); Wang, Dong [School of Civil Engineering and Architecture, University of Jinan, Jinan 250022 (China); Wang, Zhaoyang; Li, Ke; Li, Xin [School of Municipal and Environmental Engineering, Harbin Institute of Technology, Harbin 150090 (China)

    2013-02-15

    Highlights: ► Sorption functional media (SFM) were prepared using zeolite tailings. ► Two upflow BAFs were applied to treat municipal wastewater. ► SFM BAF brought a relative superiority to haydite reactor. ► SFM BAF has a stronger adaptability to low temperature (6–11°C) for NH{sub 3}-N removal. ► The application provided a promising way in zeolite tailings utilization. -- Abstract: The few reuse and large stockpile of zeolite tailings led to a series of social and environmental problems. This study investigated the possibility of using the zeolite tailings as one of principal raw materials to prepare sorption functional media (SFM) by a high temperature sintering process. The SFM was used to serve as a biomedium in a biological aerated filter (BAF) reactor for domestic wastewater treatment, and its purification performance was examined. The physical, chemical and sorption properties of SFM were also determined. The microstructure of the SFM was analyzed by scanning electron microscopy (SEM). Results revealed that: (1) zeolite tailings could be used to produce the SFM under the optimal sintering parameters; (2) the sorption and desorption isotherm of ammonia nitrogen on SFM could be well described by the Langmuir formula; (3) in terms of removing organic matter, ammonia nitrogen, turbidity and colourity, the performance of the biofilter with SFM was superior to that with haydite; and (4) SFM BAF has a stronger adaptability to low temperature (6–11 °C) for NH{sub 3}-N removal compared to haydite BAF. Therefore, the SFM produced from the zeolite tailings was suitable to serve as the biomedium in the domestic wastewater treatment.

  1. Biological consequences of environmental changes related to coastal upwelling: a simulation study

    Energy Technology Data Exchange (ETDEWEB)

    Howe, S.O.

    1979-05-01

    Two simulation models of marine ecosystem dynamics are formulated and applied to field data. The first is a time-dependent model of phytoplankton growth in nutrient-enriched batch cultures where spatial gradients of dependent variables and the effects of higher tropic level processes are not included. Rates of photosynthesis, nutrient uptake, chlorophyll synthesis and cell division for a single phytoplankton functional group are simulated as functions of photosynthetically active solar radiation, dissolved nutrient concentrations and cell quotas of carbon, nitrogen and silica. The second model combines the phytoplankton growth model with a time dependent, two-dimensional model of coastal upwelling off northwest Africa.

  2. Identifying environmental risk to male reproductive function by occupational sperm studies: logistics and design options.

    NARCIS (Netherlands)

    Bonde, J.P.; Giwercman, A.; Ernst, E.; Joffe, M.; Bisanti, L.; Hoorne M, van M.; Thonneau, P.; Zielhuis, G.; Kiss, P.; Abell, A.; Larsen, S.B.; Danscher, G.; Kolstad, H.

    1996-01-01

    Malfunction of the male reproductive system might be a sensitive marker of environmental hazards, the effects of which may extend beyond reproductive function. The testis is more vulnerable to heat and ionising radiation than any other organ of the body and several xenobiotics are known to disrupt s

  3. GST-omega genes interact with environmental tobacco smoke on adult level of lung function

    NARCIS (Netherlands)

    de Jong, Kim; Boezen, Hendrika; ten Hacken, Nicolaas; Postma, Dirkje S; Vonk, Judith M

    2013-01-01

    BACKGROUND: Lung growth in utero and lung function loss during adulthood can be affected by exposure to environmental tobacco smoke (ETS). The underlying mechanisms have not been fully elucidated. Both ETS exposure and single nucleotide polymorphisms (SNPs) in Glutathione S-Transferase (GST) Omega g

  4. Environmental effects on recruitment and implications for biological reference points of Eastern Baltic cod (Gadus morhua)

    DEFF Research Database (Denmark)

    Köster, Fritz; Vinther, Morten; MacKenzie, Brian;

    2009-01-01

    stock productivity. Long-term projections suggest that under adverse environmental conditions for reproduction, harvesting at fishing mortality determined as precautionary may not lead to a recovery of the stock to a biomass level considered precautionary. Thus, a revision of either the limit fishing......The decline of the Eastern Baltic cod (Gadus morhua) stock from highest to lowest stock levels on record throughout the 1980s and early 1990s was caused by a combination of recruitment failure and increasing fishing pressure at declining stock sizes. The processes driving the reproductive success...... of limit reference points, but according to long-term simulations also for target fishing mortalities, being central parts of harvest control rules in several management plans....

  5. NATO Advanced Research Workshop on Environmental and Biological Risks of Hybrid Organic-Silicon Nanodevices

    CERN Document Server

    Kozyrev, Sergey; Vaseashta, Ashok

    2009-01-01

    Even though there is no generally accepted definition of nanotechnologies to be defined as distinct discipline there is an emerging consensus that their advent and development is a growing in importance factor of the contemporary and future technological civilization. One of these most fundamental issues we are confronted with is the compatibility with life itself. From single cell organisms to humans, carbon is a key building block of all molecular structures of life. In contrast the man created electronic industry to build on other elements, of which silicon is the most common. Both carbon and silicon create molecular chains, although different in their internal structure. All life is built from carbon-based chains. As long as the man built technological products do not directly interfere with the physiology of life the associated risks from them are relatively easy to identify. They are primarily in the environmental pollution and the possibility of upsetting the natural balance of biocoenosis, on a planet...

  6. Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function

    OpenAIRE

    Griffiths, Bryan; Römbke, J.; Schmelz, R. M.; Scheffczyk, A.; Faber, J.H.; Bloem, J.; Peres, G.; Cluzeau, D.; Chabbi, A.; Suhadolc, M.; Sousa, J. P.; Martins da Silva, P.; F. Carvalho; Mendes, S; MORAIS, P.

    2016-01-01

    International audience; Soils provide many ecosystem services that are ultimately dependent on the local diversity and belowground abundance of organisms. Soil biodiversity is affected negatively by many threats and there is a perceived policy requirement for the effective biological monitoring of soils at the European level. The aim of this study was to evaluate and recommend policy relevant, cost-effective soil biological indicators for biodiversity and ecosystem function across Europe. A t...

  7. Expression of Recombinant Human Amelogenin in Iranian Lizard Leishmania and Its Biological Function Assay

    Directory of Open Access Journals (Sweden)

    Zahra YADEGARI

    2015-10-01

    Full Text Available Background: Amelogenins are the major components of enamel matrix proteins. Enamel matrix derivatives (EMD can be used in periodontal diseases to regenerate periodontal tissues. The main aim of this study was to evaluate ex-pression of full-length functional recombinant human amelogenin (rhAm in Iranian lizard Leishmania (I.L.L. as an alternative eukaryotic expression system.Methods: Human cDNA encoding a 175-amino acid amelogenin expression cassette was sub cloned into a pLEXSY vector. The construct was transferred into Leishmania cells by electroporation. The protein production was surveyed in the transcription and the translation levels. The expressed protein was purified and some of its biological properties were investigated in comparison to EMD and negative control.Results: Expression of rhAm was confirmed by RT-PCR and western blot test in Leishmania cells. Purified rhAm sig-nificantly inhibited the formation of tartrate-resistant acid phosphatase positive (TRAP+ multinuclear cells in calcitriol stimulated mouse marrow cultures. Moreover, it significantly promoted proliferation and DNA synthesis in L929 mouse fibroblast cells.Conclusion: Functional rhAm was successfully expressed in I.L.L. Easy handling and post translation modification were the main advantages of this expression system. It is suggested to investigate molecular properties of this rhAm in the future.

  8. SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function.

    Science.gov (United States)

    Tomer, Raju; Lovett-Barron, Matthew; Kauvar, Isaac; Andalman, Aaron; Burns, Vanessa M; Sankaran, Sethuraman; Grosenick, Logan; Broxton, Michael; Yang, Samuel; Deisseroth, Karl

    2015-12-17

    The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here, we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca(2+) imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function.

  9. Optimization of polysaccharides extraction from watermelon rinds: Structure, functional and biological activities.

    Science.gov (United States)

    Romdhane, Molka Ben; Haddar, Anissa; Ghazala, Imen; Jeddou, Khawla Ben; Helbert, Claire Boisset; Ellouz-Chaabouni, Semia

    2017-02-01

    In the present work, optimization of hot water extraction, structural characteristics, functional properties, and biological activities of polysaccharides extracted from watermelon rinds (WMRP) were investigated. The physicochemical characteristics and the monosaccharide composition of these polysaccharides were then determined using chemical composition analysis, Fourier transform infrared (FT-IR) spectroscopy, scanning electron microscopy (SEM) and gas chromatography-flame ionization detection (GC-FID). SEM images showed that extracted polysaccharides had a rough surface with many cavities. GC-FID results proved that galactose was the dominant sugar in the extracted polysaccharides, followed by arabinose, glucose, galacturonic acid, rhamnose, mannose, xylose and traces of glucuronic acid. The findings revealed that WMRP displayed excellent antihypertensive and antioxidant activities. Those polysaccharides had also a protection effect against hydroxyl radical-induced DNA damage. Functional properties of extracted polysaccharides were also evaluated. WMRP showed good interfacial dose-dependent proprieties. Overall, the results suggested that WMRP presents a promising natural source of antioxidants and antihypertensive agents. PMID:27596431

  10. Utilizing systems biology to unravel stomatal function and the hierarchies underpinning its control.

    Science.gov (United States)

    Medeiros, David B; Daloso, Danilo M; Fernie, Alisdair R; Nikoloski, Zoran; Araújo, Wagner L

    2015-08-01

    Stomata control the concomitant exchange of CO2 and transpiration in land plants. While a constant supply of CO2 is need to maintain the rate of photosynthesis, the accompanying water losses must be tightly regulated to prevent dehydration and undesired metabolic changes. The factors affecting stomatal movement are directly coupled with the cellular networks of guard cells. Although the guard cell has been used as a model for characterization of signaling pathways, several important questions about its functioning remain elusive. Current modeling approaches describe the stomatal conductance in terms of relatively few easy-to-measure variables being unsuitable for in silico design of genetic manipulation strategies. Here, we argue that a system biology approach, combining modeling and high-throughput experiments, may be used to elucidate the mechanisms underlying stomata control and to determine targets for modulation of stomatal responses to environment. In support of our opinion, we review studies demonstrating how high-throughput approaches have provided a systems-view of guard cells. Finally, we emphasize the opportunities and challenges of genome-scale modeling and large-scale data integration for in silico manipulation of guard cell functions to improve crop yields, particularly under stress conditions which are of pertinence both to climate change and water use efficiency. PMID:25689387

  11. To Build an Ecosystem: An Introductory Lab for Environmental Science & Biology Students

    Science.gov (United States)

    Hudon, Daniel; Finnerty, John R.

    2013-01-01

    A hypothesis-driven laboratory is described that introduces students to the complexities of ecosystem function. Students work with live algae, brine shrimp, and sea anemones to test hypotheses regarding the trophic interactions among species, the exchange of nutrients and gases, and the optimal ratio of producers to consumers and predators in…

  12. Critical comparison of radiometric and mass spectrometric methods for the determination of radionuclides in environmental, biological and nuclear waste samples.

    Science.gov (United States)

    Hou, Xiaolin; Roos, Per

    2008-02-11

    The radiometric methods, alpha (alpha)-, beta (beta)-, gamma (gamma)-spectrometry, and mass spectrometric methods, inductively coupled plasma mass spectrometry, accelerator mass spectrometry, thermal ionization mass spectrometry, resonance ionization mass spectrometry, secondary ion mass spectrometry, and glow discharge mass spectrometry are reviewed for the determination of radionuclides. These methods are critically compared for the determination of long-lived radionuclides important for radiation protection, decommissioning of nuclear facilities, repository of nuclear waste, tracer application in the environmental and biological researches, these radionuclides include (3)H, (14)C, (36)Cl, (41)Ca, (59,63)Ni, (89,90)Sr, (99)Tc, (129)I, (135,137)Cs, (210)Pb, (226,228)Ra, (237)Np, (241)Am, and isotopes of thorium, uranium and plutonium. The application of on-line methods (flow injection/sequential injection) for separation of radionuclides and automated determination of radionuclides is also discussed.

  13. Environmental Effect on the Biological Behavior of The Cucurbit Beetle Epilachna chrysomelina in Al-Qunfudah Province-Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Saleh A. Aldigail

    2013-08-01

    Full Text Available Epilachna chrysomelina (Coleoptera: Coccinellidae is a phytophagous insect with an economic importance damaging the agricultural crops. The Melon Ladybird Beetle, E. Chrysomelinais one of the major phytophagous insects that feed on cucurbit plants. It is considered an economic pest in agriculture and multi-habitat insect widely distributed throughout the world.The insect is abundant in the southern region of Saudi Arabia and choose the most favourable conditions for its life cycle completion. It prefers humid habitats with optimum temperature degrees. The generations of the insect are affected by changes in environmental conditions and its numbers increase or decline according to variation in temperature and relative humidity (RH. These factors play an important role in changing its biological behaviour particularly feeding, breeding, reproduction and development of its generations. There were significant differences between the different developmental stages in the periods of time of their development.

  14. Critical comparison of radiometric and mass spectrometric methods for the determination of radionuclides in environmental, biological and nuclear waste samples.

    Science.gov (United States)

    Hou, Xiaolin; Roos, Per

    2008-02-11

    The radiometric methods, alpha (alpha)-, beta (beta)-, gamma (gamma)-spectrometry, and mass spectrometric methods, inductively coupled plasma mass spectrometry, accelerator mass spectrometry, thermal ionization mass spectrometry, resonance ionization mass spectrometry, secondary ion mass spectrometry, and glow discharge mass spectrometry are reviewed for the determination of radionuclides. These methods are critically compared for the determination of long-lived radionuclides important for radiation protection, decommissioning of nuclear facilities, repository of nuclear waste, tracer application in the environmental and biological researches, these radionuclides include (3)H, (14)C, (36)Cl, (41)Ca, (59,63)Ni, (89,90)Sr, (99)Tc, (129)I, (135,137)Cs, (210)Pb, (226,228)Ra, (237)Np, (241)Am, and isotopes of thorium, uranium and plutonium. The application of on-line methods (flow injection/sequential injection) for separation of radionuclides and automated determination of radionuclides is also discussed. PMID:18215644

  15. Default mode network connectivity as a function of familial and environmental risk for psychotic disorder.

    Directory of Open Access Journals (Sweden)

    Sanne C T Peeters

    Full Text Available Research suggests that altered interregional connectivity in specific networks, such as the default mode network (DMN, is associated with cognitive and psychotic symptoms in schizophrenia. In addition, frontal and limbic connectivity alterations have been associated with trauma, drug use and urban upbringing, though these environmental exposures have never been examined in relation to DMN functional connectivity in psychotic disorder.Resting-state functional MRI scans were obtained from 73 patients with psychotic disorder, 83 non-psychotic siblings of patients with psychotic disorder and 72 healthy controls. Posterior cingulate cortex (PCC seed-based correlation analysis was used to estimate functional connectivity within the DMN. DMN functional connectivity was examined in relation to group (familial risk, group × environmental exposure (to cannabis, developmental trauma and urbanicity and symptomatology.There was a significant association between group and PCC connectivity with the inferior parietal lobule (IPL, the precuneus (PCu and the medial prefrontal cortex (MPFC. Compared to controls, patients and siblings had increased PCC connectivity with the IPL, PCu and MPFC. In the IPL and PCu, the functional connectivity of siblings was intermediate to that of controls and patients. No significant associations were found between DMN connectivity and (subclinical psychotic/cognitive symptoms. In addition, there were no significant interactions between group and environmental exposures in the model of PCC functional connectivity.Increased functional connectivity in individuals with (increased risk for psychotic disorder may reflect trait-related network alterations. The within-network "connectivity at rest" intermediate phenotype was not associated with (subclinical psychotic or cognitive symptoms. The association between familial risk and DMN connectivity was not conditional on environmental exposure.

  16. Surfactant-Assisted Nanodrop Spectrophotometer Determination of Iron(III) in a Single Drop of Food, Biological, and Environmental Samples

    Science.gov (United States)

    Sharma, A.; Tapadia, K.; Sahin, R.; Shrivas, K.

    2016-01-01

    A surfactant-assisted nanodrop spectrophotometric (NDS) method has been developed for the determination of the iron(III) content in single drops (1 μ L) of food, biological, and or environmental sample using disodium 1-nitroso-2-naphthol-3,6-sulfonate (Nitroso-R salt) as a complexing agent and Tween-80 as non-ionic surfactant at pH 4.0. This method is based on the formation of a complex between the Fe(III) present in a sample and the Nitroso-R-salt in the presence of a surfactant to form a green-colored Fe(III)-Nitroso-R salt complex, which can be measured using a NDS method at a λ max = 710 nm. This system was found to obey Beer's law at concentrations in the range of 50-5000 μ g/L with slope, intercept and correlation coefficient values of 0.683, 0.102, and 0.986, respectively. The molar absorptivity of the complex in terms of the Fe(III) content was determined to be 4.86 × 10 5 L· mol -1 · cm -1 . The detection limit and %RSD values of the method were found to be 17 × 10-3 mg/L and ±1.3706%, respectively. This newly developed method was successfully applied to the determination of the Fe(III) content in single drops of food, biological, and environmental samples, and the results were compared with those obtained by atomic absorption spectrometry.

  17. The application of environmental economics in marine functional zoning and coastal city conceptual planning

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    There are a lot of functions of marine resources.The various and competing conflicts between different users and different sectors in th euse of marine resources will cause the disorderly development of marine resources,and even destroy the marine ecosystem.Marine functional zoning is an effective tool to solve the conflicts.However,there are some shortcomings in the current understanding on marine functional zoning and its practice.In this paper,a case study on the resource-oriented marine functional zoning of Xiangshan Port is introduced.By the prmeiples of resource-oriented and public participation,Xiangshan Pon is divided into seven zones.and the main function of the whole port and seven zones are determined by the environmental economics analysis.A case study of Xiamen is also introduced for how to integrate marine functional zoning into a coastal city conceptual planning.Under the conservation prmciple,resources-oriented principle and so on,the advantages and disadvantages of natural ecosystem,social ecosystem and econnomic ecosystem are holistically analyzed,the urban orientation of Xiamen is determined as a regional international tourism ciif,and the whole city is divided into five function zones according to its leading industry-tourism.Resource-oriented marine functional zoning has a long-term guidance for sustainable use of marine resources and development strategy of a coastal city.And environmental economics analysis is an effective tool for resource-orientation.

  18. Development of Spectral Domain Optical Coherence Tomography for in vivo Functional Imaging of Biological Tissues

    Science.gov (United States)

    An, Lin

    Optical coherence tomography is a rapidly developing optical imaging modality capable of noninvasively providing depth resolved information of biological tissue at micrometer scale. In this thesis, we described several OCT technologies that can be used to double the imaging depth, realize functional vasculature imaging of biological tissue and increase the imaging speed of OCT system. Aim 1: Use of a scanner to introduce spatial frequency modulation to OCT spectral interferograms for in vivo full-range Fourier-domain optical coherence tomography. A novel method was developed that could easily introduce a modulation frequency onto the X-direction (i.e., B-scan) of the FDOCT scanning system, enabling full-range Fourier-domain Optical Coherence Tomography (frFDOCT). Compared to the conventional FDOCT system, the newly developed frFDOCT system can provide increased system sensitivity and deeper imaging depth. The previous technology that can achieve frFDOCT either needed multiple steps for data capturing, which is time consuming, or required additional components which increased the system's complexity. The newly developed method generates a modulation spatial frequency in the spectral interferogram by simply offsetting the probe beam at the X-scanner. Aim 2: Using optical micro-angiography to achieve in vivo volumetric imaging of vascular perfusion within human retina and choroids. Optical Micro-Angiography (OMAG) is a functional extension of FDOCT technology. It can achieve visualization of vasculature network of biological tissue. In order to apply the OMAG method to image vasculature map of human retina and choroid, a phase compensation algorithm was developed, which could minimize the motion artifacts generated by the movements of human eye and head. Aim 3: Developing ultrahigh sensitive optical micro-angiography to achieve micro vasculature imaging of biological tissue. To improve the vasculature image quality, we developed ultrahigh sensitive OMAG (UHS

  19. Modification of chitosan derivatives of environmental and biological interest: a green chemistry approach.

    Science.gov (United States)

    Abdelaal, Magdy Y; Sobahi, Tariq R; Al-Shareef, Hossa F

    2013-04-01

    Chitosan is a non-toxic polyaminosaccharide that is available in a variety of useful forms, and its chemical and biological properties make it a very attractive biomaterial that could be used in a wide variety of medicinal applications. This work focuses on the preparation of different chitosan derivatives by treatment with ethyl cellulose, cellulose triacetate and different carbohydrates in both neutral and slightly acidic media. It also addresses modification with glycidyltrimethyl ammonium chloride, phthalic anhydride and succinic acid derivatives. The obtained derivatives were crosslinked with glutaraldehyde. Thermo-gravimetric (TGA) and FT-IR spectroscopic analyses and electron scanning microscopy (SEM) were used to characterize the obtained products and demonstrate the success of the chitosan-modification process. The obtained products were tested for their ability to uptake transition metal ions from aqueous solutions, and their ion-uptake efficiency was determined with the aid of the ICP-AES technique. The bioactivity of some selected products was tested to study the effect of their concentrations on selected microorganisms. Burkholderia cepaci, Aspergillus niger, and Candida albicans were selected as representative examples of bacteria, yeasts and fungi, respectively.

  20. Modification of chitosan derivatives of environmental and biological interest: a green chemistry approach.

    Science.gov (United States)

    Abdelaal, Magdy Y; Sobahi, Tariq R; Al-Shareef, Hossa F

    2013-04-01

    Chitosan is a non-toxic polyaminosaccharide that is available in a variety of useful forms, and its chemical and biological properties make it a very attractive biomaterial that could be used in a wide variety of medicinal applications. This work focuses on the preparation of different chitosan derivatives by treatment with ethyl cellulose, cellulose triacetate and different carbohydrates in both neutral and slightly acidic media. It also addresses modification with glycidyltrimethyl ammonium chloride, phthalic anhydride and succinic acid derivatives. The obtained derivatives were crosslinked with glutaraldehyde. Thermo-gravimetric (TGA) and FT-IR spectroscopic analyses and electron scanning microscopy (SEM) were used to characterize the obtained products and demonstrate the success of the chitosan-modification process. The obtained products were tested for their ability to uptake transition metal ions from aqueous solutions, and their ion-uptake efficiency was determined with the aid of the ICP-AES technique. The bioactivity of some selected products was tested to study the effect of their concentrations on selected microorganisms. Burkholderia cepaci, Aspergillus niger, and Candida albicans were selected as representative examples of bacteria, yeasts and fungi, respectively. PMID:23376358

  1. Structured Development and Promotion of a Research Field: Hormesis in Biology, Toxicology, and Environmental Regulatory Science.

    Science.gov (United States)

    Mushak, Paul; Elliott, Kevin C

    2015-12-01

    The ability of powerful and well-funded interest groups to steer scientific research in ways that advance their goals has become a significant social concern. This steering ability is increasingly being recognized in the peer-reviewed scientific literature and in findings of deliberative scientific bodies. This paper provides a case study that illustrates some of the major strategies that can be used to structure and advance a controversial research field. It focuses on hormesis, described as a type of dose-response relationship in toxicology and biology showing low-dose stimulation but high-dose inhibition, or the reverse. Hormesis proponents tout its significance, arguing that substances toxic at high doses and beneficial at lower doses should be regulated less stringently. We identify five strategies employed by hormesis proponents to foster its acceptance: (1) creating institutions focused on supporting hormesis; (2) developing terminology, study designs, and data interpretations that cast it in a favorable light; (3) using bibliometric techniques and surveys to attract attention; (4) aggressively advocating for the phenomenon and challenging critics; and (5) working with outside interest groups to apply the hormesis phenomenon in the economic and political spheres. We also suggest a number of oversight strategies that can be implemented to help promote credible and socially responsible research in cases like this one.

  2. A visualization tool to support decision making in environmental and biological planning

    Science.gov (United States)

    Romañach, Stephanie S.; McKelvy, James M.; Conzelmann, Craig; Suir, Kevin J.

    2014-01-01

    Large-scale ecosystem management involves consideration of many factors for informed decision making. The EverVIEW Data Viewer is a cross-platform desktop decision support tool to help decision makers compare simulation model outputs from competing plans for restoring Florida's Greater Everglades. The integration of NetCDF metadata conventions into EverVIEW allows end-users from multiple institutions within and beyond the Everglades restoration community to share information and tools. Our development process incorporates continuous interaction with targeted end-users for increased likelihood of adoption. One of EverVIEW's signature features is side-by-side map panels, which can be used to simultaneously compare species or habitat impacts from alternative restoration plans. Other features include examination of potential restoration plan impacts across multiple geographic or tabular displays, and animation through time. As a result of an iterative, standards-driven approach, EverVIEW is relevant to large-scale planning beyond Florida, and is used in multiple biological planning efforts in the United States.

  3. Enrichment and immobilization of sulfide removal microbiota applied for environmental biological remediation of aquaculture area.

    Science.gov (United States)

    Zhao, Yang-Guo; Zheng, Yu; Tian, Weijun; Bai, Jie; Feng, Gong; Guo, Liang; Gao, Mengchun

    2016-07-01

    To remove sulfide in the deteriorating aquaculture sediment and water, sulfide-oxidizing microbiota was enriched from Jiaozhou Bay, China, by using sulfide-rich medium. Composition and structure of microbial communities in the enrichments were investigated by 16S rDNA molecular biotechniques. Results showed that microbial community structure continuously shifted and the abundance of sulfate reducing bacteria, i.e., Desulfobacterium, Desulfococcus and Desulfobacca apparently declined. Several halophile genera, Vibrio, Marinobacter, Pseudomonas, Prochlorococcus, Pediococcus and Thiobacillus predominated finally in the microbiota. The enriched microbiota was capable of removing a maximum of 1000 mg/L sulfide within 12 h with 10% inoculum at pH 7.0, 20-30 °C. After immobilized, the microbiota presented excellent resistance to impact and could completely remove 600 mg/L sulfide in 12 h. Moreover, the immobilized microbiota recovered well even recycled for five times. In conclusion, the immobilized sulfide-removing microbiota showed a quite promising application for biological restoring of sulfide-rich aquaculture environment. PMID:27105167

  4. Use of cloud-point preconcentration for spectrophotometric determination of trace amounts of antimony in biological and environmental samples.

    Science.gov (United States)

    El-Sharjawy, Abdel-Azeem M; Amin, Alaa S

    2016-01-01

    This work presents a cloud-point extraction process using the micelle-mediated extraction method for simultaneous preconcentration and determination of Sb(III) and Sb(V) species in biological and environmental samples as a prior preconcentration step to their spectrophotometric determination. The analytical system is based on the selective reaction between Sb(III) and 3-dichloro-6-(3-carboxy-2-hydroxy-1-naphthylazo)quinoxaline (DCHNAQ) in the presence of cetyltrimethylammonium bromide (CTAB) and potassium iodide at pH 4.5. Total Sb concentration was determined after reduction of Sb(V) to Sb(III) in the presence of potassium iodide and ascorbic acid. The optimal reaction conditions and extraction were studied, and the analytical characteristics of the method (e.g., limits of detection and quantification, linear range, preconcentration, improvement factors) were obtained. Linearity for Sb(III) was obeyed in the range of 0.2-20 ng ml(-1). The detection and quantification limits for the determination of Sb(III) were 0.055 and 0.185 ng ml(-1), respectively. The method has a lower detection limit and wider linear range, inexpensive instrument, and low cost, and is more sensitive compared with most other methods. The interference effect of some anions and cations was also studied. The method was applied to the determination of Sb(III) in the presence of Sb(V) and total antimony in blood plasma, urine, biological, and water samples.

  5. Metalloproteinases: A parade of functions in matrix biology and an outlook for the future.

    Science.gov (United States)

    Apte, Suneel S; Parks, William C

    2015-01-01

    This issue of Matrix Biology is devoted to exploring how metalloproteinases - here inclusive of related families of extracellular proteinases - act on extracellular matrix (ECM) proteins to influence an astonishing diversity of biological systems and diseases. Since their discovery in the 1960's, matrix metalloproteinases (MMPs) have oft and widely been considered as the principal mediators of ECM destruction. However, as becomes clear from several articles in this issue, MMPs affect processes that both promote and limit ECM assembly, structure, and quantity. Furthermore, it has become increasingly apparent that ECM proteolysis is neither the exclusive function of MMPs nor their only sphere of influence. Thus, other enzymes may be important participants in ECM proteolysis, and indeed they are. The ADAMTS (a disintegrin-like and metalloproteinase domain with thrombospondin type 1 repeat) proteinases, BMP/tolloid proteases, and meprins have all emerged as major mechanisms of ECM proteolysis. An aggregate view of proteolysis as an exquisitely specific and crucial post-translational modification of secreted proteins emerges from these reviews. The cumulative evidence strongly suggests that although some MMPs can and do cleave ECM components, notably fibrillar collagens, the majority of these proteinases are not key physiological participants in morphogenesis nor in control of matrix metabolism in homeostasis or disease. In contrast, deficiency of ADAMTS proteases leads to a remarkable array of morphogenetic defects and connective tissue disorders consistent with a specialized role in turnover of the embryonic provisional ECM and in ECM assembly. Astacin-related proteases emerge into crucial positions in ECM assembly and turnover, although they also have numerous roles related to morphogen and growth factor regulation. To further turn the traditional view on its head, it is clear that many MMPs are key participants in many, diverse immune and inflammation processes

  6. Accounting for multiple functions in environmental life cycle assessment of storm water management solutions

    DEFF Research Database (Denmark)

    Brudler, Sarah; Arnbjerg-Nielsen, Karsten; Rygaard, Martin

    The wide range of approaches to handle storm water runoff have varying effects on the environment. Local stormwater control measures for retention and treatment are increasingly used components in urban climate adaptation plans. Often, these solutions modify the multiple functions of urban...... environments by adding green and blue elements, and they change the water balance compared to traditional, underground approaches. Additionally, different implementation and maintenance processes are required. All of these transformations affect the environmental impacts of urban storm water management (SWM......) systems, which can be quantified using Life Cycle Assessment (LCA). This study aims to define the multiple functions provided by a SWM system at sub-catchment scale, and to assess the environmental impacts arising from fulfilling these functions. The approach is tested using the Nørrebro catchment...

  7. Sheep lymph-nodes as a biological indicator of environmental exposure to fluoro-edenite.

    Science.gov (United States)

    Ledda, Caterina; Loreto, Carla; Pomara, Cristoforo; Rapisarda, Giuseppe; Fiore, Maria; Ferrante, Margherita; Bracci, Massimo; Santarelli, Lory; Fenga, Concettina; Rapisarda, Venerando

    2016-05-01

    A significantly increased incidence of pleural mesothelioma in Biancavilla (Sicily, Italy) has been attributed to exposure to fluoro-edenite (FE), a fibrous amphibole extracted from a local stone quarry. The lymph-nodes draining the pulmonary lobes of sheep grazing around the town were examined, to gain insights into fibre diffusion. The pasture areas of six sheep flocks lying about 3km from Biancavilla were located using the global positioning system. The cranial tracheobronchial and one middle mediastinal lymph-node as well as four lung tissue samples were collected from 10 animals from each flock and from 10 control sheep for light and scanning electron microscopy (SEM) examination. The lymph-nodes from exposed sheep were enlarged and exhibited signs of anthracosis. Histologically, especially at the paracortical level, they showed lymph-follicle hyperplasia with large reactive cores and several macrophages (coniophages) containing grey-brownish particulate interspersed with elements with a fibril structure, forming aggregates of varying dimensions (coniophage nodules). Similar findings were detected in some peribronchiolar areas of the lung parenchyma. SEM examination showed that FE fibres measured 8-41µm in length and 0.4-1.39µm in diameter in both lymph-nodes and lung tissue. Monitoring of FE fibres in sheep lymph-nodes using appropriate techniques can help set up environmental pollution surveillance. PMID:26855127

  8. DataONE: Preserving Data and Enabling Data-Intensive Biological and Environmental Research

    Science.gov (United States)

    Cook, R. B.; DataONE Leadership Team

    2011-12-01

    Addressing grand environmental science challenges requires unprecedented access to easily understood data that cross the breadth of temporal, spatial, and thematic scales. From a scientist's perspective, the challenges lie in discovering the relevant data, dealing with data heterogeneity, and converting data to information and knowledge. Solving these challenges requires new approaches for managing, preserving, sharing and analyzing data. DataONE (Observation Network for Earth) represents a virtual organization whose goal is to enable new science and knowledge creation through preservation and access to data about life on Earth and the environment that sustains it. DataONE supports science through facilitating easy, secure, and persistent storage of data and disseminating integrated and user-friendly tools for data discovery, analysis, visualization, and decision-making. DataONE engages its community of partners through working groups focused on identifying and implementing the DataONE cyberinfrastructure, governance, and sustainability models. These working groups, which consist of a diverse group of graduate students, educators, government representatives, and leading computer, information, and library scientists: (1) adapt interoperability standards; (2) create value-added technologies (e.g., semantic mediation, scientific workflow, and visualization) that facilitate data integration, analysis, and understanding; (3) address socio-cultural barriers to sustainable data preservation and data sharing; and (4) promote the adoption of best practices for managing the full data life cycle.

  9. Exploring biological and pathological functions of TGFβ family member activin C

    International Nuclear Information System (INIS)

    Activins and their antagonists inhibins are cytokines of the transforming growth factor β family (TGFβ), with important regulatory functions in a wide array of physiological processes. Activins are homo- or heterodimers consisting of two disulfide-linked β subunits, four mammalian activin β subunits - βA, βB, βC, βE - have been identified in mammalian cells. Inhibins in contrast are heterodimers composed of an β subunit and a β subunit. Whereas the expression of βA and βB subunits is high and widely distributed in many organs, the βC and βE subunits are predominantly expressed in the liver. Activin A is by far the best investigated activin. It has been implicated for instance in reproductive biology, embryonic development, homeostasis, inflammation and tissue repair. In the liver it contributes to regulation of cell growth, apoptosis and tissue architecture. Additionally, deregulation of activin A signaling accounts for pathologic conditions such as hepatic inflammation, fibrosis and carcinogenesis. The biological functions of the other family members and their involvement in liver biology and diseases are still poorly understood. The first part of this work deals with the mRNA expression pattern of the complete inhibin gene family to obtain novel insights into possible functions of activins and inhibins in human hepatocellular carcinogenesis. Using quantitative real-time PCR analysis we found strongly increased inhibin β subunit expression comparing samples of hepatocellular carcinoma and tumor surrounding tissue to samples from healthy donors. All four β subunits were expressed in normal and patient samples, whereas expression of βB subunit increased from normal to malignant samples. This study is the first to report a significant relation of the inhibin β and inhibin βB mRNA levels to human hepatocellular carcinoma. Furthermore, these data, different from those in rodent model systems, suggest a tumor promoting role of inhibin and activin

  10. Molecular biology of environmental aromatic hydrocarbons. Progress report, September 1, 1984-June 31, 1985

    International Nuclear Information System (INIS)

    The biological activities of the (+)- and (-)-enantiomers of anti-BPDE (benzo[a]pyrene diol epoxide) and BePe (benzo[e]pyrene epoxide) were examined for their capacity to inhibit infectious single- and double-stranded 0X174 phage DNAs. For both activated PAH derivatives, the (+)-isomer was more inhibitory using either single- or double-stranded 0X DNAs. Both PAH derivatives showed a higher inhibition potency with single-stranded 0X DNA than with duplex DNA; this difference between the two phage DNA forms was much greater for BePE than with anti-BPDE. Digestion of phage DNAs reacted with the two isomers of anti-BPDE, followed by chromatography on LH20 Sephadex, showed a single major dG adduct peak for the (+)-isomer suggesting that alkylation of both 0X DNA forms is highly stereoselective. Reaction of the (-)-isomer of anti-BPDE with either form of 0X DNA showed several dG adduct peaks indicating that adduct formation was not stereoselective. A model viral DNA system was used, containing short oligonucleotide inserts as targets for PAH alkylation, to detect sequence modifications induced by anti-BPDE. A 10-base-pair oligomer (Bam HI linker) was treated with anti-BPDE and inserted into phage M13 replicative form DNA. E. coli was transfected with the recombinant DNA containing the alkylated oligomer, progeny viral plaques were selected, and their DNAs subjected to DNA sequence analysis at the region of oligomer insertion. For the alkylated inserts used in our study, the DNA sequence analysis of progeny viral DNA showed that nucleotide deletions were present in all the clones examined. These deletions occurred primarily, but not exclusively, at G dot C cluster regions, varied from 1 to 24 base pairs in length, and included both target and nontarget nucleotides. 19 refs., 4 figs

  11. Functional issues and environmental qualification of digital protection systems of advanced light-water nuclear reactors

    Energy Technology Data Exchange (ETDEWEB)

    Korsah, K.; Clark, R.L.; Wood, R.T. [Oak Ridge National Lab., TN (United States)

    1994-04-01

    Issues of obsolescence and lack of infrastructural support in (analog) spare parts, coupled with the potential benefits of digital systems, are driving the nuclear industry to retrofit analog instrumentation and control (I&C) systems with digital and microprocessor-based systems. While these technologies have several advantages, their application to safety-related systems in nuclear power plants raises key issues relating to the systems` environmental qualification and functional reliability. To bound the problem of new I&C system functionality and qualification, the authors focused this study on protection systems proposed for use in ALWRs. Specifically, both functional and environmental qualification issues for ALWR protection system I&C were addressed by developing an environmental, functional, and aging data template for a protection division of each proposed ALWR design. By using information provided by manufacturers, environmental conditions and stressors to which I&C equipment in reactor protection divisions may be subjected were identified. The resulting data were then compared to a similar template for an instrument string typically found in an analog protection division of a present-day nuclear power plant. The authors also identified fiber-optic transmission systems as technologies that are relatively new to the nuclear power plant environment and examined the failure modes and age-related degradation mechanisms of fiber-optic components and systems. One reason for the exercise of caution in the introduction of software into safety-critical systems is the potential for common-cause failure due to the software. This study, however, approaches the functionality problem from a systems point of view. System malfunction scenarios are postulated to illustrate the fact that, when dealing with the performance of the overall integrated system, the real issues are functionality and fault tolerance, not hardware vs. software.

  12. Functional issues and environmental qualification of digital protection systems of advanced light-water nuclear reactors

    International Nuclear Information System (INIS)

    Issues of obsolescence and lack of infrastructural support in (analog) spare parts, coupled with the potential benefits of digital systems, are driving the nuclear industry to retrofit analog instrumentation and control (I ampersand C) systems with digital and microprocessor-based systems. While these technologies have several advantages, their application to safety-related systems in nuclear power plants raises key issues relating to the systems' environmental qualification and functional reliability. To bound the problem of new I ampersand C system functionality and qualification, the authors focused this study on protection systems proposed for use in ALWRs. Specifically, both functional and environmental qualification issues for ALWR protection system I ampersand C were addressed by developing an environmental, functional, and aging data template for a protection division of each proposed ALWR design. By using information provided by manufacturers, environmental conditions and stressors to which I ampersand C equipment in reactor protection divisions may be subjected were identified. The resulting data were then compared to a similar template for an instrument string typically found in an analog protection division of a present-day nuclear power plant. The authors also identified fiber-optic transmission systems as technologies that are relatively new to the nuclear power plant environment and examined the failure modes and age-related degradation mechanisms of fiber-optic components and systems. One reason for the exercise of caution in the introduction of software into safety-critical systems is the potential for common-cause failure due to the software. This study, however, approaches the functionality problem from a systems point of view. System malfunction scenarios are postulated to illustrate the fact that, when dealing with the performance of the overall integrated system, the real issues are functionality and fault tolerance, not hardware vs. software

  13. Voltammetric method for sensitive determination of herbicide picloram in environmental and biological samples using boron-doped diamond film electrode

    International Nuclear Information System (INIS)

    The voltammetric behavior and determination of picloram, a member of a pyridine herbicide family, was for the first time investigated on a boron doped diamond film electrode using cyclic and differential pulse voltammetry. The influence of supporting electrolyte and scan rate on the current response of picloram was examined to select the optimum experimental conditions. It was found that picloram provided one well-shaped oxidation peak at very positive potential (+1.5 V vs. Ag/AgCl electrode) in strong acidic medium. At optimized differential pulse voltammetric parameters, the current response of picloram was proportionally linear in the concentration range from 0.5 to 48.07 μmol L−1 and the low limit of detection of 70 nmol L−1 as well as good repeatability (relative standard deviation of 2.6% at 10 μmol L−1 for n = 11) were obtained on unmodified boron-doped diamond film electrode. The proposed method was successfully applied in analysis of environmental (tap and natural water) and biological (human urine) samples spiked with picloram with good accuracy (relative standard deviations less than 5% for all samples, n = 5). By this way, the boron-doped diamond could introduce a green (environmentally acceptable) alternative to mercury electrodes for the monitoring of herbicides

  14. Illicit drugs as new environmental pollutants: cyto-genotoxic effects of cocaine on the biological model Dreissena polymorpha.

    Science.gov (United States)

    Binelli, A; Pedriali, A; Riva, C; Parolini, M

    2012-03-01

    The increase in global consumption of illicit drugs has produced not only social and medical problems but also a potential new environmental danger. Indeed, it has been established that drugs consumed by humans end up in surface waters, after being carried through the sewage system. Although many studies to measure concentrations of several drugs of abuse in freshwater worldwide have been conducted, no data have been available to evaluate their potentially harmful effects on non-target organisms until now. The present study represents the first attempt to investigate the cyto-genotoxic effects of cocaine, one of the primary drugs consumed in Western Countries, in the biological model Dreissena polymorpha by the use of a biomarker battery. We performed the following tests on Zebra mussel hemocytes: the single cell gel electrophoresis (SCGE) assay, the apoptosis frequency evaluation and the micronucleus assay (MN test) for the evaluation of genotoxicity and the lysosomal membranes stability test (neutral red retention assay; NRRA) to identify the cocaine cytotoxicity. We exposed the molluscs for 96 h to three different nominal concentrations in water (40 ng L(-1); 220 ng L(-1); and 10 μg L(-1)). Cocaine caused significant (papoptosis, which was evident in samples from even the lowest environmental cocaine concentration. Because cocaine decreased the stability of lysosomal membranes, we also highlighted its cytotoxicity and the possible implications of oxidative stress for the observed genotoxic effects. PMID:22119280

  15. Investigation of the soluble metals in tissue as biological response pattern to environmental pollutants (Gammarus fossarum example).

    Science.gov (United States)

    Filipović Marijić, Vlatka; Dragun, Zrinka; Sertić Perić, Mirela; Matoničkin Kepčija, Renata; Gulin, Vesna; Velki, Mirna; Ečimović, Sandra; Hackenberger, Branimir K; Erk, Marijana

    2016-07-01

    In the present study, Gammarus fossarum was used to investigate the bioaccumulation and toxic effects of aquatic pollutants in the real environmental conditions. The novelty of the study is the evaluation of soluble tissue metal concentrations in gammarids as indicators in early assessment of metal exposure. In the Sutla River, industrially/rurally/agriculturally influenced catchment in North-Western Croatia, physico-chemical water properties pointed to disturbed ecological status, which was reflected on population scale as more than 50 times lower gammarid density compared to the reference location, Črnomerec Stream. Significantly higher levels of soluble toxic metals (Al, As, Cd, Pb, Sb, Sn, Sr) were observed in gammarids from the Sutla River compared to the reference site and reflected the data on higher total dissolved metal levels in the river water at that site. The soluble metal estimates were supplemented with the common multibiomarker approach, which showed significant biological responses for decreased acetylcholinesterase activity and increased total soluble protein concentrations, confirming stressed environmental conditions for biota in the Sutla River. Biomarker of metal exposure, metallothionein, was not induced and therefore, toxic effect of metals was not confirmed on molecular level. Comparable between-site pattern of soluble toxic metals in gammarids and total dissolved metal levels in water suggests that prior to biomarker response and observed toxic impact, soluble metals in tissue might be used as early warning signs of metal impact in the aquatic environment and improve the assessment of water quality. PMID:27060638

  16. Functional traits and environmental filtering drive community assembly in a species-rich tropical system.

    Science.gov (United States)

    Lebrija-Trejos, Edwin; Pérez-García, Eduardo A; Meave, Jorge A; Bongers, Frans; Poorter, Lourens

    2010-02-01

    Mechanistic models of community assembly state that biotic and abiotic filters constrain species establishment through selection on their functional traits. Predicting this assembly process is hampered because few studies directly incorporate environmental measurements and scale up from species to community level and because the functional traits' significance is environment dependent. We analyzed community assembly by measuring structure, environmental conditions, and species traits of secondary forests in a species-rich tropical system. We found, as hypothesized, that community structure shaped the local environment and that strong relationships existed between this environment and the traits of the most successful species of the regeneration communities. Path and multivariate analyses showed that temperature and leaf traits that regulate it were the most important factors of community differentiation. Comparisons between the trait composition of the forest's regeneration, juvenile, and adult communities showed a consistent community assembly pattern. These results allowed us to identify the major functional traits and environmental factors involved in the assembly of dry-forest communities and demonstrate that environmental filtering is a predictable and fundamental process of community assembly, even in a complex system such as a tropical forest.

  17. Development of PVDF Membrane Nanocomposites via Various Functionalization Approaches for Environmental Applications

    OpenAIRE

    Douglas M. Davenport; Minghui Gui; Lindell R. Ormsbee; Dibakar Bhattacharyya

    2016-01-01

    Membranes are finding wide applications in various fields spanning biological, water, and energy areas. Synthesis of membranes to provide tunable flux, metal sorption, and catalysis has been done through pore functionalization of microfiltration (MF) type membranes with responsive behavior. This methodology provides an opportunity to improve synthetic membrane performance via polymer fabrication and surface modification. By optimizing the polymer coagulation conditions in phase inversion fabr...

  18. Iron-sulphur clusters, their biosynthesis, and biological functions in protozoan parasites.

    Science.gov (United States)

    Ali, Vahab; Nozaki, Tomoyoshi

    2013-01-01

    Fe-S clusters are ensembles of sulphide-linked di-, tri-, and tetra-iron centres of a variety of metalloproteins that play important roles in reduction and oxidation of mitochondrial electron transport, energy metabolism, regulation of gene expression, cell survival, nitrogen fixation, and numerous other metabolic pathways. The Fe-S clusters are assembled by one of four distinct systems: NIF, SUF, ISC, and CIA machineries. The ISC machinery is a house-keeping system conserved widely from prokaryotes to higher eukaryotes, while the other systems are present in a limited range of organisms and play supplementary roles under certain conditions such as stress. Fe-S cluster-containing proteins and the components required for Fe-S cluster biosynthesis are modulated under stress conditions, drug resistance, and developmental stages. It is also known that a defect in Fe-S proteins and Fe-S cluster biogenesis leads to many genetic disorders in humans, which indicates the importance of the systems. In this review, we describe the biological and physiological significance of Fe-S cluster-containing proteins and their biosynthesis in parasitic protozoa including Plasmodium, Trypanosoma, Leishmania, Giardia, Trichomonas, Entamoeba, Cryptosporidium, Blastocystis, and microsporidia. We also discuss the roles of Fe-S cluster biosynthesis in proliferation, differentiation, and stress response in protozoan parasites. The heterogeneity of the systems and the compartmentalization of Fe-S cluster biogenesis in the protozoan parasites likely reflect divergent evolution under highly diverse environmental niches, and influence their parasitic lifestyle and pathogenesis. Finally, both Fe-S cluster-containing proteins and their biosynthetic machinery in protozoan parasites are remarkably different from those in their mammalian hosts. Thus, they represent a rational target for the development of novel chemotherapeutic and prophylactic agents against protozoan infections. PMID:23876871

  19. Next-generation sequencing as a powerful motor for advances in the biological and environmental sciences.

    Science.gov (United States)

    Faure, Denis; Joly, Dominique

    2015-04-01

    Next-generation sequencing (NGS) provides unprecedented insight into (meta)genomes, (meta)transcriptomes (cDNA) and (meta)barcodes of individuals, populations and communities of Archaea, Bacteria and Eukarya, as well as viruses. This special issue combines reviews and original papers reporting technical and scientific advances in genomics and transcriptomics of non-model species, as well as quantification and functional analyses of biodiversity using NGS technologies of the second and third generations. In addition, certain papers also exemplify the transition from Sanger to NGS barcodes in molecular taxonomy.

  20. Thermal biology of flight in a butterfly: genotype, flight metabolism, and environmental conditions.

    Science.gov (United States)

    Mattila, Anniina L K

    2015-12-01

    Knowledge of the effects of thermal conditions on animal movement and dispersal is necessary for a mechanistic understanding of the consequences of climate change and habitat fragmentation. In particular, the flight of ectothermic insects such as small butterflies is greatly influenced by ambient temperature. Here, variation in body temperature during flight is investigated in an ecological model species, the Glanville fritillary butterfly (Melitaea cinxia). Attention is paid on the effects of flight metabolism, genotypes at candidate loci, and environmental conditions. Measurements were made under a natural range of conditions using infrared thermal imaging. Heating of flight muscles by flight metabolism has been presumed to be negligible in small butterflies. However, the results demonstrate that Glanville fritillary males with high flight metabolic rate maintain elevated body temperature better during flight than males with a low rate of flight metabolism. This effect is likely to have a significant influence on the dispersal performance and fitness of butterflies and demonstrates the possible importance of intraspecific physiological variation on dispersal in other similar ectothermic insects. The results also suggest that individuals having an advantage in low ambient temperatures can be susceptible to overheating at high temperatures. Further, tolerance of high temperatures may be important for flight performance, as indicated by an association of heat-shock protein (Hsp70) genotype with flight metabolic rate and body temperature at takeoff. The dynamics of body temperature at flight and factors affecting it also differed significantly between female and male butterflies, indicating that thermal dynamics are governed by different mechanisms in the two sexes. This study contributes to knowledge about factors affecting intraspecific variation in dispersal-related thermal performance in butterflies and other insects. Such information is needed for predictive

  1. Selective uptake and biological consequences of environmentally relevant antidepressant pharmaceutical exposures on male fathead minnows

    Science.gov (United States)

    Schultz, M.M.; Painter, M.M.; Bartell, S.E.; Logue, A.; Furlong, E.T.; Werner, S.L.; Schoenfuss, H.L.

    2011-01-01

    Antidepressant pharmaceuticals have been reported in wastewater effluent at the nanogram to low microgram-per-liter range, and include bupropion (BUP), fluoxetine (FLX), sertraline (SER), and venlafaxine (VEN). To assess the effects of antidepressants on reproductive anatomy, physiology, and behavior, adult male fathead minnows (Pimephales promelas) were exposed for 21 days either to a single concentration of the antidepressants FLX, SER, VEN, or BUP, or to an antidepressant mixture. The data demonstrated that exposure to VEN (305. ng/L and 1104. ng/L) and SER (5.2. ng/L) resulted in mortality. Anatomical alterations were noted within the testes of fish exposed to SER and FLX, both modulators of the neurotransmitter serotonin. Additionally, FLX at 28. ng/L induced vitellogenin in male fish-a common endpoint for estrogenic endocrine disruption. Significant alterations in male secondary sex characteristics were noted with single exposures. Effects of single compound exposures neither carried over, nor became additive in the antidepressant mixtures, and reproductive behavior was not affected. Analysis of brain tissues from the exposed fish suggested increased uptake of FLX, SER and BUP and minimal uptake of VEN when compared to exposure water concentrations. Furthermore, the only metabolite detected consistently in the brain tissues was norfluoxetine. Similar trends of uptake by brain tissue were observed when fish were exposed to antidepressant mixtures. The present study demonstrates that anatomy and physiology, but not reproductive behavior, can be disrupted by exposure to environmental concentrations of some antidepressants. The observation that antidepressant uptake into fish tissues is selective may have consequences on assessing the mode-of-action and effects of these compounds in future studies. ?? 2011 Elsevier B.V.

  2. Thermal biology of flight in a butterfly: genotype, flight metabolism, and environmental conditions.

    Science.gov (United States)

    Mattila, Anniina L K

    2015-12-01

    Knowledge of the effects of thermal conditions on animal movement and dispersal is necessary for a mechanistic understanding of the consequences of climate change and habitat fragmentation. In particular, the flight of ectothermic insects such as small butterflies is greatly influenced by ambient temperature. Here, variation in body temperature during flight is investigated in an ecological model species, the Glanville fritillary butterfly (Melitaea cinxia). Attention is paid on the effects of flight metabolism, genotypes at candidate loci, and environmental conditions. Measurements were made under a natural range of conditions using infrared thermal imaging. Heating of flight muscles by flight metabolism has been presumed to be negligible in small butterflies. However, the results demonstrate that Glanville fritillary males with high flight metabolic rate maintain elevated body temperature better during flight than males with a low rate of flight metabolism. This effect is likely to have a significant influence on the dispersal performance and fitness of butterflies and demonstrates the possible importance of intraspecific physiological variation on dispersal in other similar ectothermic insects. The results also suggest that individuals having an advantage in low ambient temperatures can be susceptible to overheating at high temperatures. Further, tolerance of high temperatures may be important for flight performance, as indicated by an association of heat-shock protein (Hsp70) genotype with flight metabolic rate and body temperature at takeoff. The dynamics of body temperature at flight and factors affecting it also differed significantly between female and male butterflies, indicating that thermal dynamics are governed by different mechanisms in the two sexes. This study contributes to knowledge about factors affecting intraspecific variation in dispersal-related thermal performance in butterflies and other insects. Such information is needed for predictive

  3. Environmental DNA Marker Development with Sparse Biological Information: A Case Study on Opossum Shrimp (Mysis diluviana).

    Science.gov (United States)

    Carim, Kellie J; Christianson, Kyle R; McKelvey, Kevin M; Pate, William M; Silver, Douglas B; Johnson, Brett M; Galloway, Bill T; Young, Michael K; Schwartz, Michael K

    2016-01-01

    The spread of Mysis diluviana, a small glacial relict crustacean, outside its native range has led to unintended shifts in the composition of native fish communities throughout western North America. As a result, biologists seek accurate methods of determining the presence of M. diluviana, especially at low densities or during the initial stages of an invasion. Environmental DNA (eDNA) provides one solution for detecting M. diluviana, but building eDNA markers that are both sensitive and species-specific is challenging when the distribution and taxonomy of closely related non-target taxa are poorly understood, published genetic data are sparse, and tissue samples are difficult to obtain. To address these issues, we developed a pair of independent eDNA markers to increase the likelihood of a positive detection of M. diluviana when present and reduce the probability of false positive detections from closely related non-target species. Because tissue samples of closely-related and possibly sympatric, non-target taxa could not be obtained, we used synthetic DNA sequences of closely related non-target species to test the specificity of eDNA markers. Both eDNA markers yielded positive detections from five waterbodies where M. diluviana was known to be present, and no detections in five others where this species was thought to be absent. Daytime samples from varying depths in one waterbody occupied by M. diluviana demonstrated that samples near the lake bottom produced 5 to more than 300 times as many eDNA copies as samples taken at other depths, but all samples tested positive regardless of depth.

  4. Environmental DNA Marker Development with Sparse Biological Information: A Case Study on Opossum Shrimp (Mysis diluviana)

    Science.gov (United States)

    Carim, Kellie J.; Christianson, Kyle R.; McKelvey, Kevin M.; Pate, William M.; Silver, Douglas B.; Johnson, Brett M.; Galloway, Bill T.; Young, Michael K.; Schwartz, Michael K.

    2016-01-01

    The spread of Mysis diluviana, a small glacial relict crustacean, outside its native range has led to unintended shifts in the composition of native fish communities throughout western North America. As a result, biologists seek accurate methods of determining the presence of M. diluviana, especially at low densities or during the initial stages of an invasion. Environmental DNA (eDNA) provides one solution for detecting M. diluviana, but building eDNA markers that are both sensitive and species-specific is challenging when the distribution and taxonomy of closely related non-target taxa are poorly understood, published genetic data are sparse, and tissue samples are difficult to obtain. To address these issues, we developed a pair of independent eDNA markers to increase the likelihood of a positive detection of M. diluviana when present and reduce the probability of false positive detections from closely related non-target species. Because tissue samples of closely-related and possibly sympatric, non-target taxa could not be obtained, we used synthetic DNA sequences of closely related non-target species to test the specificity of eDNA markers. Both eDNA markers yielded positive detections from five waterbodies where M. diluviana was known to be present, and no detections in five others where this species was thought to be absent. Daytime samples from varying depths in one waterbody occupied by M. diluviana demonstrated that samples near the lake bottom produced 5 to more than 300 times as many eDNA copies as samples taken at other depths, but all samples tested positive regardless of depth. PMID:27551919

  5. Environmental DNA Marker Development with Sparse Biological Information: A Case Study on Opossum Shrimp (Mysis diluviana).

    Science.gov (United States)

    Carim, Kellie J; Christianson, Kyle R; McKelvey, Kevin M; Pate, William M; Silver, Douglas B; Johnson, Brett M; Galloway, Bill T; Young, Michael K; Schwartz, Michael K

    2016-01-01

    The spread of Mysis diluviana, a small glacial relict crustacean, outside its native range has led to unintended shifts in the composition of native fish communities throughout western North America. As a result, biologists seek accurate methods of determining the presence of M. diluviana, especially at low densities or during the initial stages of an invasion. Environmental DNA (eDNA) provides one solution for detecting M. diluviana, but building eDNA markers that are both sensitive and species-specific is challenging when the distribution and taxonomy of closely related non-target taxa are poorly understood, published genetic data are sparse, and tissue samples are difficult to obtain. To address these issues, we developed a pair of independent eDNA markers to increase the likelihood of a positive detection of M. diluviana when present and reduce the probability of false positive detections from closely related non-target species. Because tissue samples of closely-related and possibly sympatric, non-target taxa could not be obtained, we used synthetic DNA sequences of closely related non-target species to test the specificity of eDNA markers. Both eDNA markers yielded positive detections from five waterbodies where M. diluviana was known to be present, and no detections in five others where this species was thought to be absent. Daytime samples from varying depths in one waterbody occupied by M. diluviana demonstrated that samples near the lake bottom produced 5 to more than 300 times as many eDNA copies as samples taken at other depths, but all samples tested positive regardless of depth. PMID:27551919

  6. Pollen tube growth test (PTGT) in environmental biomonitoring and predictive radiation biology studies: problem and prospect

    International Nuclear Information System (INIS)

    In Environmental and Human Bio monitoring studies of Hazardous xenobiotics over living system particularly at cell level, it is desirable to have easy and sensitive test system like Cell Viability assay, MNT, Cell Culture photo toxicity Test, PTGT etc. Out of these the PTGT quite better than other because the in vitro culture of pollen grain can provides a sensitive indication of toxicity at cellular level, since germination and growth of pollen tube will inhibited in presence of toxic substance like DDT, Heavy metal, even Radionuclide's. This test system is easy, economical and widely accepted through out world. In PTGT pollen tube never containing Chloroplast or other plastids so pollen tube resembles animals more than a plant organ and is therefore also a suitable as model for Genotoxicity Assessment of compounds harmful to animal and humans. Lack of plastids in PT, PTGT will not identify the toxic effect of compounds that targets Non cyclic and cyclic photoposphorylation of photosynthesis. This test system valid in International Toxicity Testing Protocol. But this method is time consuming and problem in measurement of pollen tube growing in a culture medium became usually bent and make measurement difficult. Other disadvantage of this method is requirement of DMSO to dissolve test substance of low water suitability in culture medium. DMSO shown to have no effect on PTG at Concentration not more than 1% but some extent interfere with results. Values of PTG are quantified in ED50/IC50 that is the concentration of test compounds that reduces pollen tube growth to 50% of control. So PTGT could be very sensitive and easy to assess in common lab in International way. (author)

  7. Bridging from Cells to Cognition in Autism Pathophysiology: Biological Pathways to Defective Brain Function and Plasticity

    Directory of Open Access Journals (Sweden)

    Matthew P. Anderson

    2008-01-01

    Full Text Available We review evidence to support a model where the disease process underlying autism may begin when an in utero or early postnatal environmental, infectious, seizure, or autoimmune insult triggers an immune response that increases reactive oxygen species (ROS production in the brain that leads to DNA damage (nuclear and mitochondrial and metabolic enzyme blockade and that these inflammatory and oxidative stressors persist beyond early development (with potential further exacerbations, producing ongoing functional consequences. In organs with a high metabolic demand such as the central nervous system, the continued use of mitochondria with damaged DNA and impaired metabolic enzyme function may generate additional ROS which will cause persistent activation of the innate immune system leading to more ROS production. Such a mechanism would self-sustain and possibly progressively worsen. The mitochondrial dysfunction and altered redox signal transduction pathways found in autism would conspire to activate both astroglia and microglia. These activated cells can then initiate a broad-spectrum proinflammatory gene response. Beyond the direct effects of ROS on neuronal function, receptors on neurons that bind the inflammatory mediators may serve to inhibit neuronal signaling to protect them from excitotoxic damage during various pathologic insults (e.g., infection. In autism, over-zealous neuroinflammatory responses could not only influence neural developmental processes, but may more significantly impair neural signaling involved in cognition in an ongoing fashion. This model makes specific predictions in patients and experimental animal models and suggests a number of targets sites of intervention. Our model of potentially reversible pathophysiological mechanisms in autism motivates our hope that effective therapies may soon appear on the horizon.

  8. The Elemental Analysis of Biological and Environmental Materials Using a 2MEV Proton Beam

    Science.gov (United States)

    Arshed, Waheed

    Available from UMI in association with The British Library. A programme has been developed to simulate the proton induced x-ray emission (PIXE) spectra and its uses have been described. The PIXE technique has been applied to the analysis of new biological reference materials which consist of IAEA human diet samples and NIST leaf samples. Homogeneity of these and two existing reference materials, IAEA soil -7 and Bowen's kale, has also been determined at the mug scale. A subsample representative of a material is ascertained by determination of sampling factors for the elements detected in the material. Proton induced gamma-ray emission (PIGE) analysis in conjunction with PIXE has been employed to investigate F and other elemental concentrations found in human teeth samples. The mean F concentration in enamel and dentine parts of teeth followed an age dependent model. Concentrations of Ca and P were found to be higher in the enamel than in the dentine. Analysis of blood and its components in the study of elemental models in sickle cell disease in Nigerians has been carried out. Comparisons revealed that Cl, Ca and Cu were at higher levels whereas K, Fe, Zn and Rb were at lower levels in the whole blood of the sicklers compared to controls. Similar results were obtained for the erythrocytes except that Br was found at higher concentration in erythrocytes of the sicklers. Higher concentrations of Cl, K, Fe and Cu were also observed in plasma of the sicklers compared to controls. PIXE and scanning electron microscopy (SEM) were used in the characterization of the Harmattan dust particulates collected at Kano and Ife. Most of the elements were found to be at higher concentrations as compared to those found in Recife (Brazil) and Toronto (Canada). The value of total suspended particulate was above the relevant national air quality standards. PIXE in conjunction with Rutherford backscattering spectrometry and instrumental neutron activation analysis was employed in the

  9. Synthesis, characterization and functionalization of silicon nanoparticle based hybrid nanomaterials for photovoltaic and biological applications

    Science.gov (United States)

    Xu, Zejing

    Silicon nanoparticles are attractive candidates for biological, photovoltaic and energy storage applications due to their size dependent optoelectronic properties. These include tunable light emission, high brightness, and stability against photo-bleaching relative to organic dyes (see Chapter 1). The preparation and characterization of silicon nanoparticle based hybrid nanomaterials and their relevance to photovoltaic and biological applications are described. The surface-passivated silicon nanoparticles were produced in one step from the reactive high-energy ball milling (RHEBM) of silicon wafers with various organic ligands. The surface structure and optical properties of the passivated silicon nanoparticles were systematically characterized. Fast approaches for purifying and at the same time size separating the silicon nanoparticles using a gravity GPC column were developed. The hydrodynamic diameter and size distribution of these size-separated silicon nanoparticles were determined using GPC and Diffusion Ordered NMR Spectroscopy (DOSY) as fast, reliable alternative approaches to TEM. Water soluble silicon nanoparticles were synthesized by grafting PEG polymers onto functionalized silicon nanoparticles with distal alkyne or azide moieties. The surface-functionalized silicon nanoparticles were produced from the reactive high-energy ball milling (RHEBM) of silicon wafers with a mixture of either 5-chloro-1-pentyne in 1-pentyne or 1,7 octadiyne in 1-hexyne to afford air and water stable chloroalkyl or alkynyl terminated nanoparticles, respectively. Nanoparticles with the ω-chloroalkyl substituents were easily converted to ω-azidoalkyl groups through the reaction of the silicon nanoparticles with sodium azide in DMF. The azido terminated nanoparticles were then grafted with monoalkynyl-PEG polymers using a copper catalyzed alkyne-azide cycloaddition (CuAAC) reaction to afford core-shell silicon nanoparticles with a covalently attached PEG shell. Covalently

  10. Carbohydrate/glycan-binding specificity of legume lectins in respect to their proposed biological functions

    Directory of Open Access Journals (Sweden)

    Márcio Viana Ramos

    2000-01-01

    Full Text Available The lectins, proteins which specifically recognize carbohydrate moieties, have been extensively studied in many biochemical and structural aspects in order to establish the molecular basis of this non-catalytic event. On the other hand, their clinical and agricultural potentials have been growing fast. Although lectins, mainly those from legume plants, had been investigated for biological properties, studies about the physiological functions of lectins are scarce in literature. Therefore, despite the accumulated data on lectins (as proteins, the role played by these signalizing molecules is poorly discussed. In the light of our accumulated results on legume lectins, specially those obtained from plants belonging to the Diocleinae sub-tribe and available data in literature, we discuss here the main hypothesis of their functions according to their carbohydrate/glycan-binding specificity.As lectinas, proteinas que especificamente reconhecem estruturas que contém carboidratos, têm sido extensivamente estudadas em muitos aspectos bioquímicos e estruturais, objetivando estabelecer as bases moleculares deste evento não-catalítico. Por outro lado, os potenciais clínicos e agriculturais destas proteínas têm crescido rapidamente. Embora as lectinas, principalmente aquelas de legumes tenham sido bastante investigadas em suas propriedades biológicas, estudos sobre as funcões fisiológicas de lectinas são escassos na literatura. Além disto, a despeito da quantidade de dados acumulados sobre lectinas (como proteínas, o papel desempenhado por estas moléculas de sinalização é pobremente discutido. Valendo-se de nossos estudos sobre lectinas de leguminosas, principalmente da sub-tribo Diocleinae, e outros dados presentes na literatura, discutimos aqui, as principais hipóteses de suas funções com base na especificidade por carboidratos e glicanos complexos.

  11. Somatostatin receptor expression and biological functions in endocrine pancreatic cells: review based on a doctoral thesis.

    Science.gov (United States)

    Ludvigsen, Eva

    2007-01-01

    Type 1 diabetes is resulting from the selective destruction of insulin-producing betacells within the pancreatic islets. Somatostatin acts as an inhibitor of hormone secretion through specific receptors (sst1-5). All ssts were expressed in normal rat and mouse pancreatic islets, although the expression intensity and the co-expression pattern varied between ssts as well as between species. This may reflect a difference in response to somatostatin in islet cells of the two species. The Non-Obese Diabetic (NOD) mouse model is an experimental model of type 1 diabetes, with insulitis accompanied by spontaneous hyperglycaemia. Pancreatic specimens from NOD mice at different age and stage of disease were stained for ssts. The islet cells of diabetic NOD mice showed increased islet expression of sst2-5 compared to normoglycemic NOD mice. The increase in sst2-5 expression in the islets cells may suggest either a contributing factor in the process leading to diabetes, or a defense response against ongoing beta-cell destruction. Somatostatin analogues were tested on a human endocrine pancreatic tumour cell line and cultured pancreatic islets. Somatostatin analogues had an effect on cAMP accumulation, chromogranin A secretion and MAP kinase activity in the cell line. Treatment of rat pancreatic islets with somatostatin analogues with selective receptor affinity was not sufficient to induce an inhibition of insulin and glucagon secretion. However, a combination of selective analogues or non-selective analogues via costimulation of receptors can cause inhibition of hormone production. For insulin and glucagon, combinations of sst2 + sst5 and sst1 + sst2, respectively, showed a biological effect. In summary, knowledge of islet cell ssts expression and the effect of somatostatin analogues with high affinity to ssts may be valuable in the future attempts to influence beta-cell function in type 1 diabetes mellitus, since down-regulation of beta-cell function may promote survival of

  12. Multiple functional UV devices based on III-Nitride quantum wells for biological warfare agent detection

    Science.gov (United States)

    Wang, Qin; Savage, Susan; Persson, Sirpa; Noharet, Bertrand; Junique, Stéphane; Andersson, Jan Y.; Liuolia, Vytautas; Marcinkevicius, Saulius

    2009-02-01

    We have demonstrated surface normal detecting/filtering/emitting multiple functional ultraviolet (UV) optoelectronic devices based on InGaN/GaN, InGaN/AlGaN and AlxGa1-xN/AlyGa1-yN multiple quantum well (MQW) structures with operation wavelengths ranging from 270 nm to 450 nm. Utilizing MQW structure as device active layer offers a flexibility to tune its long cut-off wavelength in a wide UV range from solar-blind to visible by adjusting the well width, well composition and barrier height. Similarly, its short cut-off wavelength can be adjusted by using a GaN or AlGaN block layer on a sapphire substrate when the device is illuminated from its backside, which further provides an optical filtering effect. When a current injects into the device under forward bias the device acts as an UV light emitter, whereas the device performs as a typical photodetector under reverse biases. With applying an alternating external bias the device might be used as electroabsorption modulator due to quantum confined Stark effect. In present work fabricated devices have been characterized by transmission/absorption spectra, photoresponsivity, electroluminescence, and photoluminescence measurements under various forward and reverse biases. The piezoelectric effect, alloy broadening and Stokes shift between the emission and absorption spectra in different InGaN- and AlGaN-based QW structures have been investigated and compared. Possibilities of monolithic or hybrid integration using such multiple functional devices for biological warfare agents sensing application have also be discussed.

  13. Unexpected functional similarities between gatekeeper tumour suppressor genes and proto-oncogenes revealed by systems biology.

    Science.gov (United States)

    Zhao, Yongzhong; Epstein, Richard J

    2011-05-01

    Familial tumor suppressor genes comprise two subgroups: caretaker genes (CTs) that repair DNA, and gatekeeper genes (GKs) that trigger cell death. Since GKs may also induce cell cycle delay and thus enhance cell survival by facilitating DNA repair, we hypothesized that the prosurvival phenotype of GKs could be selected during cancer progression, and we used a multivariable systems biology approach to test this. We performed multidimensional data analysis, non-negative matrix factorization and logistic regression to compare the features of GKs with those of their putative antagonists, the proto-oncogenes (POs), as well as with control groups of CTs and functionally unrelated congenital heart disease genes (HDs). GKs and POs closely resemble each other, but not CTs or HDs, in terms of gene structure (P<0.001), expression level and breadth (P<0.01), DNA methylation signature (P<0.001) and evolutionary rate (P<0.001). The similar selection pressures and epigenetic trajectories of GKs and POs so implied suggest a common functional attribute that is strongly negatively selected-that is, a shared phenotype that enhances cell survival. The counterintuitive finding of similar evolutionary pressures affecting GKs and POs raises an intriguing possibility: namely, that cancer microevolution is accelerated by an epistatic cascade in which upstream suppressor gene defects subvert the normal bifunctionality of wild-type GKs by constitutively shifting the phenotype away from apoptosis towards survival. If correct, this interpretation would explain the hitherto unexplained phenomenon of frequent wild-type GK (for example, p53) overexpression in tumors.

  14. Soft robotic arm inspired by the octopus: I. From biological functions to artificial requirements.

    Science.gov (United States)

    Margheri, L; Laschi, C; Mazzolai, B

    2012-06-01

    Octopuses are molluscs that belong to the group Cephalopoda. They lack joints and rigid links, and as a result, their arms possess virtually limitless freedom of movement. These flexible appendages exhibit peculiar biomechanical features such as stiffness control, compliance, and high flexibility and dexterity. Studying the capabilities of the octopus arm is a complex task that presents a challenge for both biologists and roboticists, the latter of whom draw inspiration from the octopus in designing novel technologies within soft robotics. With this idea in mind, in this study, we used new, purposively developed methods of analysing the octopus arm in vivo to create new biologically inspired design concepts. Our measurements showed that the octopus arm can elongate by 70% in tandem with a 23% diameter reduction and exhibits an average pulling force of 40 N. The arm also exhibited a 20% mean shortening at a rate of 17.1 mm s(-1) and a longitudinal stiffening rate as high as 2 N (mm s)(-1). Using histology and ultrasounds, we investigated the functional morphology of the internal tissues, including the sinusoidal arrangement of the nerve cord and the local insertion points of the longitudinal and transverse muscle fibres. The resulting information was used to create novel design principles and specifications that can in turn be used in developing a new soft robotic arm.

  15. The formation, function and regulation of amyloids: insights from structural biology.

    Science.gov (United States)

    Landreh, M; Sawaya, M R; Hipp, M S; Eisenberg, D S; Wüthrich, K; Hartl, F U

    2016-08-01

    Amyloid diseases are characterized by the accumulation of insoluble, β-strand-rich aggregates. The underlying structural conversions are closely associated with cellular toxicity, but can also drive the formation of functional protein assemblies. In recent years, studies in the field of structural studies have revealed astonishing insights into the origins, mechanisms and implications of amyloid formation. Notably, high-resolution crystal structures of peptides in amyloid-like fibrils and prefibrillar oligomers have become available despite their challenging chemical nature. Nuclear magnetic resonance spectroscopy has revealed that dynamic local polymorphisms in the benign form of the prion protein affect the transformation into amyloid fibrils and the transmissibility of prion diseases. Studies of the structures and interactions of chaperone proteins help us to understand how the cellular proteostasis network is able to recognize different stages of aberrant protein folding and prevent aggregation. In this review, we will focus on recent developments that connect the different aspects of amyloid biology and discuss how understanding the process of amyloid formation and the associated defence mechanisms can reveal targets for pharmacological intervention that may become the first steps towards clinically viable treatment strategies. PMID:27237473

  16. Expression of a Magnaporthe grisea Elicitor and Its Biological Function in Activating Resistance in Rice

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The expression of a protein elicitor from Magnaporthe griesea and its biological function in activating resistance in rice (Oryza sativa L) were reported. The gene of elicitor was expressed in Escherichia coli cells and produced a His6-fusion protein with 42 kD apparent molecular weight on SDS-PAGE. The purified protein could induce the resistance to blast disease, with the control efficiency of 46.47% and 36.41% at the 14th day and the 21st day after blast inoculation, respectively.After treatment with the expressed protein, the phenylalanine ammonia-lyase (PAL) and peroxidase (POD) activities were promoted in rice plants, meanwhile, the transcription levels of STKM, FAD, PBZ1 and PR1 genes were increased in rice plants. Moreover, after comparing the profile of total rice leaf proteins on two-dimensional eiectrophoresis gel, about 14proteins were found to be increased in expression level after the expressed protein treatment. All the results indicated that the expressed protein could act as an elicitor to trigger the resistance in rice.

  17. Predicting drug-target interaction networks based on functional groups and biological features.

    Directory of Open Access Journals (Sweden)

    Zhisong He

    Full Text Available BACKGROUND: Study of drug-target interaction networks is an important topic for drug development. It is both time-consuming and costly to determine compound-protein interactions or potential drug-target interactions by experiments alone. As a complement, the in silico prediction methods can provide us with very useful information in a timely manner. METHODS/PRINCIPAL FINDINGS: To realize this, drug compounds are encoded with functional groups and proteins encoded by biological features including biochemical and physicochemical properties. The optimal feature selection procedures are adopted by means of the mRMR (Maximum Relevance Minimum Redundancy method. Instead of classifying the proteins as a whole family, target proteins are divided into four groups: enzymes, ion channels, G-protein- coupled receptors and nuclear receptors. Thus, four independent predictors are established using the Nearest Neighbor algorithm as their operation engine, with each to predict the interactions between drugs and one of the four protein groups. As a result, the overall success rates by the jackknife cross-validation tests achieved with the four predictors are 85.48%, 80.78%, 78.49%, and 85.66%, respectively. CONCLUSION/SIGNIFICANCE: Our results indicate that the network prediction system thus established is quite promising and encouraging.

  18. Melatonin and its potential biological functions in the fruits of sweet cherry.

    Science.gov (United States)

    Zhao, Yu; Tan, Dun-Xian; Lei, Qiong; Chen, Hao; Wang, Lin; Li, Qing-tian; Gao, Yinan; Kong, Jin

    2013-08-01

    Melatonin is a well-known molecule which possesses many beneficial effects on human health. Many agriculture products provide natural melatonin in the diet. Cherry is one such fruit as they are rich in melatonin. In order to understand the biological roles of melatonin in cherry fruit, melatonin synthesis and its changes over 24 hr period were systematically monitored both during their development and in the ripe cherries in two cultivars, 'Hongdeng' (Prunus avium L. cv. Hongdeng) and 'Rainier' (Prunus avium L. cv. Rainier). It was found that both darkness and oxidative stress induced melatonin synthesis, which led to dual melatonin synthetic peaks during a 24 hr period. The high levels of malondialdehyde induced by high temperature and high intensity light exposure were directly related to up-regulated melatonin production. A primary function of melatonin in cherry fruits is speculated to be as an antioxidant to protect the cherry from the oxidative stress. Importantly, plant tryptophan decaboxylase gene (PaTDC) was identified in cherry fruits. Our data shows that PaTDC expression is positively related to the melatonin production in the cherry. This provides additional information to suggest that tryptophan decaboxylase is a rate-limiting enzyme of melatonin synthesis in plants. PMID:23480341

  19. Improved normal tissue sparing in head and neck radiotherapy using biological cost function based-IMRT.

    Science.gov (United States)

    Anderson, N; Lawford, C; Khoo, V; Rolfo, M; Joon, D L; Wada, M

    2011-12-01

    Intensity-modulated radiotherapy (IMRT) has reduced the impact of acute and late toxicities associated with head and neck radiotherapy. Treatment planning system (TPS) advances in biological cost function based optimization (BBO) and improved segmentation techniques have increased organ at risk (OAR) sparing compared to conventional dose-based optimization (DBO). A planning study was undertaken to compare OAR avoidance in DBO and BBO treatment planning. Simultaneous integrated boost treatment plans were produced for 10 head and neck patients using both planning systems. Plans were compared for tar get coverage and OAR avoidance. Comparisons were made using the BBO TPS Monte Carlo dose engine to eliminate differences due to inherent algorithms. Target coverage (V95%) was maintained for both solutions. BBO produced lower OAR doses, with statistically significant improvement to left (12.3%, p = 0.005) and right parotid mean dose (16.9%, p = 0.004), larynx V50_Gy (71.0%, p = 0.005), spinal cord (21.9%, p < 0.001) and brain stem dose maximums (31.5%, p = 0.002). This study observed improved OAR avoidance with BBO planning. Further investigations will be undertaken to review any clinical benefit of this improved planned dosimetry.

  20. Biological functions of glycosyltransferase genes involved in O-fucose glycan synthesis.

    Science.gov (United States)

    Okajima, Tetsuya; Matsuura, Aiko; Matsuda, Tsukasa

    2008-07-01

    Rare types of glycosylation often occur in a domain-specific manner and are involved in specific biological processes. Well-known examples of such modification are O-linked fucose (O-fucose) and O-linked glucose (O-glucose) glycans on epidermal growth factor (EGF) domains. In particular, O-fucose glycans are reported to regulate the functions of EGF domain-containing proteins such as urinary-type plasminogen activator and Notch receptors. Two glycosyltransferases catalyze the initiation and elongation of O-fucose glycans. The initiation process is catalyzed by O-fucosyltransferase 1, which is essential for Notch signalling in both Drosophila and mice. O-fucosyltransferase 1 can affect the folding, ligand interaction and endocytosis of Notch receptors, and both the glycosyltransferase and non-catalytic activities of O-fucosyltransferase 1 have been reported. The elongation of O-fucose monosaccharide is catalyzed by Fringe-related genes, which differentially modulate the interaction between Notch and two classes of ligands, namely, Delta and Serrate/Jagged. In this article, we have reviewed the recent reports addressing the distinctive features of the glycosyltransferases and O-glycans present on the EGF domains.

  1. Mechanically robust, rapidly actuating, and biologically functionalized macroporous poly(N-isopropylacrylamide)/silk hybrid hydrogels.

    Science.gov (United States)

    Gil, Eun Seok; Park, Sang-Hyug; Tien, Lee W; Trimmer, Barry; Hudson, Samuel M; Kaplan, David L

    2010-10-01

    A route toward mechanically robust, rapidly actuating, and biologically functionalized polymeric actuators using macroporous soft materials is described. The materials were prepared by combining silk protein and a synthetic polymer (poly(N-isopropylacrylamide) (PNIAPPm)) to form interpenetrating network materials and macroporous structures by freeze-drying, with hundreds of micrometer diameter pores and exploiting the features of both polymers related to dynamic materials and structures. The chemically cross-linked PNIPAAm networks provided stimuli-responsive features, while the silk interpenetrating network formed by inducing protein β-sheet crystallinity in situ for physical cross-links provided material robustness, improved expansion force, and enzymatic degradability. The macroporous hybrid hydrogels showed enhanced thermal-responsive properties in comparison to pure PNIPAAm hydrogels, nonporous silk/PNIPAAm hybrid hydrogels, and previously reported macroporous PNIPAAm hydrogels. These new systems reach near equilibrium sizes in shrunken/swollen states in less than 1 min, with the structural features providing improved actuation rates and stable oscillatory properties due to the macroporous transport and the mechanically robust silk network. Confocal images of the hydrated hydrogels around the lower critical solution temperature (LCST) revealed macropores that could be used to track changes in the real time morphology upon thermal stimulus. The material system transformed from a macroporous to a nonporous structure upon enzymatic degradation. To extend the utility of the system, an affinity platform for a switchable or tunable system was developed by immobilizing biotin and avidin on the macropore surfaces.

  2. Danish consumers' attitudes to the functional and environmental characteristics of food packaging

    DEFF Research Database (Denmark)

    Bech-Larsen, Tino

    1996-01-01

    This paper presents the results of a study of Danish consumers' attitudes to packaging and the importance of the environmental and functional characteristics of packaging for their purchasing decisions. The aim is to evaluate whether and how purch behaviour can be influenced in such a way...... as to limit the environmental problems caused by packaging. The study deals with consumers' attitudes to (a) packaging in general, and (b) the specific packaging which consumers take home with them (primar packaging). Consumers' attitudes to various industrial, transportation and storage packgaging...... are not explicitly included in the analysis. The paper concludes with a discussion of the implications of the results for the environmental authorities a and packaging manufacturers....

  3. Fluorescence response of hypocrellin B to the environmental changes in a mimic biological membrane--liposome

    Institute of Scientific and Technical Information of China (English)

    JIN; Xuanye; ZHAO; Yuewei; XIE; Jie; ZHAO; Jingquan

    2004-01-01

    , Photochem.Photobiol., 2001, 73 (5): 482-488.[13]Mang, T. S., Dougherty, T. J., Potter, W. R. et al., Photobleaching of porphyrins used in photodynamic therapy and implications for therapy, Photochem. Photobiol., 1987, 45: 501-506.[14]Shoko, Y., Tadahiro, T., Masahiko, A., Preparation of ganglioside GM3 liposomes and their membrane properties, Colloid Surface B, 2002, 27: 181-187.[15]Murakami, S., Packer, L., The role of cations in the organization of chloroplast membranes, Arch. Biochem. Biophys., 1971, 146:337-347.[16]Angeli, N. G., Lagorio, M. G., San Román, E. et al., Meso-substituted cationic porphyrins of biological interest, Photophysical and physicochemical properties in solution and bound to liposomes,Photochem. Photobiol., 2000, 72(1 ): 49-56.

  4. Usefulness and limitations of dK random graph models to predict interactions and functional homogeneity in biological networks under a pseudo-likelihood parameter estimation approach

    OpenAIRE

    Luan Yihui; Nunez-Iglesias Juan; Wang Wenhui; Sun Fengzhu

    2009-01-01

    Abstract Background Many aspects of biological functions can be modeled by biological networks, such as protein interaction networks, metabolic networks, and gene coexpression networks. Studying the statistical properties of these networks in turn allows us to infer biological function. Complex statistical network models can potentially more accurately describe the networks, but it is not clear whether such complex models are better suited to find biologically meaningful subnetworks. Results ...

  5. The hidden function of photosynthesis: a sensing system for environmental conditions that regulates plant acclimation responses.

    Science.gov (United States)

    Pfannschmidt, Thomas; Yang, Chunhong

    2012-06-01

    Plants convert light energy from the sun into chemical energy by photosynthesis. Since they are sessile, they have to deal with a wide range of conditions in their immediate environment. Many abiotic and biotic parameters exhibit considerable fluctuations which can have detrimental effects especially on the efficiency of photosynthetic light harvesting. During evolution, plants, therefore, evolved a number of acclimation processes which help them to adapt photosynthesis to such environmental changes. This includes protective mechanisms such as excess energy dissipation and processes supporting energy redistribution, e.g. state transitions or photosystem stoichiometry adjustment. Intriguingly, all these responses are triggered by photosynthesis itself via the interplay of its light reaction and the Calvin-Benson cycle with the residing environmental condition. Thus, besides its primary function in harnessing and converting light energy, photosynthesis acts as a sensing system for environmental changes that controls molecular acclimation responses which adapt the photosynthetic function to the environmental change. Important signalling parameters directly or indirectly affected by the environment are the pH gradient across the thylakoid membrane and the redox states of components of the photosynthetic electron transport chain and/or electron end acceptors coupled to it. Recent advances demonstrate that these signals control post-translational modifications of the photosynthetic protein complexes and also affect plastid and nuclear gene expression machineries as well as metabolic pathways providing a regulatory framework for an integrated response of the plant to the environment at all cellular levels.

  6. Short term recovery of soil biological functions in a new vineyard cultivated in organic farming

    Science.gov (United States)

    Costantini, Edoardo; Agnelli, Alessandro; Fabiani, Arturo; Gagnarli, Elena; Mocali, Stefano; Priori, Simone; Simoni, Sauro; Valboa, Giuseppe

    2014-05-01

    soil biological classes). Physical soil characteristics remained unchanged after the first year from the earthworks and did not change under grass cover. Chemical analysis only indicated a significant effect of earthworks. Over the 2010-2013 period, the new vineyard showed a slight increase of TOC and total N contents; as compared to the old vineyard, it averaged lower TOC and total N, and higher CaCO3 contents, suggesting still evolving equilibrium conditions. Microarthropod analysis showed significant different abundances and communities' structures both by management system and by year, increasing where the land use pressure was reduced by permanent grass cover and along with the aging of vineyard. Though the euedaphic forms, well adapted to soil life, were always rare. Microbiological analysis showed a different structure of eubacterial communities and a lower microbial activity in the new vineyard, especially during 2010-2012. In contrast, significant differences were not observed between the two vineyards in 2013, and grass cover effect was controversial. To sum up, the consequence of deep earthworks on chemical and biological properties were still evident after four years from planting and more time was needed to recover soil functions. Permanent grass cover did not always show a consistent positive effect.

  7. Contribution of personal and environmental factors on positive psychological functioning in adolescents.

    Science.gov (United States)

    Fadda, Daniela; Scalas, L Francesca; Meleddu, Mauro

    2015-08-01

    This study examined self-esteem as mediator in the relations of personal (extraversion, neuroticism) and environmental (maternal, paternal, peer-relationships) variables with domains of positive psychological functioning (PPF) in adolescence (Satisfaction with life, Mastery, Vigor, Social Interest, Social Cheerfulness). We compared one-sided and multidimensional models using a sample of 1193 high school students (592 males and 601 females). We examined variations in adolescent PPF as a function of parenting styles via independent examination of maternal and paternal bonding. Results supported the multidimensional models, which indicated direct effects of personality traits, maternal care and peer relationships, as well as indirect effects, mediated by self-esteem, of all predictors on most PPF dimensions. Overall, our study provided a broader picture of personal and environmental predictors on different dimensions of PPF, which supported the mediating role of self-esteem and emphasized the importance of considering multidimensional models to characterize PPF in adolescents.

  8. Contribution of personal and environmental factors on positive psychological functioning in adolescents.

    Science.gov (United States)

    Fadda, Daniela; Scalas, L Francesca; Meleddu, Mauro

    2015-08-01

    This study examined self-esteem as mediator in the relations of personal (extraversion, neuroticism) and environmental (maternal, paternal, peer-relationships) variables with domains of positive psychological functioning (PPF) in adolescence (Satisfaction with life, Mastery, Vigor, Social Interest, Social Cheerfulness). We compared one-sided and multidimensional models using a sample of 1193 high school students (592 males and 601 females). We examined variations in adolescent PPF as a function of parenting styles via independent examination of maternal and paternal bonding. Results supported the multidimensional models, which indicated direct effects of personality traits, maternal care and peer relationships, as well as indirect effects, mediated by self-esteem, of all predictors on most PPF dimensions. Overall, our study provided a broader picture of personal and environmental predictors on different dimensions of PPF, which supported the mediating role of self-esteem and emphasized the importance of considering multidimensional models to characterize PPF in adolescents. PMID:26093819

  9. Single Fluorescent Molecules as Nano-Illuminators for Biological Structure and Function

    Science.gov (United States)

    Moerner, W. E.

    2011-03-01

    Since the first optical detection and spectroscopy of a single molecule in a solid (Phys. Rev. Lett. {62}, 2535 (1989)), much has been learned about the ability of single molecules to probe local nanoenvironments and individual behavior in biological and nonbiological materials in the absence of ensemble averaging that can obscure heterogeneity. Because each single fluorophore acts a light source roughly 1 nm in size, microscopic imaging of individual fluorophores leads naturally to superlocalization, or determination of the position of the molecule with precision beyond the optical diffraction limit, simply by digitization of the point-spread function from the single emitter. For example, the shape of single filaments in a living cell can be extracted simply by allowing a single molecule to move through the filament (PNAS {103}, 10929 (2006)). The addition of photoinduced control of single-molecule emission allows imaging beyond the diffraction limit (super-resolution) and a new array of acronyms (PALM, STORM, F-PALM etc.) and advances have appeared. We have used the native blinking and switching of a common yellow-emitting variant of green fluorescent protein (EYFP) reported more than a decade ago (Nature {388}, 355 (1997)) to achieve sub-40 nm super-resolution imaging of several protein structures in the bacterium Caulobacter crescentus: the quasi-helix of the actin-like protein MreB (Nat. Meth. {5}, 947 (2008)), the cellular distribution of the DNA binding protein HU (submitted), and the recently discovered division spindle composed of ParA filaments (Nat. Cell Biol. {12}, 791 (2010)). Even with these advances, better emitters would provide more photons and improved resolution, and a new photoactivatable small-molecule emitter has recently been synthesized and targeted to specific structures in living cells to provide super-resolution images (JACS {132}, 15099 (2010)). Finally, a new optical method for extracting three-dimensional position information based on

  10. Decreased Pulmonary Function Measured in Children Exposed to High Environmental Relative Moldiness Index Homes

    OpenAIRE

    Vesper, Stephen J.; Wymer, Larry; Kennedy, Suzanne; Grimsley, L. Faye

    2013-01-01

    Background: Exposures to water-damaged homes/buildings has been linked to deficits in respiratory health. However, accurately quantifying this linkage has been difficult because of the methods used to assess water damage and respiratory health. Purpose: The goal of this analysis was to determine the correlation between the water-damage, as defined by the Environmental Relative Moldiness Index (ERMI) value in an asthmatic child’s home, and the child’s pulmonary function measured by spirometry,...

  11. The influence of demographic, environmental and physical factors on functional independence post stroke

    OpenAIRE

    M.V. Mamabolo; W. Mudzi; A.S. Stewart; N. P. Mbambo; S. Olorunju

    2008-01-01

    Purpose: The magnitude of disability observed in strokesurvivors is believed to be dependent in part, on the severity of neurological deficits incurred. A s important but less well understood, is thecontribution of demographic, physical and environmental factors. The objective of this study was to establish what demographic, environmentaland physical factors influence functional independence post stroke. Method: Convenience sampling was used in the selection of subjects from four stroke outpa...

  12. Bridging from Cells to Cognition in Autism Pathophysiology: Biological Pathways to Defective Brain Function and Plasticity

    Energy Technology Data Exchange (ETDEWEB)

    Anderson, Matthew; Hooker, Brian S.; Herbert, Martha

    2008-01-01

    We review evidence to support the model that autism may begin when a maternal environmental, infectious, or autoantibody insult causes inflammation which increases reactive oxygen species (ROS) production in the fetus, leading to fetal DNA damage (nuclear and mitochondrial), and that these inflammatory and oxidative stressors persist beyond early development (with potential further exacerbations), producing ongoing functional consequences. In organs with a high metabolic demand such as the central nervous system, the continued use of mitochondria with DNA damage may generate additional ROS which will activate the innate immune system leading to more ROS production. Such a mechanism would self-sustain and possibly progressively worsen. The mitochondrial dysfunction and altered redox signal transduction pathways found in autism would conspire to activate both astroglia and microglia. These activated cells can then initiate a broad-spectrum proinflammatory gene response. Neurons may have acquired receptors for these inflammatory signals to inhibit neuronal signaling as a protection from excitotoxic damage during various pathologic insults (e.g., infection). In autism, over-zealous neuroinflammatory responses could not only influence neural developmental processes, but may more significantly impair neural signaling involved in cognition in an ongoing fashion. This model makes specific predictions in patients and experimental animal models and suggests a number of targets sites of intervention. Our model of potentially reversible pathophysiological mechanisms in autism motivates our hope that effective therapies may soon appear on the horizon.

  13. Quality of life and biological communities: Analysis of the study of environmental impact of the metro in the city of Quito

    Directory of Open Access Journals (Sweden)

    Cristina Aguilar

    2013-10-01

    Full Text Available This work shows a critique review of the Informe de Impacto Ambiental del Metro de Quito (Report of environmental impact of subway of Quito, in its variables: quality of life and biological communities. From an ecosistemic perspective of comprehension and understanding of the city, we see that the report holds a reductionist vision of the environmental dimension. Assuming that the subway constitutes an improvement in urban mobility, we argue that this project is an opportunity to generate instances of promotion and articulation of biodiversity within the city. We discuss the necessity of counteracting the dependency of the environmental approach of production and reproduction of the city.

  14. Development of Voltammetric Double-Polymer-Modified Electrodes for Nanomolar Ion Detection for Environmental and Biological Applications

    Science.gov (United States)

    Kim, Yushin

    Qualitative and quantitative electrochemical methods for trace ion analysis of organic and inorganic species with environmental and biological attention have been developed and reported during past decades. The development of fast and accurate electrochemical methods is critical for field applications with various blocking contaminants. Voltammetric method is attractive not only to analyze selective ion species due to its characteristic based on ion lipophilicity, but also to lower the limit of detection by combining with stripping analysis. In my PhD work, I have developed and studied a highly selective and sensitive electrochemical method that can be used to characterize fundamental transport dynamics and to develop electrochemical sensors at liquid/liquid interfaces based on electrochemically-controlled ion transfer and recognition. The understanding of the kinetic and thermodynamic properties of the voltammetric ion transfer through polymer-modified ion-selective electrodes leads to realize the highly selective and sensitive analytical method. The ultrathin polymer membrane is used to maximize a current response by complete exhaustion of preconcentrated ions. Therefore, nanomolar detection is achieved and confirmed by a thermodynamic mechanism that controls the detection limit. It was also demonstrated experimentally and theoretically that more lipophilic ionic species gives a significantly lower detection limit. The voltammetric method was expanded into inexpensive and disposable applications based on pencil lead modified with the thin polymer membrane. In the other hand, micropipet/nanopipet voltammetry as an artificial cell membrane was used to study the interface between two immiscible solutions for environmental and biomedical applications. It is very useful to get quantitative kinetic and thermodynamic information by studying numerical simulations of ion transfer and diffusion. Molecular recognition and transport of heparin and low

  15. Environmental and socio-economic analysis of treatment of biological waste; Miljoe- och samhaellsekonomisk analys av behandling av biologiskt avfall

    Energy Technology Data Exchange (ETDEWEB)

    Ljungkvist, Hanna

    2008-01-15

    Biogas is a renewable fuel that can be extracted from anaerobic digestion of many different substrates, for example biological household waste. An alternative handling of the waste is to mix it with other wastes and incinerate it in a combined heat and power (CHP) plant. This study uses life cycle assessment to investigate which type of waste handling that is better from an environmental point of view, anaerobic digestion with biogas production or incineration. The results are based on a case study of a biogas production plant owned by the company Ragn-Sells in Vaenersborg. The alternative is incineration at a CHP plant in Gothenburg. Three different weighting methods were used, which produced different results on the detailed level. Overall however, the alternative with digestion and biogas production had significantly lower potential environmental impact than incineration according to all three methods. An economic valuation of the biogas production potential showed that the biggest societal savings would result from using all the produced biogas in heavy vehicles or to replace fuel oil for heating. However, since biogas is a high quality fuel it should be used as transportation fuel rather than for heating. By digestion and biogas production many potential services are gained from the organic waste. Waste volumes are reduced, emissions from the transport sector are reduced, local air quality is improved and valuable nutrients are returned to farmland through the organic fertilizer produced. The infrastructure and knowledge built up around the biogas system is also very valuable as a bridge to future gas based transport systems

  16. Multivariate benthic ecosystem functioning in the Arctic – benthic fluxes explained by environmental parameters in the southeastern Beaufort Sea

    Directory of Open Access Journals (Sweden)

    H. Link

    2013-09-01

    Full Text Available The effects of climate change on Arctic marine ecosystems and their biogeochemical cycles are difficult to predict given the complex physical, biological and chemical interactions among the ecosystem components. We studied benthic biogeochemical fluxes in the Arctic and the influence of short-term (seasonal to annual, long-term (annual to decadal and other environmental variability on their spatial distribution to provide a baseline for estimates of the impact of future changes. In summer 2009, we measured fluxes of dissolved oxygen, nitrate, nitrite, ammonia, soluble reactive phosphate and silicic acid at the sediment–water interface at eight sites in the southeastern Beaufort Sea at water depths from 45 to 580 m. The spatial pattern of the measured benthic boundary fluxes was heterogeneous. Multivariate analysis of flux data showed that no single or reduced combination of fluxes could explain the majority of spatial variation, indicating that oxygen flux is not representative of other nutrient sink–source dynamics. We tested the influence of eight environmental parameters on single benthic fluxes. Short-term environmental parameters (sinking flux of particulate organic carbon above the bottom, sediment surface Chl a were most important for explaining oxygen, ammonium and nitrate fluxes. Long-term parameters (porosity, surface manganese and iron concentration, bottom water oxygen concentrations together with δ13Corg signature explained most of the spatial variation in phosphate, nitrate and nitrite fluxes. Variation in pigments at the sediment surface was most important to explain variation in fluxes of silicic acid. In a model including all fluxes synchronously, the overall spatial distribution could be best explained (57% by the combination of sediment Chl a, phaeopigments, δ13Corg, surficial manganese and bottom water oxygen concentration. We conclude that it is necessary to consider long-term environmental variability along with

  17. Environmental Impacts of Wind Power Development on the Population Biology of Greater Prairie-Chickens

    Energy Technology Data Exchange (ETDEWEB)

    Sandercock, Brett K. [Kansas State University

    2013-05-22

    Executive Summary 1. We investigated the impacts of wind power development on the demography, movements, and population genetics of Greater Prairie-Chickens (Tympanuchus cupido) at three sites in northcentral and eastern Kansas for a 7-year period. Only 1 of 3 sites was developed for wind power, the 201MW Meridan Way Wind Power Facility at the Smoky Hills site in northcentral Kansas. Our project report is based on population data for prairie chickens collected during a 2-year preconstruction period (2007-2008), a 3-year postconstruction period (2009-2011) and one final year of lek surveys (2012). Where relevant, we present preconstruction data from our field studies at reference sites in the northern Flint Hills (2007-2009) and southern Flint Hills (2006-2008). 2. We addressed seven potential impacts of wind power development on prairie chickens: lek attendance, mating behavior, use of breeding habitat, fecundity rates, natal dispersal, survival rates, and population numbers. Our analyses of pre- and postconstruction impacts are based on an analysis of covariance design where we modeled population performance as a function of treatment period, distance to eventual or actual site of the nearest wind turbine, and the interaction of these factors. Our demographic and movement data from the 6-year study period at the Smoky Hills site included 23 lek sites, 251 radio-marked females monitored for 287 bird-years, and 264 nesting attempts. Our genetic data were based on genotypes of 1,760 females, males and chicks that were screened with a set of 27 microsatellite markers that were optimized in the lab. 3. In our analyses of lek attendance, the annual probability of lek persistence during the preconstruction period was ~0.9. During the postconstruction period, distance to nearest turbine did not have a significant effect on the probability of lek persistence. However, the probability of lek persistence increased from 0.69 at 0 m to 0.89 at 30 km from turbines, and most

  18. Mercury in Environmental and Biological Samples Using Online Combustion with Sequential Atomic Absorption and Fluorescence Measurements: A Direct Comparison of Two Fundamental Techniques in Spectrometry

    Science.gov (United States)

    Cizdziel, James V.

    2011-01-01

    In this laboratory experiment, students quantitatively determine the concentration of an element (mercury) in an environmental or biological sample while comparing and contrasting the fundamental techniques of atomic absorption spectrometry (AAS) and atomic fluorescence spectrometry (AFS). A mercury analyzer based on sample combustion,…

  19. Environmental Impacts of Wind Power Development on the Population Biology of Greater Prairie-Chickens

    Energy Technology Data Exchange (ETDEWEB)

    Sandercock, Brett K. [Kansas State University

    2013-05-22

    Executive Summary 1. We investigated the impacts of wind power development on the demography, movements, and population genetics of Greater Prairie-Chickens (Tympanuchus cupido) at three sites in northcentral and eastern Kansas for a 7-year period. Only 1 of 3 sites was developed for wind power, the 201MW Meridan Way Wind Power Facility at the Smoky Hills site in northcentral Kansas. Our project report is based on population data for prairie chickens collected during a 2-year preconstruction period (2007-2008), a 3-year postconstruction period (2009-2011) and one final year of lek surveys (2012). Where relevant, we present preconstruction data from our field studies at reference sites in the northern Flint Hills (2007-2009) and southern Flint Hills (2006-2008). 2. We addressed seven potential impacts of wind power development on prairie chickens: lek attendance, mating behavior, use of breeding habitat, fecundity rates, natal dispersal, survival rates, and population numbers. Our analyses of pre- and postconstruction impacts are based on an analysis of covariance design where we modeled population performance as a function of treatment period, distance to eventual or actual site of the nearest wind turbine, and the interaction of these factors. Our demographic and movement data from the 6-year study period at the Smoky Hills site included 23 lek sites, 251 radio-marked females monitored for 287 bird-years, and 264 nesting attempts. Our genetic data were based on genotypes of 1,760 females, males and chicks that were screened with a set of 27 microsatellite markers that were optimized in the lab. 3. In our analyses of lek attendance, the annual probability of lek persistence during the preconstruction period was ~0.9. During the postconstruction period, distance to nearest turbine did not have a significant effect on the probability of lek persistence. However, the probability of lek persistence increased from 0.69 at 0 m to 0.89 at 30 km from turbines, and most

  20. Rapidly restoring biological soil crusts and ecosystem functions in a severely disturbed desert ecosystem.

    Science.gov (United States)

    Chiquoine, Lindsay P; Abella, Scott R; Bowker, Matthew A

    2016-06-01

    Restoring biological soil crusts (biocrusts) in degraded drylands can contribute to recovery of ecosystem functions that have global implications, including erosion resistance and nutrient cycling. To examine techniques for restoring biocrusts, we conducted a replicated, factorial experiment on recently abandoned road surfaces by applying biocrust inoculation (salvaged and stored dry for two years), salvaged topsoil, an abiotic soil amendment (wood shavings), and planting of a dominant perennial shrub (Ambrosia dumosa). Eighteen months after treatments, we measured biocrust abundance and species composition, soil chlorophyll a content and fertility, and soil resistance to erosion. Biocrust addition significantly accelerated biocrust recovery on disturbed soils, including increasing lichen and moss cover and cyanobacteria colonization. Compared to undisturbed controls, inoculated plots had similar lichen and moss composition, recovered 43% of total cyanobacteria density, had similar soil chlorophyll content, and exhibited recovery of soil fertility and soil stability. Inoculation was the only treatment that generated lichen and moss cover. Topsoil application resulted in partial recovery of the cyanobacteria community and soil properties. Compared to untreated disturbed plots, topsoil application without inoculum increased cyanobacteria density by 186% and moderately improved soil chlorophyll and ammonium content and soil stability. Topsoil application produced 22% and 51% of the cyanobacteria density g⁻¹ soil compared to undisturbed and inoculated plots, respectively. Plots not treated with either topsoil or inoculum had significantly lower cyanobacteria density, soil chlorophyll and ammonium concentrations, and significantly higher soil nitrate concentration. Wood shavings and Ambrosia had no influence on biocrust lichen and moss species recovery but did affect cyanobacteria composition and soil fertility. Inoculation of severely disturbed soil with native